�m -10PEHVPSBDS000392 20-Feb-2002 (last modified) uchi�� "-10 promoter element" found in the barley (H.v.) chloroplastpsbD gene promoter; Involved in the expression of the plastidgene psbD which encodes a photosystem II reaction centerchlorophyll-binding protein that is activated by blue, white orUV-A light;psbDchloroplast gene expressioncircadian rhythmslight
regulationbarley (Hordeum vulgare)8Thum KE, Kim M, Morishige DT, Eibl C, Koop HU, Mullet JE_Analysis of barley chloroplast psbD light-responsive promoterelements in transplastomic tobacco"Plant Mol Biol 47: 353-366 (2001)PubMed: 11587507; TATTCT -141NTG13S000335 16-Feb-2001 (last modified) seki��"-141 sequence"; Binding site of tobacco (N.t.) TGA1a-relatedprotein,PG13, found in the G13 gene promoter; PG13 (Proteinencoded by G13) shows high homology to TGA1a; ASF-1, PG13, andTGA1a bind to the same target sequence in the 5' upstream regionof G13 suggesting that autoregulation of transcription mayinvolved in the control of G13 expression; TGA1a ispreferentially expressed in root tip meristems; TGA1a maycontribute to the expression of GST isoenzymes, especially inroot tip meristems;TGA1aG13ASF1ASF-1bZipxenobiotic stressrootmeristemtobacco (Nicotiana tabacum)PFromm H, Katagiri F, Chua NHKlinedinst S, Pascuzzi P, Redman J, Desai M, Arias J� The tobacco transcription activator TGA1a binds to a sequence inthe 5' upstream region of a gene encoding a TGA1a-relatedproteinA xenobiotic-stress-activated transcription factor and itscognate target genes are preferentially expressed in root tipmeristemsBMol Gen Genet 229: 181-188 (1991)Plant Mol Biol 42: 679-688 (2000)2PubMed: 1921969; GenBank: M62855;PubMed: 10809441; GCTTTTGATGACTTCAAACAC-284MOTIFZMSBE1S000285 10-Feb-2000 (last modified) seki�Located between -284 and -255 region of maize (Z.m.) Sbe1 genepromoter; Critical positive cis element; Important for thehigh-level, sugar-responsive expression of the Sbe1 gene in maizeendosperm cells; Recognized by nuclear protein; See S000284; Starch-branching enzyme (Sbe1)starchkernelsugar endospermseedmaize (Zea mays)Kim K-N, Guiltinan MJvIdentification of cis-acting elements important for expression ofthe starch-branching enzyme I gene in Maize endosperm"Plant Physiol 121: 225-236 (1999)PubMed: 10482678 CGTGCAAGCCCAAAGGCCAATCGGCCCAGA-300CORES000001 10-May-2006 (last modified) kehi�>"TGTAAAG core motif" in "-300 elements" of alpha-zein genes ofmaize; "-300 element core"; "prolamin box" by Vicente-Carbajosaet al. (Proc Natl Acad Sci USA 94:7685 (1997)); P-box; Binds withP-box binding factor (PBF); Binds with BPBF (Barley PBF); PBF isa DNA-binding protein of the DOF class of transcription factors; zein
core motifmaize -300 elementpromoter prolamin-boxP-boxseed endospermamaize (Zea mays); wheat (Triticum aestivum); barley (Hordeumvulgare); tobacco (Nicotiana tabacum)�Forde BG, Heyworth A, Pywell J, Kreis MColot V, Robert LS, Kavanagh TA, Bevan MW, Thompson RDThomas MS, Flavell RBThompson GA, Boston RS, Lyznik LA, Hodges TK, Larkins BAVicente-Carbajosa J, Moose SP, Parsons RL, Schmidt RMena M, Vicente-Carbajosa J, Schmidt RJ, Carbonero PSingh KB��Nucleotide sequence of a B1 hordein gene and the identificationof possible upstream regulatory elements in endosperm storageprotein genes from barley, wheat and maize.Localization of sequences in wheat endosperm protein genes whichconfer tissue-specific expression in tobacco.Identification of an enhancer element for the endosperm-specificexpression of high molecular weight glutenin.Analysis of promoter activity from an alpha-zein gene 5' flankingsequence in transient expression assays.A maize zinc-finger protein binds the prolamin box in zein genepromoters and interacts with the basic leucine zippertranscriptional activator Opaque2.An endosperm-specific DOF protein from barley, highly conservedin wheat, binds to and activates transcription from theprolamin-box of a native B-hordein promoter in barley endospermTranscriptional regulation in plants: the importance ofcombinatorial control.�Nucleic Acids Res 13:7327-7339 (1985)EMBO J 6:3559-3564 (1987)Plant Cell 2:1171-1180 (1990)Plant Mol Biol 15:755-764 (1990)Proc Natl Acad Sci USA 94:7685-7690 (1997)Plant J 16:53-62 (1998)Plant Physiol 118: 1111-1120 (1998)�PubMed: 4059057; GenBank: X03103;PubMed: 15467781PubMed: 2152160;PubMed: 2102884;PubMed: 9207153; GenBank: U82230;PubMed: 9807827; GenBank: AJ012284, AJ000991PubMed: 9847085reviewTGTAAAG-314MOTIFZMSBE1S000284 10-Feb-2000 (last modified) seki�Located between -314 and -295 region of maize (Z.m.) Sbe1 genepromoter; Critical positive cis element; Important for thehigh-level, sugar-responsive expression of the Sbe1 gene in maizeendosperm cells; Recognized by nuclear protein; See S000285; Starch-branching enzyme (Sbe1)kernelsugar endospermseedmaize (Zea mays)Kim K-N, Guiltinan MJvIdentification of cis-acting elements important for expression ofthe starch-branching enzyme I gene in maize endosperm"Plant Physiol 121: 225-236 (1999)PubMed: 10482678 ACATAAAATAAAAAAAGGCA
14BPATERD1S000412 03-Jun-2003 (last modified) kehi~"14 bp region" (from -599 to -566) necessary for expression oferd1 (early responsive to dehydration) in dehydratedArabidopsis; water-stresserdArabidopsis thalianaOSimpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K,Yamaguchi-Shinozaki K.�Two different novel cis-acting elements of erd1, a clpAhomologous Arabidopsis gene function in induction by dehydrationstress and dark-induced senescence.Plant J. 33: 259-270 (2003)PubMed: 12535340; CACTAAATTGTCAC 20NTNTNOSS000312 7-Sep-2000 (last modified) seki�"20nt (20 nucleotide sequence)" found in the promoter on tobacco(N.t.) nopalin synthase (nos) gene promoter; Containing twohexamer motifs (TGAGCT) and a spacer region; The spacer regionbetween two hexamer motifs is essential; Important for the geneexpression; Essential for response to wounding, auxin, MJ, andSA; Very similar to ASF-1 binding site (See S000073); SeeS000053(ACGTCA);nopalin synthasenosauxinwoundingmethyl jasmonatetobacco (Nicotiana tabacum) Kim Y, Buckley K, Costa MA, An G^A 20 nucleotide upstream element is essential for the nopalinesynthase (nos) promoter activity Plant Mol Biol 24:105-117 (1994)PubMed: 8111010; TGAGCTAAGCACATACGTCA23BPUASNSCYCB1S000283 10-Feb-2000 (last modified) seki�,"23 bp UAS (Upstream activating sequence)" found in the promoterof Nicotiana sylvestris (N.s.) CycB1 gene; Located between -386and -409; Contains a 5 bp element identical to the MYB bindingcore (ACGT); Required for M-phase-specific expression; Bindsprotein complexes in a cell cycle-regulated manner;B-type cyclinsMYB
Cell cycleM-phase tobacco (Nicotiana sylvestris)8Trehin C, Glab N, Perennes C, Planchais S, Bergounioux CoM phase-specific activation of the Nicotiana sylvestris Cyclin B1promoter involves multiple regulatory elementsPlant J 17: 263-273 (1999) TTTATTTACCAAACGGTAACATC23BPZM27KDAZEINS000341 7-Sep-2000 (last modified) seki�z23 bp sequence found in the maize (Z.m.) gamma-class 27kDa zeingene promoter; Contains -300 element (also called the endospermbox or prolamin box); Binding site of nuclear protein; Confers ahigh level of transcriptional activity in anorientation-dependent manner; -300 element is involved in thecommon regulatory mechanisms mediating the coordinated expressionof the zein genes;gamma-class 27kDa zein -300 element prolamin box endospermboxseedmaize (Zea mays)!Ueda T, Wang Z, Pham N, Messing JqIdentification of a transcriptional activator-binding element inthe 27-kilodalton zein promoter, the -300 element"Mol Cell Biol 14: 4350-4359 (1994)PubMed: 8007944; GACGTGTAAAGTAAATTTACAAC2SSEEDPROTBANAPAS000143 10-May-1998 (last modified) kehiiConserved in many storage-protein gene promoters; May beimportant for high activity of the napA promoter;storage proteinABREnapA2SseedBrassica napus;3Stalberg K, Ellerstom M, Ezcurra I, Ablov S, Rask L�Disruption of an overlapping E-box/ABRE motif abolished hightranscription of the napA storage-protein promoter in transgenicBrassica napus seeds.Planta 199:515-519 (1996)PubMed: 8818291; CAAACAC3AF1BOXPSRBCS3S000004 17-May-1998 (last modified) kehi�"3AF1 binding site"; tetramer in the light-responsive promoter ofpea (P.s.) rbcS-3A gene; "Box VI"; One of "AT-rich sequences"which have been found in numerous light-regulated promoters(Terzaghi & Cashmore, 1995); 3AF1 site includes a GATA motif;3AF1 boxpromoterAT-rich sequencesGATArbcsrbcs-3leafshootpea (Pisum sativum){Lam E, Kano-Murakami Y, Gilmartin P, Niner B, Chua N-HGilmartin PM, Sarokin L, Memelink J, Chua N-HTerzaghi WB, Cashmore AR�A metal-dependent DNA-binding protein interacts with aconstitutive element of a light-responsive promoter.Molecular light switches for plant genes.Light-regulated transcriptionmPlant Cell 2:857-866 (1990)Plant Cell 2:369-378 (1990)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)1PubMed: 2152132; GenBank: X62746;PubMed: 2152164;ReviewAAATAGATAAATAAAAACATT5256BOXLELAT5256S000279 27-Feb-2000 (last modified) kehi��"52/56 box"; A sequence motif shared between the tomato (L.e.)LAT(Late Anther Tomato)52 and LAT56 promoters; Encompassing "PBcore motif" (TGTGGTT), and is closely related to the box IIsequence motif in the pea rbcS-3A gene promoter; Involved inmodulating the activity of the LAT gene promoters in pollen;Dispensable for the developmental regulation of the LAT52 gene inpollen; 52/56 box may be a target for the binding of a member ofthe GT-1 transcription factor family;52/56latlat52lat56GT-1pollenanther tomato (Lycopersicon esculentum)rTwell D, Yamaguchi J, Wing RA, Ushiba J, McCormick SEyal Y, Curie C, McCormick SVillain P, Mache R, Zhou DXZhou DX��Promoter analysis of genes that are coordinately expressed duringpollen development reveals pollen-specific enhancer sequences andshared regulatory elementsPollen specificity elements reside in 30 bp of the proximalpromoters of two pollen-expressed genesThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�Genes Dev 5:496-507 (1991)Plant Cell 7:373-384 (1995)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)RPubMed: 1840556; GenBank: X56487;PubMed: 7734969;PubMed: 8955086;PubMed: 10366876Review TGTGGTTATATAAACACOREOSGLUB1S000353 16-Feb-2001 (last modified) seki�OCore of AACA motifs found in rice (O.s.) glutelin genes, involvedin controlling the endosperm-specific expression; AACA is alsoclosely associated with the GCN4 motif in all rice glutelin genesand together have been shown to confer endosperm-specificenhancement to the truncated -90 CaMV 35S promoter; See alsoS000045, S000181, S000276;glutelinAACAGCN4seed endospermrice (Oryza sativa)/Wu C, Washida H, Onodera Y, Harada K, Takaiwa F�Quantitative nature of the Prolamin-box, ACGT and AACA motifs ina rice glutelin gene promoter: minimal cis-element requirementsfor endosperm-specific gene expressionPlant J 23: 415-421 (2000)PubMed: 10929134; AACAAAC AACAOSGLUB1S000276 15-Oct-1999 (last modified) kehi�"AACA motif" found in GluB-1 gene in rice (O.s.); Required forendosperm-specific expression; Highly conserved in the5'-flanking region of glutelin genes; See S000277;GluB-1glutelin endospermseedstorage protein
AACA motifrice (Oryza sativa)GWashida H, Wu CY, Suzuki A, Yamanouchi U, Akihama T, Harada K,Takaiwa F{Identification of cis-regulatory elements required for endospermexpression of the rice storage protein glutelin gene GluB-1 Plant Mol Biol 40:1-12 (1999)PubMed: 10394940; CAACAAACTATATCAAGACGTAGATACL12S000344 7-Sep-2000 (last modified) sekiwSequence found in Arabidopsis (A.t.) acyl carrier protein (ACP),Acl1.2, gene promoter; Contains bZIP core motif (ACGT);Acl1.2bZIPacyl carrier proteinArabidopsis thaliana'Baerson SR, Vander Heiden MG, Lamppa GK|Identification of domains in an Arabidopsis acyl carrier proteingene promoter required for maximal organ-specific expression#Plant Mol Biol 26: 1947-1959 (1994)PubMed: 7858229; AAGACGTAGABADESI2S000008 29-Sep-1999 (last modified) kehi�Synthetic element (hex-3) related to response to ABA and todesiccation; seed expression; Gene: synthetic; hex-3, mutant ofhex-1 sequence from wheat histone H3 promoter; transactingfactor: bZIP ?;ABASEEDbZIPhex-1hex-3histone.rice (Oryza sativa); wheat (Triticum aestivum)(Lam E, Chua N-HThomas TLBusk PK, Pages M�
Tetramer of a 21-base pair synthetic element confers seedexpression and transcriptional enhancement in response to waterstress and abscisic acid.Gene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcription_J Biol Chem 266:17131-17135 (1991)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998)/PubMed: 1832669;PubMed: 8281041;PubMed: 9617810 ReviewReview GGACGCGTGGCABAREG2S000009 29-Sep-1999 (last modified) kehiXMotif related to ABA regulation; Gene: sunflower helianthinin;transacting factor: bZIP ?ABAbZIPseed sunflower (Helianthus annuus)TNunberg A, Li Z, Bogue M, Vivekananda J, Reddy A, Thomas TLThomas TLBusk PK, Pages MxGene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcriptionwunpublished results (cited in a review by Thomas TL, 1993)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998) PubMed: 8281041;PubMed: 9617810 ReviewReview ATGTACGAAGCABASEED1S000011 29-Sep-1999 (last modified) kehibABA regulation; seed expression; Gene: carrot Dc3; Transactingfactor: bZIP ?; Contains ACGT motif;Dc3ABAABREbZIPseedACGTcarrot (Daucus carota)+Chung H, Thomas TLThomas TLBusk PK, Pages MxGene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcriptionwunpublished results (cited in a review by Thomas TL, 1993)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998) PubMed: 8281041;PubMed: 9617810 ReviewReview TGTTACGTGCCABFOSS000190 11-Oct-1999 (last modified) kehi�1ABF (as-1-like box binding factor) binding site; as-1-like (ASL)box is found at -98 to -79 of RTBV (rice tungro bacilliformvirus) promoter; ASL box is required for phloem-specific geneexpression of Rice Tungro Bacilliform Virus (RTBV); See alsoRNFG1OS (S000188), and RNFG2OS (S000189); See as-1 (S000023);ASLas-1phloemRTBVABFstemphloem9RTBV; rice tungro bacilliform virus; rice (Oryza sativa);Yin Y, Chen L, Beachy R\Promoter elements required for phloem-specific gene expressionfrom the RTBV promoter in ricePlant J 12:1179-1188 (1997)PubMed: 9418055; GCATCTTTACTTTAGCATC ABRE2HVA1S000134 29-Sep-1999 (last modified) kehi�ABA responsive element, ABRE2, found in barley (H.v.) HVA1 geneencoding a class 3 late embryogenesis-abundant protein; stressresponse;ABREABAHVA1ABRE2seedembryobarley (Hordeum vulgare);)Straub PF, Shen Q, Ho THDBusk PK, Pages M�Structure and promoter analysis of an ABA- and stress-regulatedbarley gene, HVA1.Regulation of abscisic acid-induced transcription@Plant Mol Biol 26:617-630 (1994)Plant Mol Biol 37:425-435 (1998)1PubMed: 7948917; GenBank: X78205;PubMed: 9617810;Review CCTACGTGGCGG
ABRE2HVA22S000117 29-Sep-1999 (last modified) kehi�"ABRE2" of barley HVA22 gene; G-box; component of ABA responsecomplex in HVA22 gene; see S0118 (ABRE3 of HVA22 gene); see CE1(coupling element 1 = TGCCACCGG); See S000014;ABREG-boxcoupling elementCE1HVA22barley (Hordeum vulgare); Shen Q, Ho THBusk PK, Pages M�Functional dissection of an abscisic acid(ABA)-inducible genereveals two independent ABA-responsive complexes each containinga G-box and a novel cis-acting element.Regulation of abscisic acid-induced transcription;Plant Cell 7:295-307 (1995)Plant Mol Biol 37:425-435 (1998) PubMed: 7734964;PubMed: 9617810;Review
CGCACGTGTC ABRE3HVA1S000135 29-Sep-1999 (last modified) kehi�ABA responsive element, ABRE3, found in barley (H.v.) HVA1 geneencoding a class 3 late embryogenesis-abundant protein; stressresponse;ABREABAHVA1ABRE3seedembryobarley (Hordeum vulgare);)Straub PF, Shen Q, Ho THDBusk PK, Pages M�Structure and promoter analysis of an ABA- and stress-regulatedbarley gene, HVA1.Regulation of abscisic acid-induced transcription@Plant Mol Biol 26:617-630 (1994)Plant Mol Biol 37:425-435 (1998)1PubMed: 7948917; GenBank: X78205;PubMed: 9617810;Review
GCAACGTGTC
ABRE3HVA22S000118 17-May-2001 (last modified) uchi�R"ABRE3" of barley HVA22 gene; Newly designated "A3" by Shen etal., Plant Cell 8:1107 (1996); G-box; component of ABA responsecomplex in HVA22 gene; see S0117 (ABRE2 of HVA22 gene); see CE1(coupling element 1 = TGCCACCGG); See S000014; ABA responsecomplex 1(ABRC1)=A3(previously designated ABRE3)+CE1 (Shen etal., Plant Cell 8:1107(1996));ABREG-boxcoupling elementCE1HVA22barley (Hordeum vulgare);=Shen Q, Ho THDShen Q, Zhang P, Ho THDBusk PK, Pages MSingh KB��Functional dissection of an abscisic acid(ABA)-inducible genereveals two independent ABA-responsive complexes each containinga G-box and a novel cis-acting element.Modular nature of abscisic acid (ABA) response complexes:composite promoter units that are necessary and sufficient forABA induction of gene expression in barley.Regulation of abscisic acid-induced transcriptionTranscriptional Regulation in Plants: The Importance ofCombinatorial ComtroltPlant Cell 7:295-307 (1995)Plant Cell 8:1107-1119 (1996)Plant Mol Biol 37:425-435 (1998)Plant Physiol 118: 1111-11200PubMed: 7734964;PubMed: 8768371;PubMed: 9617810; Reviewreview
GCCACGTACA ABRE3OSRAB16S000120 29-Sep-1999 (last modified) kehiCABA-responsive element of rice (O.s.) rab16 and alpha-amylasegenes;ABArab16
alpha-amylaseABREseedrice (Oryza sativa);7Skriver K, Olsen FL, Rogers JC, Mundy JBusk PK, Pages M�Cis-acting DNA elements responsive to gibberellin and itsantagonist abscisic acid.Regulation of abscisic acid-induced transcriptionJProc Natl Acad Sci USA 88:7266-7270 (1991)Plant Mol Biol 37:425-435 (1998) PubMed: 1831269;PubMed: 9617810;Review GTACGTGGCGC
ABREA2HVA1S000140 17-May-2001 (last modified) uchi�A2 of ABRC3; ABRC3 (ABA response complex 3) of HVA1 consists ofCE3 and A2; ABA responsive element; stress response; Found inbarley HVA1 gene encoding a class 3 late embryogenesis-abundant(Lea) protein; ABRC1 OF HVA22 consists of CE1 and A3;CE1=S000014; A3=ABRE3=S000118; See S000118;A2ABRC3ABREABAHVA1Leaseedbarley (Hordeum vulgare)'Shen Q, Zhang P, Ho THDBusk PK, Pages M�Modular nature of abscisic acid (ABA) response complexes:composite promoter units that are necessary and sufficient forABA induction of gene expression in barley.Regulation of abscisic acid-induced transcription=Plant Cell 8:1107-1119 (1996)Plant Mol Biol 37:425-435 (1998) PubMed: 8768371;PubMed: 9617810;Review
CCTACGTGGC ABREAZMRAB28S000218 11-May-2006 (last modified) kehi�ABA-responsive element (ABRE A) found at -148 to -139 in maizerab28 (Busk & Pages, 1997); Maize rab28 is ABA-inducible inembryos and vegetative tissues;ABAABRErab28seedshootmaize (Zea mays) Busk PK, Pages MBusk PK, Pages M�Protein binding to the abscisic acid-responsive element isindependent of VIVIPAROUS1 in vivoRegulation of abscisic acid-induced transcription=Plant Cell 9:2261-2270 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 11407411PubMed: 9617810;Review
GCCACGTGGG
ABREBNNAPAS000145 16-Feb-2001 (last modified) seki��ABRE of napA storage-protein gene of Brassica napus (B.n.); ABAresponsive element; dist B ABRE mediated transactivation by ABI3adn ABI3-dependent response to ABA; a tetramer of the compositeRY/G complex mediated only ABA-independent transactivation byABI3; B2 domain of ABI3 is necessary for ABA-independent andABA-dependent activation through the dist B ABRE; B3 domain ofABI3 interacts with the RY/G complex;napAstorage proteinABREnapinseedBrassica napus;xStalberg K, Ellerstom M, Ezcurra I, Ablov S, Rask LBusk PK, Pages MEzcurra I, Wycliffe P, Nehlin L, Ellerstrom M, Rask L��Disruption of an overlapping E-box/ABRE motif abolished hightranscription of the napA storage-protein promoter in transgenicBrassica napus seeds.Regulation of abscisic acid-induced transcriptionTransactivation of the Brassica napus napin promoter by ABI3requires interaction of the conserved B2 and B3 domains of ABI3with different cis-elements: B2 mediates activation through anABRE, whereas B3 interacts with an RY/G-boxPPlanta 199:515-519 (1996)Plant Mol Biol 37:425-435 (1998)Plant J 24:57-66 (2000)1PubMed: 8818291;PubMed: 9617810;PubMed: 11029704;Review CGCCACGTGTCC ABREBZMRAB28S000219 11-May-2006 (last modified) kehi�ABA-responsive element (ABRE B) found at -105 to -96 in maize(Z.m.) rab28 (Busk & Pages, 1997); Maize rab28 is ABA-induciblein embryos and vegetative tissues;ABAABRErab28embryoseedshootmaize (Zea mays) Busk PK, Pages MBusk PK, Pages M�Protein binding to the abscisic acid-responsive element isindependent of VIVIPAROUS1 in vivoRegulation of abscisic acid-induced transcription=Plant Cell 9:2261-2270 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 11407411PubMed: 9617810;Review
TCCACGTCTC ABRECE1HVA22S000014 03-Jun-2003 (last modified) kehi�CE1(coupling element 1) of barley HVA22 gene; possible bindingsite for nuclear bZIP protein; ABA responsive complex consists ofa G-box, namely ABRE3 (GCCACGTACA), and CE1;ABACE1bZIPG boxG-boxABREshootbarley (Hordeum vulgare)7Shen Q, Ho THBray EABusk PK, Pages MCasaretto J, Ho TH.�wFunctional dissection of an abscisic acid(ABA)-inducible genereveals two independent ABA-responsive complexes each containinga G-box and a novel cis-acting element.Plant responses to water deficitRegulation of abscisic acid-induced transcriptionThe transcription factors HvABI5 and HvVP1 are required for theabscisic acid induction of gene expression in barley aleuronecells.~Plant Cell 7:295-307 (1995)Trends in Plant Science 2:48-54 (1997)Plant Mol Biol 37:425-435 (1998)Plant Cell 15: 271-284 (2003)1PubMed: 7734964;PubMed: 9617810;PubMed: 12509536;Review TGCCACCGG ABRECE3HVA1S000141 03-jun-2003 (last modified) kehi�DCE3 (coupling element 3) of ABRC3 in barley HVA1 gene; ABRC3 (ABAresponse complex 3) of HVA1 consists of CE3 and A2; ABAresponsive element; stress response; Found in barley HVA1 geneencoding a class 3 late embryogenesis-abundant (Lea) protein;ABRC1 OF HVA22 consists of CE1 and A3; CE1=S000014;A3=ABRE3=S000118; See S000118;CE3coupling elementABRC3ABREABAHVA1Leaseedbarley (Hordeum vulgare);AShen Q, Zhang P, Ho THDBray EABusk PK, Pages MCasaretto J, Ho TH.�uModular nature of abscisic acid (ABA) response complexes:composite promoter units that are necessary and sufficient forABA induction of gene expression in barley.Plant responses to water deficitRegulation of abscisic acid-induced transcriptionThe transcription factors HvABI5 and HvVP1 are required for theabscisic acid induction of gene expression in barley aleuronecells.�Plant Cell 8:1107-1119 (1996)Trends in Plant Science 2:48-54 (1997)Plant Mol Biol 37:425-435 (1998)Plant Cell 15: 271-284 (2003)1PubMed: 8768371;PubMed: 9617810;PubMed: 12509536;Review ACGCGTGTCCTCABRECE3ZMRAB28S000221 11-May-2006 (last modified) kehi�CE3 (coupling element 3) in maize (Z.m.) rab28 gene promoter; ABAresponsive element; stress response; Similar (10 of 12) to CE3 inA1 gene of barley; See S000141 (ABRECE3HVA1); Found at -126 to-115;CE3coupling elementRAB28rabABREABAseedmaize (Zea mays) Busk PK, Pages MBusk PK, Pages M�Protein binding to the abscisic acid-responsive element isindependent of VIVIPAROUS1 in vivoRegulation of abscisic acid-induced transcription=Plant Cell 9:2261-2270 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 11407411PubMed: 9617810;Review ACGCGCCTCCTCABREDISTBBNNAPAS000262 16-Feb-2001 (last modified) seki��"dist B (distal portion of B-box)" found in napA gene of Brassicanapus (B.n.); Shows similarity to ABRE; Found between -148 and-124; Required for seed specific expression and ABAresponsiveness; See S000263, S000264; dist B ABRE mediatedtransactivation by ABI3 adn ABI3-dependent response to ABA; atetramer of the composite RY/G complex mediated onlyABA-independent transactivation by ABI3; B2 domain of ABI3 isnecessary for ABA-independent and ABA-dependent activationthrough the dist B ABRE;ABREABAdistBB-boxseednapAnapinBrassica napus|Ezcurra I, Ellerstrom M, Wycliffe P, Stalberg K, Rask LBusk PK, Pages MEzcurra I, Wycliffe P, Nehlin L, Ellerstrom M, Rask L��Interaction between composite elements in the napA promoter: boththe B-box ABA-responsive complex and the RY/G complex arenecessary for seed-specific expressionRegulation of abscisic acid-induced transcriptionTransactivation of the Brassica napus napin promoter by ABI3requires interaction of the conserved B2 and B3 domains of ABI3with different cis-elements: B2 mediates activation through anABRE, whereas B3 interacts with an RY/G-boxYPlant Mol Biol 40:699-709 (1999)Plant Mol Biol 37:425-435 (1998)Plant J 24:57-66 (2000)2PubMed: 10480393;PubMed: 9617810;PubMed: 11029704;
GCCACTTGTC ABRELATERD1S000414#01-August-2006 (last modified) kehi�ABRE-like sequence (from -199 to -195) required foretiolation-induced expression of erd1 (early responsive todehydration) in Arabidopsis;ABRE
etiolationerdArabidopsis thaliana�Simpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K,Yamaguchi-Shinozaki K.Nakashima K, Fujita Y, Katsura K, Maruyama K, Narusaka Y, Seki M,Shinozaki K, Yamaguchi-Shinozaki K.�+Two different novel cis-acting elements of erd1, a clpAhomologous Arabidopsis gene function in induction by dehydrationstress and dark-induced senescence.Transcriptional regulation of ABI3- and ABA-responsive genesincluding RD29B and RD29A in seeds, germinating embryos, andseedlings of Arabidopsis.;Plant J. 33: 259-270 (2003)Plant Mol Biol. 60:51-68 (2006).!PubMed: 12535340;PubMed: 16463099 ACGTGABREMOTIFAOSOSEMS000299 16-Feb-2001 (last modified) seki�"motif A" ABRE-like sequence found in rice (O.s.) Osem genepromoter; Essential for activation by VP1; Important forregulation by ABA; See S000102, S000300; TRAB1, bZIPtranscription factor, interacts with VP1 and mediates abscisicacid-induced transcritption;ABREEmOsemABAVP1seedrice (Oryza sativa);Hattori T, Terada t, Hamasuna SHobo T, Kowyama Y, Hattori T�Regulation of the Osem gene by abscisic acid and thetranscriptional activator VP1: analysis of cis-acting promoterelements required for regulation by abscisic acid and VP1A bZIP factor, TRAB1, interacts with VP1 and mediates abscisicacid-induced transcriptionFPlant J 7: 913-925 (1995)Proc Natl Acad Sci USA 96: 15348-15353 (1999)1PubMed: 7599651; GenBank: U22102PubMed: 10611387; TACGTGTCABREMOTIFIIIOSRAB16BS000291 10-Feb-2000 (last modified) seki�"Motif III" found in the promoter of rice (O.s.) rab16B gene;Motif I (S000290) and motif III are both required for ABAresponsiveness; However, each can substitute for the other;ABAABRE motif IIIrab16Brice (Oryza sativa)%Ono A, Izawa T, Chua N-H, Shimamoto KRThe rab16B promoter of rice contains two distinct abscisicacid-responsive elements!Plant Physiol 112: 483-491 (1996)PubMed: 8883374
GCCGCGTGGCABREMOTIFIOSRAB16BS000290 10-Feb-2000 (last modified) seki�"Motif I" found in the promoter of rice (O.s.) rab16B gene; MotifI and motif III (S000291) are both required for ABAresponsiveness; However, each can substitute for the other; SeeS000019, S000120;ABAABREmotif Irab16Brice (Oryza sativa)%Ono A, Izawa T, Chua N-H, Shimamoto KRThe rab16B promoter of rice contains two distinct abscisicacid-responsive elements!Plant Physiol 112: 483-491 (1996)PubMed: 8883374
AGTACGTGGCABRETAEMS000015 29-Sep-1999 (last modified) kehi�"ABRE (ABA responsive element)" found in wheat (T.a.) Em gene;transacting factor: EMBP-1; EMBP-1 binds to CACGTGGC; See S000119EMBP1;ABAABREEMBP-1seedwheat (Triticum aestivum)BGuiltinan MJ, Marcotte WR Jr, Quatrano RSThomas TLBusk PK, Pages M�A plant leucine zipper protein that recognizes an abscisic acidresponse elementGene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcriptionWScience 250:267-270 (1990)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998)HPubMed: 2145628; GenBank: M62893, M63999;PubMed: 8281041;PubMed: 9617810 ReviewReview GGACACGTGGC ABREZMRAB28S000133!23-June-2006 (last modified) kehi��ABRE; ABA and water-stress responses; Found in maize (Z.m.)rab28; maize rab28 is ABA-inducible in embryos and vegetativetissues; Found in the Arabidopsis (A.t.) alcohol dehydrogenase(Adh) gene promoter; "ABRE2"; Found in the maize (Z.m.) Cat1 genepromoter; Responsible for the induction by ABA; Binding site ofCBF2; Arabidopsis CBF1 overexpression induces COR genes andenhances freezing tolerance; The CBF genes do not appear to beautoregulated through the CRT/DRE sequence;ABRErab28G-boxAdhCat1ABACBF1DRERGA1CORfreezing toleranceseedshootCBF2Imaize (Zea mays); Arabidopsis thaliana; rice (Oryza sativa);Populus spp.;��Suzuki M, Ketterling MG, McCarty DR.Busk PK, Pages MAlonso-Blanco C, Gomez-Mena C, Llorente F, Koornneef M, SalinasJ, Martinez-Zapater JMGuan LM, Zhao J, Scandalios JGBenedict C, Skinner JS, Meng R, Chang Y, Bhalerao R, Huner NPA,Finn CE, Chen THH, Hurry VJaglo-Ottosen KR, Gilmour SJ, Zarka DG, Schabenberger O,Thomashow MFGilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM,Thomashow MF�aQuantitative statistical analysis of cis-regulatory sequences inABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis.Regulation of abscisic acid-induced transcriptionGenetic and Molecular Analyses of Natural Variation Indicate CBF2as a Candidate Gene for Underlying a Freezing ToleranceQuantitative Trait Locus in ArabidopsisCis-elements and trans-factors that regulate expression of themaize Cat1 antioxidant gene in response to ABA and osmoticstress: H2O2 is the likely intermediary signaling molecule forthe responseThe CBF1-dependent low temperature signalling pathway, regulonand increase in freeze tolerance are conserved in Populus spp.Arabidopsis CBF1 overexpression induces COR genes and enhancesfreezing toleranceLow temperature regulation of the Arabidopsis CBF family of AP2transcriptional activators as an early step in cold-induced CORgene expression�Plant Physiol.139: 437-447 (2005)Plant Mol Biol 37:425-435 (1998)Plant Physiology 139: 1304-1312 (2005)Plant J 22: 87-95 (2000)Plant, Cell and Environment 29:1259-1272 (2006)Science 1998 3: 104-106 (1998)Plant J 16: 433-442 (1998)aPubMed: 16113229PubMed: 9617810;PubMed: 16244146PubMed: 10792824;PubMed: 9525853;PubMed: 9881163;in silicoReviewCCACGTGGACEATCHSS000355#02-August-2006 (last modified) kehi��"ACEAtCHS (ACGT containing element)" found in the LRU(light-responsive unit) in Arabidopsis (A.t.) chalcone synthase(CHS) gene promoter; Required for UV-B and UV-1/blue lightresponsiveness; See S000356; Transcriptional repression by AtMYB4controls production of UV-protecting sun screens in Arabidopsis;AtMYB4 mutant shows enhanced levels of sinapate ester in leavesand tolerance of UV-B irradiation; AtMYB4 expression isdownregulated by exposure to UV-B light; CHSACEMYBlightUV-AUV-BMYB4leafshootArabidopsis thaliana�Hartmann U, Valentine WJ, Christie JM, Hays J, Jenkins GI,Weisshaar BJin H, Cominelli E, Bailey P, Parr A, Mehrtens F, Jones J,Tonelli C, Weisshaar B, Martin CHartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B.��Identification of UV/blue light-response elements in theArabidopsis thaliana chalcone synthase promoter using ahomologous protoplast transient expression systemTranscriptional repression by AtMYB4 controls production ofUV-protecting sunscreens in ArabidopsisDifferential combinatorial interactions of cis-acting elementsrecognized by R2R3-MYB, BZIP, and BHLH factors controllight-responsive and tissue-specific activation ofphenylpropanoid biosynthesis genes._Plant Mol Biol (1998) 36: 741-754EMBO J 19: 6150-6161 (2000)Plant Mol Biol. 57: 155-171 (2005).1PubMed: 9526507;PubMed: 11080161;PubMed: 15821875
GACACGTAGAACGTABOXS000130 7-Sep-2000 (last modified) seki�p"A-box" according to the nomenclature of ACGT elements by Fosteret al. (FASEB J 8:192-200 (1994)); One of ACGT elements; Found inocs gene; RITA-1 binding site (Izawa et al. 1994); "G motif" byToyofuku et al. (1998); G motif and TATCCAY motif (a GATA motifas its antisense sequence; see S000256) are responsible forsugar repression (Toyofuku et al. 1998); See S000346;A-box ACGT elementG motifsugar
repressionseedplant; rice (Oryza sativa);qFoster R, Izawa T, Chua N-HIzawa T, Foster R, Nakajima M, Shimamoto K, Chua N-HToyofuku K, Umemura T, Yamaguchi J�Plant bZIP Proteins gather at ACGT elements.The rice bZIP transcriptional activator RITA-1 is highlyexpressed during seed development.Promoter elements required for sugar-repression of the RAmy3Dgene for alpha-amylase in riceRFASEB J 8:192-200 (1994)Plant Cell 6:1277-1287 (1994)FEBS Lett 428:275-280 (1998)@PubMed: 8119490;PubMed: 7919992; GenBank: L34551;PubMed: 9654148ReviewTACGTAACGTABREMOTIFAOSOSEMS000281 16-Feb-2001 (last modified) seki�="ABRE motif A" found in the promoter of the rice (O.s.) Osemgene; ACGT-containing ABRE; Required for ABA-responsiveness andVP1 activation; Binding site of TRAB1; Motif A and CE3 (S000282)are functionally equivalent; TRAB1, bZIP transcription factor,interacts with VP1 and mediates abscisic acid-inducedtranscritption;
Motif AABRECE3ABAVP1TRAB1OsemEmbZIPseedrice (Oryza sativa)AHobo T, Asada M, Kowyama Y, Hattori THobo T, Kowyama Y, Hattori T�ACGT-containing abscisic acid response element (ABRE) andcoupling element 3 (CE3) are functionally equivalentA bZIP factor, TRAB1, interacts with VP1 and mediates abscisicacid-induced transcriptionHPlant J 19: 679-689 (1999)Proc Natl Acad Sci USA 96: 15348-15353 (1999)"PubMed: 10571853;PubMed: 10611387; TACGTGTC
ACGTATERD1S000415 03-Jun-2003 (last modified) kehi�ACGT sequence (from -155 to -152) required for etiolation-inducedexpression of erd1 (early responsive to dehydration) inArabidopsis;ACGT
etiolationerdArabidopsis thalianaOSimpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K,Yamaguchi-Shinozaki K.�Two different novel cis-acting elements of erd1, a clpAhomologous Arabidopsis gene function in induction by dehydrationstress and dark-induced senescence.Plant J. 33: 259-270 (2003)PubMed: 12535340; ACGTACGTCBOXS000131 16-Jan-1998 (last modified) kehi�"C-box" according to the nomenclature of ACGT elements by Fosteret al. (FASEB J 8:192-200 (1994)); One of ACGT elements; Factorsgroups 1, 2 and 3 have affinity for C-box (Izawa et al. J MolBiol. 230:1131-1144 (1993)); RITA-1 binding site (Izawa et al.1994);C-box ACGT elementseedplant;jFoster R, Izawa T, Chua N-HIzawa T, Foster R, Nakajima M, Shimamoto K, Chua N-HIzawa T, Foster R, Chua N-H�Plant bZIP Proteins gather at ACGT elements.The rice bZIP transcriptional activator RITA-1 is highlyexpressed during seed development.Plant bZIP protein DNA binding specificity.TFASEB J 8:192-200 (1994)Plant Cell 6:1277-1287 (1994)J Mol Biol 230:1131-1144 (1993)BPubMed: 8119490;PubMed: 7919992; GenBank: L345501;PubMed: 8487298;ReviewGACGTC ACGTOSGLUB1S000278 16-Feb-2001 (last modified) seki�<"ACGT motif" found in GluB-1 gene in rice (O.s.); Required forendosperm-specific expression; Conserved in the 5'-flankingregion of glutelin genes; See S000276, S000277; SeeS000019;Combination of GCN4, AACA and ACGT motifs was foundsufficient to confer a detectable level of endosperm expression;See S000353, S000354;GluB-1glutelin endospermseedstorage protein
ACGT motifrice (Oryza sativa)vWashida H, Wu CY, Suzuki A, Yamanouchi U, Akihama T, Harada K,Takaiwa FWu C, Washida H, Onodera Y, Harada K, Takaiwa F� Identification of cis-regulatory elements required for endospermexpression of the rice storage protein glutelin gene GluB-1Quantitative nature of the Prolamin-box, ACGT and AACA motifs ina rice glutelin gene promoter: minimal cis-element requirementsfor endosperm-specific gene expression7Plant Mol Biol 40:1-12 (1999)Plant J 23: 415-421 (2000)"PubMed: 10394940;PubMed: 10929134; GTACGTG ACGTROOT1S000016 31-Jul-2001 (last modified) uchi�S"ACGT motif" related to root expression; Gene: synthetic; perfectpalindromic sequence (PA) containing G-box-related sequence;transacting factor: TAF-1 ?; Binding of SGBF-1 (a Soybean G-boxbinding bZIP transcription factor) to ABRE is enhanced by SCOF-1(a zinc finger protein ); Transcription of SCOF-1 is induced bylow temperature and ABA;
rootACGTG boxG-box
ABRE motifbZIP binding enhancementcold toleranceCORSGBF-1SCOF-12tobacco (Nicotiana tabacum); soybean (Glycine max)~Salinas J, Oeda K, Chua N-HThomas TLKim JC, Lee SH, Cheong YH, Yoo CM, Lee SI, Chun HJ, Yun DJ, HongJC, Lee SY, Lim CO, Cho MJ�Two G-box-related sequences confer different expression patternsin transgenic tobaccoGene expression during plant embryogenesis and germination: Anoverview.A novel cold-inducible zinc finger protein from soybean, SCOF-1,enhances cold tolerance in transgenic plantsTPlant Cell 4:1485-1493 (1992)Plant Cell 5:1401-1410 (1993)Plant J 25: 247-259 (2001)1PubMed: 1467649;PubMed: 8281041;PubMed: 11208017;Review
GCCACGTGGC ACGTSEED2S000018 17-May-1998 (last modified) kehi\"ACGT motif" related to seed expression; Gene: French beanphaseolin; transacting factor: 02; phaseolinseedACGT&French bean; bean (Phaseolus vulgaris)Bustos MThomas TLGGene expression during plant embryogenesis and germination: Anoverview.Zpersonal communication (cited in a review by Thomas TL, 1993)Plant Cell 5:1401-1410 (1993)PubMed: 8281041;Review ACACACGTCAA ACGTSEED3S000019 10-Feb-2000 (last modified) seki�"ACGT motif" related to seed expression; Gene: synthetic;wild-type motif (Iwt) containing G-box-related sequence;transacting factor: bZIP ?; A tobacco bZip transcriptionactivator (TAF-1) binding site;seedACGTG-boxG boxtobacco?Salinas J, Oeda K, Chua N-HThomas TLOeda K, Salinas J, Chua N-H�� Two G-box-related sequences confer different expression patternsin transgenic tobacco.Gene expression during plant embryogenesis and germination: Anoverview.A tobacco bZip transcription activator (TAF-1) binds to aG-box-like motif conserved in plant genesUPlant Cell 4:1485-1493 (1992)Plant Cell 5:1401-1410 (1993)EMBO J 10: 1792-1802 (1991)/PubMed: 1467649;PubMed: 8281041;PubMed: 2050116Review
GTACGTGGCGACGTTBOXS000132 18-Mar-1998 (last modified) kehi�"T-box" according to the nomenclature of ACGT elements by Fosteret al. (FASEB J 8:192-200 (1994)); One of ACGT elements; See alsoACGTABOX (S000130), ACGTCBOX (S000131), and CACGTGMOTIF(S000042);T-boxT box
ACGT element:plant;Foster R, Izawa T, Chua N-H,Plant bZIP Proteins gather at ACGT elements.FASEB J 8:192-200 (1994)PubMed: 8119490;ReviewAACGTT ACIIIPVPAL2S000194&15-September-2006 (last modified) kehi��ACIII element found at -246 to -238 of bean (P.v.) PAL2 promoter;ACIII element is required for vascular-specific gene expression;See also ACIPVPAL2 (S000192) and ACIIPVPAL2 (S000193); ThreeAC-elements, which are possible Myb protein binding sites,together with a G-box, interact to direct the complex patterns oftissu-specific expression of pAL2 gene; Implicated in thexylem-localized regulation of genes encoding lignin biosyntheticenzymes in loblolly pine (Patzlaff et al., 2003);
vascularPALPAL2ACIIIphloemxylemstemligninMYBR2R3-MYB7bean (Phaseolus vulgaris); Pinus taeda (loblolly pine);�Hatton D, Sablowski R, Yung MH, Smith C, Schuch W, Bevan MPatzlaff A, Newman LJ, Dubos C, Whetten RW, Smith C, McInnis S,Bevan MW, Sederoff RR, Campbell MMGomez-Maldonado J, Avila C, Torre F, Canas R, Canovas FM,Campbell MM�Tow classes of cis sequences contribute to tissue-specificexpression of a PAL2 promoter in transgenic tobaccoCharacterisation of Pt MYB1, an R2R3-MYB from pine xylem.Functional interactions between a glutamine synthetase promoterand MYB proteins.UPlant J 7:859-876 (1995)Plant Mol Biol. 53:597-608 (2003).Plant J. 39:513-526 (2004).0PubMed: 7599647;PubMed: 15010621PubMed: 15272871 GTTAGGTTC
ACIIPVPAL2S000193&15-September-2006 (last modified) kehi��ACII element found at -131 to -120 of bean (P.v.) PAL2 promoter;ACII element is required for vascular-specific gene expression;See also ACIPVPAL2 (S000192) and ACIIIPVPAL2 (S000194); ThreeAC-elements, which are possible Myb protein binding sites,together with a G-box, interact to direct the complex patterns oftissu-specific expression of pAL2 gene; Implicated in thexylem-localized regulation of genes encoding lignin biosyntheticenzymes in loblolly pine (Patzlaff et al., 2003); vascularPALACIIphloemxylemstemligninMYBR2R3-MYB7bean (Phaseolus vulgaris); Pinus taeda (loblolly pine);�Hatton D, Sablowski R, Yung MH, Smith C, Schuch W, Bevan MPatzlaff A, Newman LJ, Dubos C, Whetten RW, Smith C, McInnis S,Bevan MW, Sederoff RR, Campbell MMGomez-Maldonado J, Avila C, Torre F, Canas R, Canovas FM,Campbell MM�Tow classes of cis sequences contribute to tissue-specificexpression of a PAL2 promoter in transgenic tobaccoCharacterisation of Pt MYB1, an R2R3-MYB from pine xylem.Functional interactions between a glutamine synthetase promoterand MYB proteins.UPlant J 7:859-876 (1995)Plant Mol Biol. 53:597-608 (2003).Plant J. 39:513-526 (2004).0PubMed: 7599647;PubMed: 15010621PubMed: 15272871 CCACCAACCCCC ACIPVPAL2S000192&15-September-2006 (last modified) kehi��ACI element found at -83 to -74 of bean (P.v.) PAL2 promoter;AC-rich element; ACI element is required for vascular-specificgene expression; See also ACIIPVPAL2 (S000193) and ACIIIPVPAL2(S000194); Three AC-elements, which are possible Myb proteinbinding sites, together with a G-box, interact to direct thecomplex patterns of tissue-specific expression of pAL2 gene;Implicated in the xylem-localized regulation of genes encodinglignin biosynthetic enzymes in loblolly pine (Patzlaff et al.,2003); vascularPALACIphloemxylemstemligninMYBR2R3-MYB6Phaseolus vulgaris(bean); Pinus taeda (loblolly pine);�Hatton D, Sablowski R, Yung MH, Smith C, Schuch W, Bevan MPatzlaff A, Newman LJ, Dubos C, Whetten RW, Smith C, McInnis S,Bevan MW, Sederoff RR, Campbell MMGomez-Maldonado J, Avila C, Torre F, Canas R, Canovas FM,Campbell MM�Tow classes of cis sequences contribute to tissue-specificexpression of a PAL2 promoter in transgenic tobaccoCharacterisation of Pt MYB1, an R2R3-MYB from pine xylem.Functional interactions between a glutamine synthetase promoterand MYB proteins.UPlant J 7:859-876 (1995)Plant Mol Biol. 53:597-608 (2003).Plant J. 39:513-526 (2004).0PubMed: 7599647;PubMed: 15010621PubMed: 15272871
CCCACCTACC AGCBOXNPGLBS000232#02-August-2006 (last modified) kehi��"AGC box" repeated twice in a 61 bp enhancer element in tobacco(N.p.) class I beta-1,3-glucanase (GLB) gene; See S000036,S000089; "GCC-box"; Binding sequence of Arabidopsis AtERFs;AtERF1,2 and 5 functioned as activators of GCC box-dependenttranscription; AtERF3 and 4 acted as repressors; AtERF proteinsare stress signal-response factors; EREBP2 binding site;Conserved in most PR-protein genes; Rice MAPK (BWMK1)phosphorylates OS EREBP1, which enhance DNA-binding activity ofthe factor to the GCC box; AGC boxGLBEREERFsEthyleneGCC-box Neutral PR-5osmotin-like proteinEREBP2MAPKBWMK1PR box{tobacco (Nicotiana plumbaginifolia); Arabidopsis (Arabidopsisthaliana); tobacco (Nicotiana sylvestris); Oryza sativa; rice;��Hart CM, Nagy F, Meins Jr FFujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi MSato F, Kitajima S, Koyama T, Yamada YOhme-Takagi M, Suzuki K, Shinshi HRushton PJ, Reinstadler A, Lipka V, Lippok B, Somssich IECheong YH, Moon BC, Kim JK, Kim CY, Kim MC, Kim IH, Park CY, KimJC, Park BO, Koo SC, Yoon HW, Chung WS, Lim CO, Lee SY, Cho MJZhang H, Huang Z, Xie B, Chen Q, Tian X, Zhang X, Zhang H, Lu X,Huang D, Huang R.��A 61 bp enhancer element of the tobacco beta-1,3-glucanase B geneinteracts with one or more regulated nuclear proteinsArabidopsis ethylene-responsive element binding factors act astranscriptional activators or repressors of GCC box-mediated geneexpressionEthylene-induced gene expression of osmotin-like protein, aneutral isoform of tobacco PR-5, is mediated by the AGCCGCCcis-sequenceRegulation of Ethylene-Induced Transcription of Defense GenesSynthetic plant promoters containing defined regulatory elementsprovide novel insights into pathogen- and wound-inducedsignalingBWMK1, a rice mitogen-activated protein kinase, locates in thenucleus and mediates pathogenesis-related gene expression byactivation of a transcription factor.The ethylene-, jasmonate-, abscisic acid- and NaCl-responsivetomato transcription factor JERF1 modulates expression of GCCbox-containing genes and salt tolerance in tobacco.�Plant Mol Biol 21:121-131 (1993)Plant Cell 12:393-404 (2000)Plant Cell Physiol 37: 249-255 (1996)Plant Cell Physiol 41: 1187-1192 (2000)Plant Cell 14: 749-762 (2002)Palnt Physiol. 132: 1961-1972 (2003)Planta. 220: 262-270 (2004)tPubMed: 8425042;PubMed: 10715325;PubMed: 8673338;PubMed: 11092902;PubMed: 11971132;PubMed: 12913152;PubMed: 15300440 AGCCGCC
AGMOTIFNTMYB2S000444 28-Jan-2004 (last modified) kehi�+AG-motif found at -114 of the promoter of NtMyb2 gene; NtMyb2 isa regulator of the tobacco retrotransposon Tto1 and thedefence-related gene phenylalanine ammonia lyase (PAL), which areinduced by various stress such as wounding or elicitor treatment;AGP1 (GATA-type zinc finger protein) binding site;MYBTto1PALAGP1GATANicotiana tabacum (tobacco)!Sugimoto K, Takeda S, Hirochika H�Transcriptional activation mediated by binding of a plantGATA-type zinc finger proteinAGP1 to the AG-motif (AGATCCAA) ofthe wound-inducible Myb gene NtMyb2.Plant J, 36: 550-564 (2003)PubMed: 14617085; AGATCCAAAGTACSAOS000258 14-Oct-1999 (last modified) kehi�"AGTA repeat" in pumpkin (C.s.) ascorbate oxidase gene (AO)promoter; Found in silencer region; AOBP (AGTA repeat bindingprotein) binding site; AOBP protein has DOF domain; Required forrepression of expression of AO gene; AGTA repeatDOFAOBPascorbate oxidasesilencer regionpumpkin (Cucurbita sp.)1Kisu Y, Ono T, Shimofurutani N, Suzuki M, Esaka M|Characterization and expression of a new class of zinc fingerprotein that binds to silencer region of ascorbate oxidase gene&Plant Cell Physiol 39:1054-1064 (1998)"PubMed: 9871365; GenBank: D45066; AAAAAGTAAAAAGTAAAAAAGTAAAAAG
ALF1NTPARCS000238 11-Oct-1999 (last modified) kehi�"ALF-1 (as-1-like sequence binding factor)" binding site found intobacco (N.t.) parC gene; Found in auxin-responsive regions;as-1-like sequences in parA, parB and parC bind with ASF-1,ALF-2, and ALF-1, respectively; See S000190 (ABFOS);as-1ALF-1parauxin tobacco (Nicotiana tabacum); Sakai T, Takahashi Y, Nagata T{The identification of DNA binding factor specific for as-1-likesequences in auxin-responsive regions of parA, parB and parC%Plant Cell Physiol 39:731-739 (1998)PubMed: 9729895; TTACGCAAGCAATGACA
ALF2NTPARBS000239 11-Oct-1999 (last modified) kehi�"ALF-2 (as-1-like sequence binding factor 2)" binding site foundin tobacco (N.t.) parB gene; Found in auxin-responsive regions;as-1-like sequences in parA, parB and parC bind with ASF-1,ALF-2, and ALF-1, respectively; See S000190 (ABFOS);as-1ALF-2parauxin tobacco (Nicotiana tabacum); Sakai T, Takahashi Y, Nagata T{The identification of DNA binding factor specific for as-1-likesequences in auxin-responsive regions of parA, parB and parC%Plant Cell Physiol 39:731-739 (1998)PubMed: 9729895; TGAGGAGACTTGTGAGGTAMMORESIVDCRNIA1S000375 31-Jul-2001 (last modified) uchi�Motif (IVD) found in the Chlamydomonas (C.R.) Nia1 gene promoter;Located between -51 and -42; Involved in Nia1 transcriptionrepression;nitrate reductaseammonium responseChlamydomonas reinhardtiiLoppes R, Radoux M�Identification of short promoter regions involved in thetranscriptional expression of the nitrate reductase gene inChlamydomonas reinhardtii!Plant Mol Biol 45: 215-227 (2001)PubMed: 11289512; CGAACTTAMMORESVDCRNIA1S000376 31-Jul-2001 (last modified) uchi�Motif (VD) found in the Chlamydomonas (C.R.) Nia1 gene promoter;Located between -33 and -8; Involved in Nia1 transcriptionactivation;nitrate reductaseammonium responseChlamydomonas reinhardtiiLoppes R, Radoux M�Identification of short promoter regions involved in thetranscriptional expression of the nitrate reductase gene inChlamydomonas reinhardtii!Plant Mol Biol 45: 215-227 (2001)PubMed: 11289512; GGCCCCGGGAMYBOX2S000021 17-May-1998 (last modified) kehi�"amylase box"; "amylase element"; Conserved sequence found in5'upstream region of alpha-amylase gene of rice, wheat, barley;"amylase box" (Huang et al. 1990); "amylase element" (Hwang etal., 1998);amylaseseedGbarley (Hordeum vulgare); rice (Oryza sativa); wheat (Triticumaestivum)_Huang N, Sutliff TD, Litts JC, Rodriguez RLHwang YS, Karrer EE, Thomas BR, Chen L, Rodriguez RL�Classification and characterization of the rice alpha-amylasemultigene family.Three cis-elements required for rice alpha-amylase Amy3Dexpression during sugar starvation@Plant Mol Biol 14:655-668 (1990)Plant Mol Biol 36:331-341 (1998)1PubMed: 2102847; GenBank: X16509;PubMed: 9484474; TATCCATANAERO1CONSENSUSS000477%05-November-2005 (last modified) kehi�One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway (anaerobic set1)(Mohanty et al., 2005); Arbitrary named ANAERO1CONSENSUS by thePLACEdb curator; See also S000478, S000479, S000480, S000481; anaerobic�Zea mays (maize); Arabidopsis thaliana; Pisum sativum (pea);Hordeum vulgare (barley); Oryza sativa (rice); Petunia hybrida(petunia); Lycopersicon esculentum (tomato);+Mohanty B, Krishnan SP, Swarup S, Bajic VB.sDetection and preliminary analysis of motifs in promoters ofanaerobically induced genes of different plant species.!Ann Bot (Lond).96: 669-681 (2005)PubMed: 16027132 in silicoAAACAAAANAERO2CONSENSUSS000478%05-November-2005 (last modified) kehi�One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway (anaerobic set1)(Mohanty et al., 2005); Arbitrary named ANAERO2CONSENSUS by thePLACEdb curator; See also S000477, S000479, S000480, S000481; anaerobic�Zea mays (maize); Arabidopsis thaliana; Pisum sativum (pea);Hordeum vulgare (barley); Oryza sativa (rice); Petunia hybrida(petunia); Lycopersicon esculentum (tomato);+Mohanty B, Krishnan SP, Swarup S, Bajic VB.sDetection and preliminary analysis of motifs in promoters ofanaerobically induced genes of different plant species.!Ann Bot (Lond).96: 669-681 (2005)PubMed: 16027132 in silicoAGCAGCANAERO3CONSENSUSS000479%05-November-2005 (last modified) kehi�One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway (anaerobic set1)(Mohanty et al., 2005); Arbitrary named ANAERO3CONSENSUS by thePLACEdb curator; See also S000477, S000478, S000480, S000481; anaerobic�Zea mays (maize); Arabidopsis thaliana; Pisum sativum (pea);Hordeum vulgare (barley); Oryza sativa (rice); Petunia hybrida(petunia); Lycopersicon esculentum (tomato);+Mohanty B, Krishnan SP, Swarup S, Bajic VB.sDetection and preliminary analysis of motifs in promoters ofanaerobically induced genes of different plant species.!Ann Bot (Lond).96: 669-681 (2005)PubMed: 16027132 in silicoTCATCACANAERO5CONSENSUSS000481%05-November-2005 (last modified) kehi�One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway (anaerobic set1)(Mohanty et al., 2005); Arbitrary named ANAERO5CONSENSUS by thePLACEdb curator; See also S000477, S000478, S000479, S000480; anaerobic�Zea mays (maize); Arabidopsis thaliana; Pisum sativum (pea);Hordeum vulgare (barley); Oryza sativa (rice); Petunia hybrida(petunia); Lycopersicon esculentum (tomato);+Mohanty B, Krishnan SP, Swarup S, Bajic VB.sDetection and preliminary analysis of motifs in promoters ofanaerobically induced genes of different plant species.!Ann Bot (Lond).96: 669-681 (2005)PubMed: 16027132 in silico TTCCCTGTTANAEROBICCISZMGAPC4S000350 16-Feb-2001 (last modified) seki�20 bp anaerobic cis-regulatory sequence found in the maize (Z.m.)GapC4 (Glyceraldehyde-3-phosphate dehydrogenase 4) gene promoter;Located between -286 and -266; Required for anaerobic geneexpression in transgenic tobacco; See S000351; anaerobicGapC4(Glyceraldehyde-3-phosphate dehydrogenasemaize (Zea mays)Geffers R, Cerff R, Hehl RuAnaerobiosis-specific interaction of tobacco nuclear factors withcis-regulatory sequences in the maize GapC4 promoter Plant Mol Biol 43: 11-21 (2000)PubMed: 10949370; CGAAACCAGCAACGGTCCAGARECOREZMGAPC4S000393 21-May-2002 (last modified) uchi�Putative binding site for a Myb found in the promoter of maizeglycolytic glyceraldehyde-3-phospate dehydrogenase 4 (GapC4)gene; Essential for anaerobic induction; anaerobicGapC4 Myb proteinmaize (Zea mays)"Geffers R, Sell S, Cerff R, Hehl RvThe TATA box and a Myb binding site are essential for anaerobicexpression of a maize GapC4 minimal promoter in tobacco)Biochim Biophys Acta 1521: 120-125 (2001)PubMed: 11690643;
AGCAACGGTCARELIKEGHPGDFR2S000437%28-November-2004 (last modified) kehi�Sequence highly similar to ARE (anthocyanin regulatory element)found in maize anthocyanin promoter (Tuerck and Fromm 1994;Lesnick and Chandler 1998); Binding site of R2R3-type MYB factor,GMYB 10 of G. hybrida; anthocyaninaAREDRFC1R2R3MYBa2-Gerbera hybrida (Astraceae); Zea mays (maize)�Elomaa P, Uimari A, Mehto M, Albert VA, Latinen RAE, Teeri TH.Hernandez JM, Heine GF, Irani NG, Feller A, Kim MG, Matulnik T,Chandler VL, Grotewold E.Lesnick ML, Chandler VL.��Activation of anthocyanin biosynthesis in Gerbera hybrida(Asteraceae) suggests conserved protein-protein andprotein-promoter interactions between the anciently divergedmonocots and eudicots.Different mechanisms participate in the R-dependent activity ofthe R2R3 MYB transcription factor C1.Activation of the maize anthocyanin gene a2 is mediated by anelement conserved in many anthocyanin promoters.lPlant Physiol. 133: 1831-1842 (2003)J Biol Chem. 279: 48205-48213 (2004).Plant Physiol. 117: 437-445 (1998).0PubMed: 14605235;PubMed: 15347654PubMed: 9625696 AGTTGAATGGGGGTGCAARFATS000270#01-August-2006 (last modified) kehi��ARF (auxin response factor) binding site found in the promotersof primary/early auxin response genes of Arabidopsis thaliana(A.t.); AuxRE; See S000337; Binding site of Arabidopsis ARF1(Auxin response factor1); Sequence found in NDE element inSoybean (G.m.) SAUR (Small Auxin-Up RNA) 15A gene promoter; SeeS000359, S000360; Found in D1 or D4 element in Soybean (G.m.) GH3promoter; This element was enriched in the 5'-flanking region ofgenes up-regulated by both IAA and BL (Goda et al., 2004);
auxinAuxREARFARF1Aux/IAASAURNDEGH3D1D4@Arabidopsis thaliana; Soybean (Glycine max); Oryza sativa (rice)�xUlmasov T, Hagen G, Guilfoyle TJNag R, Maity MK, Dasgupta M.Inukai Y, Sakamoto T, Ueguchi-Tanaka M, Shibata Y, Gomi K,Umemura I, Hasegawa Y, Ashikari M, Kitano H, Matsuoka M.Harper RM, Stowe-Evans EL, Luesse DR, Muto H, Tatematsu K,Watahiki MK, Yamamoto K, Liscum ENemhauser JL, Mockler TC, Chory J.Goda H, Sawa S, Asami T, Fujioka S, Shimada Y, Yoshida S.Hagen G, Guilfoyle T��Dimerization and DNA binding of auxin response factorsDual DNA binding property of ABA insensitive 3 like factorstargeted to promoters responsive to ABA and auxin.Crown rootless1, Which Is Essential for Crown Root Formation inRice, Is a Target of an AUXIN RESPONSE FACTOR in AuxinSignaling.The NPH4 locus encodes the auxin response factor ARF7, aconditional regulator of differential growth in aerialArabidopsis tissueInterdependency of brassinosteroid and auxin signaling inArabidopsis.Comprehensive comparison of auxin-regulated andbrassinosteroid-regulated genes in Arabidopsis.Auxin-responsive gene expression: genes, promoters and regulatoryfactors�Plant J 19:309-319 (1999)Plant Mol Biol. 59: 821-838 (2005).Plant Cell 17: 1387-1396 (2005)Plant Cell 12: 757-770 (2000)PLoS Biol. 2(9):E258. (2004)Plant Physiol. 134: 1555-1573 (2004).Plant Mol Biol. 49 :373-385 (2002)sPubMed: 10476078;PubMed: 16270233PubMed: 15829602PubMed: 10810148;PubMed: 15328536PubMed: 15047898PubMed: 12036261;ReviewTGTCTCAS1CAMVS000023 16-Jan-1998 (last modified) kehi�"as-1 (activation sequence 1)" in CaMV 35S promoter; from -85 to-58 (subdomain AI); Binding with ASF-1 (activation sequencefactor 1) from pea and tobacco; Expression in root and leaf;CaMV 35S promoterASF-1leafrootas-1 Cauliflower mosaic virus; CaMV;DLam E, Benfey PN, Gilmartin PM, Fang R-X, Chua N-HBenfey PN, Chua NH�Site-specific mutations alter in vitro factor binding and changepromoter expression pattern in transgenic plants.The cauliflower mosaic virus 35S promoter: combinatorialregulation of transcription in plantsFProc Natl Acad Sci USA 86:7890-7894 (1989)Science 250:959-966 (1990)PubMed: 2813365; CCACTGACGTAAGGGATGACGCACAATCC
AS1LIKECSHPRAS000260 14-Oct-1999 (last modified) kehi�as-1-like motif found in cucumber (C.s.) hydroxypyruvatereductase (hprA) gene; Required for cytokinin responsiveness;Also see S000261 (CYTOSITECSHPRA); cytokininas-1as-1 TGACG motifcucumber (Cucumis sativus)CJin G, Davey MC, Ertl JR, Chen R, Yu Z, Daniel SG, Becker WM,Chen CInteraction of DNA-binding proteins with the 5'-flanking regionof a cytokinin-responsive cucumber hydroxypyruvate reductasegene Plant Mol Biol 38:713-724 (1998)PubMed: 9862489; AAATGACGAAAATGC ASF1ATNOSS000073 7-Sep-2000 (last modified) seki�Tobacco ASF-1 binding site in nopaline synthase (NOS) promoter ofTi-plasmid of Agrobacterium tumefaciens (A.t.); From -131 to-111; See S000312; Containing two hexamer motifs; Essential forthe nos promoter activity;nopaline synthaseASF-1auxinmethyl jasmonate salicylicacidAgrobacterium tumefaciens:Lam E, Katagiri F, Chua NHKim Y, Buckley K, Costa MA, An G�Plant nuclear factor ASF-1 binds to an essential region of thenopaline synthase promoter.A 20 nucleotide upstream element is essential for the nopalinesynthase (nos) promoter activityAJ Biol Chem 265:9909-9913 (1990)Plant Mol Biol 24: 105-117 (1994) PubMed: 2351681;PubMed: 8111010; TGAGCTAAGCACATACGTCAG
ASF1MOTIFCAMVS000024 11-May-2006 (last modified) kehi��"ASF-1 binding site" in CaMV 35S promoter; ASF-1 binds to twoTGACG motifs; See S000023 (AS1); Found in HBP-1 binding site ofwheat histone H3 gene; TGACG motifs are found in many promotersand are involved in transcriptional activation of several genesby auxin and/or salicylic acid; May be relevant to lightregulation; Binding site of tobacco TGA1a; TGA1a and b showhomology to CREB; TGA6 is a new member of the TGA family; Abioticand biotic stress differentially stimulate "as-1 element"activity;TGACGrootleafCaMV35Spromoterauxinsalicylic acidlightas-1 TGA1a, TGA1bCREBASF1TGA6shoot
xenobioticstressSARSADisease resistanceXCaMV; Cauliflower mosaic virus; plant; tobacco (Nicotianatabacum); Arabidopsis thaliana;�� Despres C, Chubak C, Rochon A, Clark R, Bethune T, Desveaux D,Fobert PR.Terzaghi WB, Cashmore ARBenfey PN, Chua NHKatagiri F, Lam E, Chua NHXiang C, Miao Z, Lam EKlinedinst S, Pascuzzi P, Redman J, Desai M, Arias JRedman J, Whitcraft J, Johnson C, Arias J��The Arabidopsis NPR1 disease resistance protein is a novelcofactor that confers redox regulation of DNA binding activity tothe basic domain/leucine zipper transcription factor TGA1.Light-regulated transcriptionThe cauliflower mosaic virus 35S promoter: combinatorialregulation of transcription in plantsTwo tobacco DNA-binding proteins with homology to the nuclearfactor CREBDNA-binding properties, genomic organization and expressionpattern of TGA6,a new member of the TGA family of bZIPtranscription factors in Arabidopsis thalianaA xenobiotic-stress-activated transcription factor and itscognate target genes are preferentially expressed in root tipmeristemsAbiotic and biotic stress differentially stimulate as-1 elementactivity in Arabidopsis�Plant Cell 15: 2181-2191 (2003)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)Science 250:959-966 (1990)Nature 31: 727-730 (1989)Plant Mol Biol 34: 403-415 (1997)Plant Mol Biol 42: 679-688 (2000)Plant Cell Rep. 21: 180-185 (2002)APubMed: 12953119;PubMed: 2528073;PubMed: 9225852PubMed: 10809441; TGACG
ASF1NTPARAS000240 11-Oct-1999 (last modified) kehi�"ASF-1 (as-1 binding nuclear factor)" binding site found intobacco (N.t.) parA gene; Found in auxin-responsive regions;as-1-like sequences in parA, parB and parC bind with ASF-1,ALF-2, and ALF-1, respectively; See S000190 (ABFOS), S000238(ALF1NTPARC), S000239 (ALF2NTPARB);as-1ASF-1parauxin tobacco (Nicotiana tabacum); Sakai T, Takahashi Y, Nagata T{The identification of DNA binding factor specific for as-1-likesequences in auxin-responsive regions of parA, parB and parC%Plant Cell Physiol 39:731-739 (1998)PubMed: 9729895; TTACGCAAGCAATGACATAT1BOXS000025!17-May-1998 (last modified) kehi;��"AT-1 box (AT-rich element)" found in the promoter region of thegenes for tobacco ( N.p.) chlorophyll a/b binding protein (cab)and small subunit of ribulose-1,5-bisphosphate carboxylase(rbcS); Deletion of a region containing the AT-1 site in thetomato RBCS3A gene strongly inhibited reporter gene expression,whereas AT-1 site in N. plumbaginifolia CAB gene (cab-E) is in anegative element (Terzaghi & Cashmore, 1995);AT-1cabrbcSphotoregulated geneslight-regulated geneslightleafshootZpea (Pisum sativum); tobacco (Nicotiana plumbaginifolia); tomato(Lycopersicon esculentum);�Datta N, Cashmore ARGilmartin PM, Sarokin L, Memelink J, Chua N-HCastresana C, Garcia-Luque I, Alonso E, Malik VS, Cashmore ARUeda T, Pichersky E, Malik VS, Cashmore ARTerzaghi WB, Cashmore AR��Binding of a pea nuclear protein to promoters of certainphotoregulated genes is modulated by phosphorylation.Molecular light switches for plant genes.Both positive and negative regulatory elements mediate expressionof a photoregulated CAB gene from Nicotiana plumbaginifolia.The level of expression of the tomato rbcs-3A gene is modulatedby a far-upstream promoter element in a developmentary regulatedmanner.Light-regulated transcription�Plant Cell 1:1069-1077 (1989)Plant Cell 2:369-378 (1990)EMBO J 7:1929-1936 (1988)Plant Cell 1:217-227 (1989)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)bPubMed: 2562560;PubMed: 2152164;PubMed: 2901343; GenBank: X12512;PubMed: 2535544; GenBank: S44160;Review AATATTTTTATT ATHB6COREATS000399 27-Aug-2002 (last modified) uchi�Consensus binding sequence for Arabidopsis (A.T.)homeodomain-leucine zipper protein, ATHB6; ATHB6 is a target ofthe protein phosphatase ABI1 and regulates hormone responses; SeeS000371;ATHB6ABAABI1homeodomain-leucine zipperArabidopsis thaliana5Himmelbach A, Hoffmann T, Leube M, Hohener B, Grill EsHomeodomain protein ATHB6 is a target of the protein phosphataseABI1 and regulates hormone responses in ArabidopsisEMBO J. 21:3029-3038 (2002)PubMed: 12065416; CAATTATTA ATRICHPSPETES000248 11-Oct-1999 (last modified) kehi�A/T-rich sequences found in pea (P.s.) plastocyanin gene (petE)promoter; Act as quantitative enhancer; Found at -289 to -255 ofpea PetE gene;A/T-richAT-richAT richenhancerpea (Pisum sativum) Sandhu JS, Webster CI, Gray JCjA/T-rich sequences act as quantitative enhancers of geneexpression in transgenic tobacco and potato plants!Plant Mol Biol 37:885-896 (1998)PubMed: 9678583; AATATACTAGTATTATTTACTAAAAAAAATCAUXRETGA1GMGH3S000234 7-Sep-2000 (last modified) seki�"TGA-box #1" in putative auxin-resonsive element (AUXRE) ofsoybean (G.m.) GH3 promoter; Strong binding site for proteins inplant nuclear extracts;TGAAUXREauxinGH3soybean (Glycine max)vLiu ZB, Ulmasov T, Shi X, Hagen G, Guilfoyle TJLiu ZB, Hagen G, Guilfoyle TJGuilfoyle T, Hagen G, Ulmasov T, Murfett J�Soybean GH3 promoter contains multiple auxin-inducible elementsA G-box-binding protein from soybean binds to the E1auxin-response element in the Soybean GH3 promoter and contains aproline-rich repression domainHow does auxin turn on genes?\Plant Cell 6:645-657 (1994)Plant Physiol 115:397-407 (1997)Plant Physiol 118: 341-347 (1998)0PubMed: 8038604;PubMed: 9342862;PubMed: 9765520;ReviewTGACGTAAAUXRETGA2GMGH3S000235 7-Sep-2000 (last modified) seki�"TGA-box #2" in putative auxin-resonsive element (AUXRE) E1 ofsoybean (G.m.) GH3 promoter; Strong binding site for proteins inplant nuclear extracts; Hex-like element; E1 element=-249 to-203; E2 element=-241 to -224; Called G-box by Liu et al.(1997);TGAAUXREauxinGH3E1G-boxsoybean (Glycine max)vLiu ZB, Ulmasov T, Shi X, Hagen G, Guilfoyle TJLiu ZB, Hagen G, Guilfoyle TJGuilfoyle T, Hagen G, Ulmasov T, Murfett J�Soybean GH3 promoter contains multiple auxin-inducible elementsA G-box-binding protein from soybean binds to the E1auxin-response element in the Soybean GH3 promoter and contains aproline-rich repression domainHow does auxin turn on genes?\Plant Cell 6:645-657 (1994)Plant Physiol 115:397-407 (1997)Plant Physiol 118: 341-347 (1998)0PubMed: 8038604;PubMed: 9342862;PubMed: 9765520;Review TGACGTGGC B2GMAUX28S000325 7-Sep-2000 (last modified) seki�"B2"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; Located between -310 and-301; Contains a TGACGACA sequence which is similar to TGACGT/Csequence found in Ocs, CaMV35S and histone H3 promoter; Containsas-1 motif;auxinAux28as-1soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133;
CTTGTCGTCABBOXSITE1STPATS000398 27-Aug-2002 (last modified) uchi�"10 base pair motif (site 1)" within the B-box found in thepotato patatin gene promoter; Involved in potato tuber-specificand sucrose-inducible gene expression; Storekeeper (STK) binds tothis region and regulates patatin expression in potato;STK (Storekeeper)tuberpatatinB-boxSolanum tuberosum (potato)3Zourelidou M, de Torres-Zabala M, Smith C, Bevan MWwStorekeeper defines a new class of plant-specific DNA-bindingproteins and is a putative regulator of patatin expressionPlant J. 30 :489-497 (2002)PubMed: 12028578;
GCTAAACAATBIHD1OSS000498#02-August-2006 (last modified) kehiEBinding site of OsBIHD1, a rice BELL homeodomain transcriptionfactor;HD homeodomainOryza sativa (rice)#Luo H, Song F, Goodman RM, Zheng Z.wUp-regulation of OsBIHD1, a rice gene encoding BELL homeodomaintranscriptional factor, in disease resistance responses.'Plant Biol (Stuttg). 7: 459-468 (2005).PubMed: 16163610FElectrophoretic mobility shift assays with recombinant OsBIHD1protein;TGTCA BOX1PSGS2S000222#19-August-2004 (last modified) kehi�,Box 1 element in pea (P.s.) glutamine synthetase (GS2) gene; Anelement in a 33-bp AT-rich sequence (box 1) of the 5' end of aGS2 promoter; Located at -837 to -827 of pea GS2; Multimer of box1 element was used to isolate a cDNA encoding an AT-rich DNAbinding protein (ATBP-1) (Tjaden & Coruzzi, 1994);Box 1glutamine synthetaseGS2ATBpATBP-1pea (Pisum sativum)4Tjaden G, Coruzzi GMTjaden G, Edwards JW, Coruzzi GM�� A novel AT-rich DNA binding protein that combines an HMG I-likeDNA binding domain with a putative transcription domaincis elements and trans-acting factors affecting regulation of anonphotosynthetic light-regulated gene for chloroplast glutaminesynthetase=Plant Cell 6:107-118 (1994)Plant Physiol 108:1109-1117 (1995)1PubMed: 7907505;PubMed: 7630938; GenBank: U22971; ATAGAAATCAA BOX1PVCHS15S000208 11-May-2006 (last modified) kehi��Box 1 of bean (P.v.) chs15 promoter; one of SBF-1 binding sitesin chs15 promoter; Located at -318 to -305; Involved inorgan-specific expression in plant development; Functions as atranscriptional silencer in electroporated protoplasts derivedfrom undifferentiated suspension-cultured soybean cells; Resemblethe binding site for the GT-1 factor in light-responsiveelements; For a compilation of related GT elements and factors,see Villain et al. (1996);
Box 1chschs15CHSSBF-1silencerorgan-specificGtGT-1GTbean (Phaseolus vulgaris)�Lawton MA, Dean SM, Dron M, Kooter JM, Kragh KM, Harrison MJ, YuL, Tanguay L, Dixon RA, Lamb CJVillain P, Mache R, Zhou DXZhou DX�Silencer region of a chalcone synthase promoter contains multiplebinding sites for a factor, SBF-1, closely related to GT-1The mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorskPlant Mol Biol 16:235-249 (1991)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)BPubMed: 1893099; GenBank: X59469;PubMed: 8955086;PubMed: 10366876ReviewTAAAAGTTAAAAAC BOX2PSGS2S000204 17-May-1998 (last modified) kehi�Box 2 in glutamine synthetase (GS2) gene in pea (P.s.); Repeatedin tandem with a partial palindrome located between the repeats;Located at ca. -300 of pea GS2;Box 2glutamine synthetaseGS2pea (Pisum sativum); Tjaden G, Edwards JW, Coruzzi GM�cis elements and trans-acting factors affecting regulation of anonphotosynthetic light-regulated gene for chloroplast glutaminesynthetase"Plant Physiol 108:1109-1117 (1995)!PubMed: 7630938; GenBank: U22971; TCTAAGCAAAG BOX2PVCHS15S000209 11-May-2006 (last modified) kehi�Box 2 of bean (P.v.) chs15 promoter; SBF-1 binding site; For acompilation of related GT elements and factors, see Villain etal. (1996);Box 2chschs15CHSSBF-1GT-1GTbean (Phaseolus vulgaris)�Lawton MA, Dean SM, Dron M, Kooter JM, Kragh KM, Harrison MJ, YuL, Tanguay L, Dixon RA, Lamb CVillain P, Mache R, Zhou DXZhou DX�Silencer region of a chalcone synthase promoter contains multiplebinding sites for a factor, SBF-1, closely related to GT-1The mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorskPlant Mol Biol 16:235-249 (1991)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)BPubMed: 1893099; GenBank: X59469;PubMed: 8955086;PubMed: 10366876ReviewCTGTGATTAAATAT BOX3PVCHS15S000210 11-May-2006 (last modified) kehi�Box 3 of bean (P.v.) chs15 promoter; SBF-1 binding site; For acompilation of related GT elements and factors, see Villain etal. (1996);Box 3chschs15CHSSBF-1GT-1GTbean (Phaseolus vulgaris)�Lawton MA, Dean SM, Dron M, Kooter JM, Kragh KM, Harrison MJ, YuL, Tanguay L, Dixon RA, Lamb CJVillain P, Mache R, Zhou DXZhou DX�Silencer region of a chalcone synthase promoter contains multiplebinding sites for a factor, SBF-1, closely related to GT-1The mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorskPlant Mol Biol 16:235-249 (1991)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)BPubMed: 1893099; GenBank: X59469;PubMed: 8955086;PubMed: 10366876ReviewTATTGGTTACTAAA BOXBPSAS1S000225 17-May-1998 (last modified) kehi�Box B in pea (P.s.) asparagine synthetase (AS1) gene; Found at-61; AS1 is negatively regulated by light; Box B binds withnuclear proteins;BOX BASAS1light
repressionnegative regulationpea (Pisum sativum)Ngai N, Tsai FY, Coruzzi GlLight-induced transcriptional repression of the pea AS1 gene:identification of cis-elements and transfactorsPlant J 12:1021-1234 (1997)PubMed: 9418044; AAACGACACCGTTT
BOXC'PSAS1S000227 17-May-1998 (last modified) kehi�Box C' in pea asparagine synthetase (AS1) gene; Found at -88; AS1is negatively regulated by light; Box C' binds with nuclearproteins, which was competed by a putative repressor element RE1(see S000195);BOX C'ASAS1pea (Pisum sativum);Ngai N, Tsai FY, Coruzzi GlLight-induced transcriptional repression of the pea AS1 gene:identification of cis-elements and transfactorsPlant J 12:1021-1234 (1997)PubMed: 9418044; TCCCGGTACACACTTCTT BOXCPSAS1S000226 10-May-1998 (last modified) kehi�Box C in pea (P.s.) asparagine synthetase (AS1) gene; Found at-45; AS1 is negatively regulated by light; Box C binds withnuclear proteins, which was competed by a putative repressorelement RE1 (see S000195);BOX CASAS1pea (Pisum sativum)Ngai N, Tsai FY, Coruzzi GlLight-induced transcriptional repression of the pea AS1 gene:identification of cis-elements and transfactorsPlant J 12:1021-1234 (1997)PubMed: 9418044; CTCCCAC BOXIINTPATPBS000296 10-Feb-2000 (last modified) seki�"Box II" found in the tobacco (N.t.) plastid atpB gene promoter;Conserved in several NCII (nonconsensus type II) promoters ofplastid genes; Important for the activity of this NCII promoter;See S000295;plastidNEPatpBPatpBNCIIBox IBox IItobacco (Nicotiana tabacum)Kapoor S, Sugiura M�Identification of two essential sequence elements in thenonconsensus type II PatpB-290 plastid promoter by using plastidtranscription extracts from cultured tobacco BY-2 cells Plant Cell 11: 1799-1810 (1999)PubMed: 10488244 ATAGAA
BOXIIPCCHSS000229#01-August-2006 (last modified) kehi�Core of "Box II/G box" found in the parsley (P.c.) chs genes;Essential for light regulation (Terzaghi & Cashmore, 1995); SeeS000345;Box IIBox 2CHSchslight regulation parsley (Petroselinum crispum)�Block A, Dangl JL, Hahlbrock K, Schulze-Lefert PTerzaghi WB, Cashmore ARNakashima K, Fujita Y, Katsura K, Maruyama K, Narusaka Y, Seki M,Shinozaki K, Yamaguchi-Shinozaki K.�JFunctional borders, genetic fine structure, and distancerequirements of cis elements mediating light responsiveness ofthe parsley chalcone synthase promoterLight-regulated transcriptionTranscriptional regulation of ABI3- and ABA-responsive genesincluding RD29B and RD29A in seeds, germinating embryos, andseedlings of Arabidopsis.�Proc Natl Acad Sci USA 87:5387-5391(1990)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)Plant Mol Biol. 60: 51-68 (2006) PubMed: 2371277PubMed: 16463099ReviewACGTGGC BOXINTPATPBS000295 10-Feb-2000 (last modified) seki�"Box I" found in the tobacco (N.t.) plastid atpB gene promoter;Conserved in several NCII (nonconsensus type II) promoters ofplastid genes; Important for the activity of this NCII promoter;See S000296;plastidNEPatpBPatpBNCIIBox IBox IItobacco (Nicotiana tabacum)Kapoor S, Sugiura M�Identification of two essential sequence elements in thenonconsensus type II PatpB-290 plastid promoter by using plastidtranscription extracts from cultured tobacco BY-2 cells Plant Cell 11: 1799-1810 (1999)PubMed: 10488244 AATTCCATAGAATAGATAATABP5OSWXS000436 27-Jan-2004 (last modified) kehi3OsBP-5 (a MYC protein) binding site in Wx promoter;MYCWxWaxyOryza sativa (rice);#Zhu Y, Cai X-L, Wang Z-Y, Hong M-M.wAn interaction between a MYC protein and an EREBP protein isinvolved in transcriptional regulation of the rice Wx gene.&J. Biol. Chem. 278: 47803-47811 (2003)PubMed: 12947109; CAACGTGBS1EGCCRS000352 16-Feb-2001 (last modified) seki�"BS1 (binding site 1)" found in E. gunnii Cinnamoyl-CoA reductase(CCR) gene promoter; nuclear protein binding site; Required forvascular expression;cinnamoyl-CoA reductasevascularBS1stemEucalyptus gunniiELacombe E, Van Doorsselaere J, Boerjan W, Boudet AM,Grima-Pettenati J�Characterization of cis-elements required for vascular expressionof the cinnamoyl CoA reductase gene and for protein-DNA complexformationPlant J 23: 663-676 (2000)PubMed: 10972892; AGCGGG C1GMAUX28S000326 7-Sep-2000 (last modified) seki�"C1"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; Located between -463 and-448; A/T-rich sequence;AuxinAux28soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133; TGAAAACAGTGAGTTA C2GMAUX28S000327 7-Sep-2000 (last modified) seki�"C2"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; Located between -552 and-553; Contains (ATT)4 sequence;AuxinAux28soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133; AATAATAATAATAATAAATACAATBOX1S000028 17-May-1998 (last modified) kehi="CAAT promoter consensus sequence" found in legA gene of pea;CAATlegAseedpea (Pisum sativum)'Shirsat A, Wilford N, Croy R, Boulter D`Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco. Mol Gen Genet 215:326-331 (1989)PubMed: 2710102; CAATCAATBOX2S000029 5-Jun-1997 (last modified) kehiZ"CAAT box" found in the 5' upstream region (-80) of manyeukaryotic genes; GGC(or T)CAATCT;eukaryotic geneCAAT
eukaryote; GGCCAATCT
CACGCAATGMGH3S000368 16-Feb-2001 (last modified) seki�Sequence found in D4 element in Soybean (G.m.) GH3 gene promoter;Showed constitutive activity with TGTCTC element (See S000270);Confers auxin inducibility; Binding site of nuclear protein; Seealso S000369;D1D4GH3AuxinSoybean (Glycine max)(Ulmasov T, Liu ZB, Hagen G, Guilfoyle TJ.Composite structure of auxin response elements Plant Cell 7: 1611-1623 (1995)PubMed: 7580254; CACGCAAT CACGTGMOTIFS000042$06-January-2006 (last modified) kehi��"CACGTG motif"; "G-box"; Binding site of Arabidopsis GBF4; C.roseus G-box binding factor 1 (CrGBF1) and 1 (CrGBF2) can act astranscriptional repressors of the Str promoter via directinteraction with the G-box; See S000345; Essential for expressionof beta-phaseolin gene during embryogenesis in bean, tobacco,Arabidopsis; Tomato Pti4 (ERF) regulates defense-related geneexpression via GCC box and non-GCC box cis-element (Myb1(GTTAGTT) and G-box (CACGTG)); A prominent hit by in silicoanalysis in both induced and repressed phyA-responsive promoters(Hudson and Quail 2003); Review by Terzaghi WB, Cashmore AR."Light-regulated transcription" in Annu Rev Plant Physiol PlantMol Biol 46:445-474 (1995);G boxG-boxrbcschs ACGT elementadhBz-2R-motifSTRGT-1GBFelicitorbZIPnapinstrictosidine synthasecellleafshootPti4ERFPR�tomato (Lycopersicon esculentum); Arabidopsis thaliana;snapdragon (Antirrhinum majus); wheat (Triticum aestivum);parsley: maize (Zea mays); periwinkle (Catharanthus roseus);Brassica napus; bean (Phaseolus vulgaris);�SChandrasekharan MB, Bishop KJ, Hall TC.Busk PK, Pages MHudson ME, Quail PH.Pasquali G, Erven ASW,Ouwerkerk PBF, Menke FLH, Memelink JMenkens AE, Schindler U, Cashmore ARChakravarthy S, Tuori RP, DAscenzo MD, Fobert PR, Despres C,Martin GBSiberil Y, Benhamron S, Memelink J, Giglioli-Guivarc'h N,Thiersault M, Boisson B, Doireau P, Gantet P�Module-specific regulation of the beta-phaseolin promoter duringembryogenesis.Regulation of abscisic acid-induced transcriptionIdentification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.The promoter of the strictosidine synthase gene from periwinkleconfers elicitor-inducible expression in transgenic tobacco andbinds nuclear factors GT-1 and GBFThe G-box: a ubiquitous regulatory DNA element in plants bound bythe GBF family of bzip proteinsThe tomato transcription factor Pti4 regulates defence-relatedgene expression via GCC box and non-GCC box cis elementsCatharanthus roseus G-box binding factors 1 and 2 act asrepressors of strictosidine synthase gene expression in cellcultures�Plant J. 33: 853-866 (2003)Plant Mol Biol 37:425-435 (1998)Plant Physiol. 133: 1605-1616 (2003)Plant Mol Biol 39:1299-1310 (1999)Trends in Biochemistry 20:506-510 (1995)Plant Cell 15: 3033-3050 (2003)Plant Mol Biol 45: 477-488 (2001)tPubMed: 12609027;PubMed: 9617810;PubMed: 14681527PubMed: 10380815;PubMed: 8571452;PubMed: 14630974;PubMed: 11352466;.Reviewin silico; over-represented motif;ReviewCACGTG
CAREOSREP1S000421%28-November-2004 (last modified) kehin"CAREs (CAACTC regulatory elements)" found in the promoter regionof a cystein proteinase (REP-1) gene in rice;aleuroneGARE gibberellinseedOryza sativa (rice)Sutoh K, Yamauchi D.oTwo cis-acting elements necessary and sufficient forgibberellin-upregulated proteinase expression in rice seedsPlant J. 34:635-645 (2003)PubMed: 12787245; CAACTC
CARG1ATAP3S000347 31-May-2006 (last modified) kehi�#"CArG1" found in the Arabidopsis (A.t.) APETALA3 (AP3) genepromoter; Binding site of AP3/PI heterodimer; Binding site ofAP3/PI heterodimer; Binding site for a positively acting factors;MADS domain transcription factors bind with a consensus sequencecalled the CArG box; See S000348, S000349;APETALA3MADSCArG boxPIflowerArabidopsis thalianabTilly JJ, Allen DW, Jack THill TA, Day CD, Zondlo SC, Thackeray AG, Irish VFFolter S, Angenent GC.�The CArG boxes in the promoter of the Arabidopsis floral organidentity gene APETALA3 mediate diverse regulatory effectsDiscrete spatial and temporal cis-acting elements regulatetranscription of the Arabidopsis floral homeotic gene APETALA3trans meets cis in MADS science.dDevelopment 125: 1647-1657 (1998)Development125: 1711-1721 (1998)Trends Plant Sci. 11:224-231 (2006)0PubMed: 9521903;PubMed: 9521909;PubMed: 16616581ReviewGTTTACATAAATGGAAAA
CARG2ATAP3S000348 31-May-2006 (last modified) kehi�"CArG2" found in the Arabidopsis (A.t.) APETALA3 (AP3) genepromoter; Mutations in CArG2 result in a decrease in theexpression in petals, but the expression pattern in stamens isunchanged; See S000348, S000349;APETALA3MADSCArG boxPIflowerArabidopsis thalianabTilly JJ, Allen DW, Jack THill TA, Day CD, Zondlo SC, Thackeray AG, Irish VFFolter S, Angenent GC.�The CArG boxes in the promoter of the Arabidopsis floral organidentity gene APETALA3 mediate diverse regulatory effectsDiscrete spatial and temporal cis-acting elements regulatetranscription of the Arabidopsis floral homeotic gene APETALA3trans meets cis in MADS science.cDevelopment 125: 1647-1657 (1998)Development125: 1711-1721 (1998)Trends Plant Sci. 11:224-231(2006)0PubMed: 9521903;PubMed: 9521909;PubMed: 16616581 CTTACCTTTCATGGATTA
CARG3ATAP3S000349 31-May-2006 (last modified) kehi�~"CArG3" found in the Arabidopsis (A.t.) APETALA3 (AP3) genepromoter; Binding site of AP3/PI heterodimer; Binding site for anegatively acting factors; Binding sequence of Arabidopsis (A.t.)MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA, andAGAMOUS; AP1, AG, and AP3-PI complexes induce similarconformational changes on a CArG-box sequence; See S000347,S000348, S000338;APETALA3MADSCArG boxPI
PISTILLATAAPETALA1flowerArabidopsis thaliana�Tilly JJ, Allen DW, Jack THill TA, Day CD, Zondlo SC, Thackeray AG, Irish VFRiechmann JL, Wang M, Meyerowitz EMFolter S, Angenent GC.�|The CArG boxes in the promoter of the Arabidopsis floral organidentity gene APETALA3 mediate diverse regulatory effectsDiscrete spatial and temporal cis-acting elements regulatetranscription of the Arabidopsis floral homeotic gene APETALA3DNA-binding properties of Arabidopsis MADS domain homeoticproteins APETALA1, APETALA3, PISTILLATA and AGAMOUStrans meets cis in MADS science.�Development 125: 1647-1657 (1998)Development125: 1711-1721 (1998)Nucleic Acids Res 24: 3134-3141 (1996)Trends Plant Sci. 11:224-231(2006)@PubMed: 9521903;PubMed: 9521909;PubMed: 8774892;PubMed: 16616581 CTTTCCATTTTTAGTAAC CATATGGMSAURS000370 11-Mar-2001 (last modified) kehi�Sequence found in NDE element in soybean (G.m.) SAUR (SmallAuxin-Up RNA) 15A gene promoter; Involved in auxinresponsiveness; See S000359, S000360;SAURNDEauxinsoybean (Glycine max)Xu N, Hagen G, Guilfoyle T@Multiple auxin response modules in the soybean SAUR 15A promoter Plant Sci 126: 193-201 (1997) CATATG CCAATBOX1S000030$04-January-2007 (last modified) kehi�Common sequence found in the 5'-non-coding regions of eukaryoticgenes; "CCAAT box" found in the promoter of heat shock proteingenes; Located immediately upstream from the most distal HSE ofthe promoter; "CCAAT box" act cooperatively with HSEs to increasethe hs promoter activity;HSE (Heat shock element) CCAAT box!eukaryotes; Glycine max (Soybean)�Rieping M, Schoffl FHaralampidis K, Milioni D, Rigas S, Hatzopoulos PWenkel S, Turck F, Singer K, Gissot L, Le Gourrierec J, Samach A,Coupland G.�}Synergistic effect of upstream sequences, CCAAT box elements, andHSE sequences for enhanced expression of chimaeric heat shockgenes in transgenic tobaccoCombinatorial interaction of cis elements specifies theexpression of the Arabidopsis AtHsp90-1 geneCONSTANS and the CCAAT Box Binding Complex Share a FunctionallyImportant Domain and Interact to Regulate Flowering ofArabidopsis.eMol Gen Genet. 231: 226-232 (1992)Plant Physiol. 129: 1138-1149 (2002)Plant Cell. 18:2971-2984 (2006)1PubMed: 1736093;PubMed: 12114568;PubMed: 17138697 CCAATCCTCGTGTCTCGMGH3S000369 16-Feb-2001 (last modified) seki�Sequence found in D1 element in Soybean (G.m.) GH3 gene promoter;Showed constitutive activity with TGTCTC element (See S000270);Confers auxin inducibility; Binding site of nuclear protein; Seealso S000368;D1D4GH3AuxinSoybean (Glycine max)(Ulmasov T, Liu ZB, Hagen G, Guilfoyle TJ.Composite structure of auxin response elements Plant Cell 7: 1611-1623 (1995)PubMed: 7580254; CCTCGTGTCTC
CDA1ATCAB2S000440 28-Jan-2004 (last modified) kehi�CDA-1 (CAB2 DET1-associated factor 1) binding site in DtRE (darkresponse element) f of chlorophyll a/b-binding protein2 (CAB2)gene in Arabidopsis;
dark responseCAB2Arabidopsis thaliana4Maxwell BB, Andersson CR, Poole DS, Kay SA, Chory J.�HY5, circadian clock-assosiated 1, and a cis-lelement, DET1 darkresponse element, mediate DET1 regulation of chlorophylla/b-binding protein2 expression.$Plant Physiol. 133: 1565-1577 (2003)PubMed: 14563928; CAAAACGC CE3OSOSEMS000282 16-Feb-2001 (last modified) seki�3"CE3 (Coupling Element 3)" found in the promoter of the rice(O.s.) Osem gene; Required for ABA-responsiveness and VP1activation; Binding site of TRAB1; Motif A and CE3 (S000281) arefunctionally equivalent; TRAB1, bZIP transcription factor,interacts with VP1 and mediates abscisic acid-inducedtranscritption; CE3Motif AAVRECE3ABAVP1TRAB1OsemEmbZIPseedrice (Oryza sativa)AHobo T, Asada M, Kowyama Y, Hattori THobo T, Kowyama Y, Hattori T�ACGT-containing abscisic acid response element (ABRE) andcoupling element 3 (CE3) are functionally equivalentA bZIP factor, TRAB1, interacts with VP1 and mediates abscisicacid-induced transcriptionHPlant J 19: 679-689 (1999)Proc Natl Acad Sci USA 96: 15348-15353 (1999)"PubMed: 10571853;PubMed: 10611387;
AACGCGTGTC CELLCYCLESCS000031 17-May-1998 (last modified) kehiv"cell cycle box" found in URS2 (-940/-200) of HO gene ofS.cerevisiae; cell-cycle-specific activation of transcription;cell cycle boxURS2HO gene yeast (Saccharomyces cerevisiae):Breeden L, Nasmyth KNasmyth K, Adolf G, Lydall D, Seddon A�Cell cycle control of the yeast HO gene: cis- and trans-actingregulators.The identification of a second cell cycle control on the HOpromoter in yeast: cell cycle regulation of SW15 nuclear entry.,Cell 48:389-397 (1987)Cell 62:631-647 (1990) PubMed: 3542227;PubMed: 2167175; CACGAAAACEREGLUBOX1PSLEGAS000032 17-May-1998 (last modified) kehi�"cereal glutenin box" in pea legumin gene (legA); sequencehomologous to the cereal glutenin gene control element ("-300element");cerealgluteninleguminlegAseedpea (Pisum sativum)'Shirsat A, Wilford N, Croy R, Boulter D`Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco. Mol Gen Genet 215:326-331 (1989)PubMed: 2710102; TGTTAAAGTCEREGLUBOX2PSLEGAS000033 17-May-1998 (last modified) kehi�"cereal glutenin box" in pea legumin gene (legA); sequencehomologous to the cereal glutenin gene control element ("-300element");leguminglutenincereallegAseedpea (Pisum sativum)'Shirsat A, Wilford N, Croy R, Boulter D`Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco. Mol Gen Genet 215:326-331 (1989)PubMed: 2710102; TGAAAACTCEREGLUBOX3PSLEGAS000034 17-May-1998 (last modified) kehiy"cereal glutenin box" in pea (P.s.) legumin gene (legA); sequencehomologous to the cereal glutenin gene control elements;legumincerealgluteninseedpea (Pisum sativum)'Shirsat A, Wilford N, Croy R, Boulter D`Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco. Mol Gen Genet 215:326-331 (1989)PubMed: 2710102; TGTAAAAGT CGACGOSAMY3S000205 17-May-1998 (last modified) kehi�"CGACG element" found in the GC-rich regions of the rice (O.s.)Amy3D and Amy3E amylase genes, but not in Amy3E gene; Mayfunction as a coupling element for the G box element;amylaserice (Oryza sativa);4Hwang YS, Karrer EE, Thomas BR, Chen L, Rodriguez RLZThree cis-elements required for rice alpha-amylase Amy3Dexpression during sugar starvation Plant Mol Biol 36:331-341 (1998)PubMed: 9484474; CGACG
CGF1ATCAB2S000213 11-May-2006 (last modified) kehi��CGF-1 binding site in the Arabidopsis (A.t.) cab2 gene promoter;CGF-1=CAB GATA Factor 1; Found at -74 to -42; Contains a highlyconserved, repeated GATA motif termed I-box (see S000124,S000199); For GATA motif, see S000039; The binding specificity ofCGF-1 appears to be related to GT-family of DNA-binding proteins;For a compilation of related GT elements and factors, see Villainet al. (1996);CGFcabcab2CGF-1GTleafshootArabidopsis thaliana;QAnderson SL, Teakle GR, Martino-Catt SJ, Kay SAVillain P, Mache R, Zhou DXZhou DX� Circadian clock- and phytochrome-regulated transcription isconferred by a 78 bp cis-acting domain of the Arabidopsis CAB2promoterThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorscPlant J 6:457-470 (1994)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)0PubMed: 7987408;PubMed: 8955086;PubMed: 10366876review!GATAAAGATTACTTCAGATATAACAAACGTTAC CGTGTSPHZMC1S000294 10-Feb-2000 (last modified) seki�Sequence found in the maize (Z.m.) C1 gene promoter; Locatedbetween -147 to -132; Containing Sph element; Required for ABAresponsiveness; See S000154, S000293;C1anthocyanin pathwayABAVP1lightSphmaize (Zea mays)+Kao CY, Cocciolone SM, Vasil IK, McCarty DR�Localization and interaction of the cis-acting elements forabscisic acid, VIVIPAROUS1, and light activation of the C1 geneof maize Plant Cell 8: 1171-1179 (1996)PubMed: 8768375 CGTGTCGTCCATGCAT CMSRE1IBSPOAS000511$04-January-2007 (last modified) kehizCMSRE-1 (Carbohydrate Metabolite Signal Responsive Element 1)found in the promoter of sweet potato (I.b.) sporamin A gene;sucrosesporamin
sugar-inducedSpoA Ipomoea batatas (sweet potato)@Morikami A, Matsunaga R, Tanaka Y, Suzuki S, Mano S, Nakamura K.�Two cis-acting regulatory elements are involved in thesucrose-inducible expression of the sporamin gene promoter fromsweet potato in transgenic tobacco.&Mol Genet Genomics. 272:690-699 (2005)PubMed: 15654621 TGGACGGCONSERVED11NTZMATP1S000301 10-Feb-2000 (last modified) seki�Conserved 11 nt sequence found in the maize (Z.m.) mitochondrialatp1 promoter; Located between -5 and +6; Essential for theexpression; mitochondriaatp1maize (Zea mays)Rapp WD, Stern DBmA conserved 11 nucleotide sequence contains an essential promoterelement of the maize mitochondrial atp1 geneEMBO J 11: 1065-1073 (1992)PubMed: 1372246 ACGTATTAAAACPBCSPORS000491%30-November-2005 (last modified) kehi�The sequence critical for Cytokinin-enhanced Protein Binding invitro, found in -490 to -340 of the promoter of the cucumber (CS)POR (NADPH-protochlorophyllide reductase) gene; cytokinin chlorophyll chloroplast Cucumis sativus L. (cucumber)<Fusada N, Masuda T, Kuroda H, Shimada H, Ohta H, Takamiya K.�Identification of a Novel Cis-Element ExhibitingCytokinin-Dependent Protein Binding in Vitro in the 5'-region ofNADPH-Protochlorophyllide Oxidoreductase Gene in Cucumber.#Plant Mol Biol. 59: 631-645 (2005).PubMed: 16244912 TATTAG CPRFPCCHSS000313$8-February-2006 (last modified) kehi��"BoxII"; Binding site of CPRF-1, -2, -3 and -4(Common PlantRegulatory Factor) in the parsley (P.c.) light responsivechalcone synthase (CHS) gene promoter; CPRF proteins are bZIPclass transcription factors; CPRF proteins participates in thelight-mediated activation of the CHS gene in parsley; "ACE"; Theproline-rich domains of CPRF1 and 4 activate transcription;CPRF1-containing bZIP heterodimer interacts with ACE in vivo; BoxIICPRFbZIPleafshootCHSACElightbZIP Parsley (Petroselinum crispum)cWeisshaar B, Armstrong GA, Block A, da Costa e Silva O, HahlbrockK.Sprenger-Haussels M, Weisshaar B�Light-inducible and constitutively expressed DNA-binding proteinsrecognizing a plant promoter element with functional relevance inlight responsivenessTransactivation properties of parsley proline-rich bZIPtranscription factors2EMBO J 10: 1777-1786 (1991)Plant J 22: 1-8 (2000)!PubMed: 2050115;PubMed: 10792815;
CCACGTGGCC CRTDREHVCBF2S000411!22-June-2006 (last modified) kehi� Preferred sequence for AP2 transcriptional activator HvCBF2 ofbarley; "Core CRT/DRE motif"; HvCBF2 bound to a (G/a)(T/c)CGACcore motif (Xue, 2003); DNA binding is regulated by temperature;This motif was erroneously ID-labeled in PLACEdb as CDTDREHVCBF2,and was corrected on 22 June, 2006;coldAP2CRT/DRECBFHordeum vulgare (barley)Xue GP�The DNA-binding activity of an AP2 transcriptional activatorHvCBF2 involved in regulation of low-temperature responsive genesin barley is modulated by temperature.Plant J. 33: 373-383 (2003)PubMed: 12535350; GTCGAC CTRMCAMV35SS000460"27-March-2004 (last modified) kehi�CT-rich motif (inverted GAGA) found in a 60-nucleotide region(S1) downstream of the transcription start site of the CaMV 35SRNA; Can enhance gene expression; Inverted GAGA; See alsoS000405, S000427 (GAGA); (TC)4T;CaMV 35Senhancer Cauliflower mosaic virus (CaMV)*Pauli S, Rothnie HM, Chen G, He X, Hohn T.MThe cauliflower mosaic virus 35S promoter extends into thetranscribed region. J Virol. 78: 12120-12128.(2004)PubMed: 15507598 TCTCTCTCT
CURECORECRS000493"11-April-2006 (last modified) kehi�GTAC is the core of a CuRE (copper-response element) found inCyc6 and Cpx1 genes in Chlamydomonas; Also involved inoxygen-response of these genes; For CuRE, see Quin and Merchant,1995;copperoxygenhypoxicChlamydomonas reinhardtii�Quinn JM, Barraco P, Eriksson M, Merchant S.Quinn JM, Eriksson M, Moseley JL, Merchant S.Quinn JM, Merchant S.Kropat J, Tottey S, Birkenbihl RP, Depege N, Huijser P, MerchantS.��Coordinate copper- and oxygen-responsive Cyc6 and Cpx1 expressionin Chlamydomonas is mediated by the same element.Oxygen deficiency responsive gene expression in Chlamydomonasreinhardtii through a copper-sensing signal transductionpathway.Two copper-responsive elements associated with the ChlamydomonasCyc6 gene function as targets for transcriptional activators.A regulator of nutritional copper signaling in Chlamydomonas isan SBP domain protein that recognizes the GTAC core of copperresponse element.�J Biol Chem. 275: 6080-6089 (2000).Plant Physiol. 128 :463-471 (2002).Plant Cell. 7 :623-628 (1995).Proc Natl Acad Sci U S A. 102: 18730-18735.(2005)?PubMed: 10692397PubMed: 11842150PubMed: 7780310PubMed: 16352720 GTACCYTOSITECSHPRAS000261 14-Oct-1999 (last modified) kehi�13 bp sequence of unknown function found in cucumber (C.s.)hydroxypyruvate reductase (hprA) gene promoter; Protein bindingsite; Required for cytokinin responsiveness; See S000260(AS1LIKECSHPRA) found in the same region; Also involved in lightresponsiveness; see also S000260; cytokininas-1lightcucumber (Cucumis sativus)CJin G, Davey MC, Ertl JR, Chen R, Yu Z, Daniel SG, Becker WM,Chen CInteraction of DNA-binding proteins with the 5'-flanking regionof a cytokinin-responsive cucumber hydroxypyruvate reductasegene Plant Mol Biol 38:713-724 (1998)PubMed: 9862489;
AAGATTGATTGAG D1GMAUX28S000328 20-Feb-2002 (last modified) uchi��"D1"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; D1 and D4 share a verysimilar core sequence TAGTXXCTGT and TAGTXCTGT, respectively;D1/D4-like sequence were identified in several otherauxin-responsive genes; Binding site of GmGT-2 which is the GT-2family of transcription factors; GmGT-2 are down-regulated bylight in a phytochrome-dependent manner; See 000331;AuxinAux28GT-2 phytochromeD1 hypocotylsoybean (Glycine max)WNagao RT, Goekjian VH, Hong JC, Key JLO'Grady K, Goekjian VH, Naim CJ, Nagao RT, Key JL�Identification of protein-binding DNA sequences in anauxin-regulated gene of soybeanThe transcript abundance of GmGT-2, a new member of the GT-2family of transcription factors from soybean, is down-regulatedby light in a phytochrome-dependent mannerEPlant Mol Biol 21: 1147-1162 (1993)Plant Mol Biol 47: 367-378 (2001)!PubMed: 8490133;PubMed: 11587508;
ACAGTTACTA D2GMAUX28S000329 7-Sep-2000 (last modified) seki�"D2"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; Located between -703 and-716; A/T-rich sequence;AuxinAux28soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133; ATTTATATAAAT D3GMAUX28S000330 7-Sep-2000 (last modified) seki�"D3"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; Located between -750 and-760; A/T-rich sequence;AuxinAux28soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133; TATTTGCTTAA D4GMAUX28S000331 7-Sep-2000 (last modified) seki�"D4"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; D1 and D4 share a verysimilar core sequence TAGTXXCTGT and TAGTXCTGT, respectively;D1/D4-like sequence were identified in several otherauxin-responsive genes; See 000328;AuxinAux28soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133; TAGTGCTGT DE1PSPRA2S000379 21-May-2001 (last modified) uchi�""DE1" found in the pea(P.S) pra2 gene promoter; Involved in pra2down-regulation by phytochrome A, phytochrome B and blue-lightphotoreceptors; pra2 encodes a small GTPase belonging to theYPT/rab family; DF1 has DNA-binding domain specifically binds totwo types of DNA sequences, DE1 and GT2;pra2light responsedark inductiondown regulationDF1pea (Pisum sativum)LInaba T, Nagano Y, Reid JB, Sasaki YNagano Y, Inaba T, Furuhashi H, Sasaki Y�5DE1, a 12-base pair cis-regulatory element sufficient to conferdark-inducible and light down-regulated expression to a minimalpromoter in peaTrihelix DNA-binding protein with specificities for two distinctcis-elements: both important for light down-regulated anddark-inducible gene expression in higher plantsFJ Biol Chem 275: 19723-19727 (2000)J Biol Chem 276: 22238-22243 (2001)"PubMed: 10777499;PubMed: 11301338; GGATTTTACAGT DOFCOREZMS000265 7-Sep-2000 (last modified) seki��Core site required for binding of Dof proteins in maize (Z.m.);Dof proteins are DNA binding proteins, with presumably only onezinc finger, and are unique to plants; Four cDNAs encoding Dofproteins, Dof1, Dof2, Dof3 and PBF, have been isolated frommaize; PBF is an endosperm specific Dof protein that binds toprolamin box; Maize Dof1 enhances transcription from thepromoters of both cytosolic orthophosphate kinase (CyPPDK) and anon-photosynthetic PEPC gene; Maize Dof2 supressed the C4PEPCpromoter;DofC4PEPCCyPPDKPEPCC4leafshootmaize (Zea mays)$Yanagisawa S, Schmidt RJYanagisawa S�Diversity and similarity among recognition sequences of Doftranscription factorsDof1 and Dof2 transcription factors are associated withexpression of multiple genes involved in carbon metabolism inmaize3Plant J 17:209-214 (1999)Plant J 21:281-288 (2000)"PubMed: 10074718;PubMed: 10758479; AAAGDR5GMGH3S000337 7-Sep-2000 (last modified) seki�"DR5"; A highly active synthetic auxin response element; Createdby site-directed mutations in a natural composite AuxRE found inthe soybean GH3 promoter; The DR5 showed greater auxinresponsiveness; Binding site of ARF1; See S000270;Aux/IAADR5AuxinARF1AUXRESoybean (Glycine max)+Ulmasov T, Murfett J, Hagen G, Guilfoyle TJ{Aux/IAA proteins repress expression of reporter genes containingnatural and highly active synthetic auxin response elements Plant Cell 9: 1963-1971 (1997)PubMed: 9401121; CCTTTTGTCTCDRE1COREZMRAB17S000401 27-Aug-2002 (last modified) uchi�3"DRE1" core found in maize (Z.M.) rab17 gene promoter; "DRE1" wasprotected, in in vivo footprinting, by a protein in embryosspecifically, but in leaves, was protected when was treated withABA and drought; rab17 is expressed during late embryogenesis,and is induced by ABA; See S000150, S000200 and S000402;rab17ABAdrought responsemaize (Zea mays)+Busk PK, Jensen AB, Pages MKizis D, Pages M�Regulatory elements in vivo in the promoter of the abscisic acidresponsive gene rab17 from maizeMaize DRE-binding proteins DBF1 and DBF2 are involved in rab17regulation through the drought-responsive element in anABA-dependent pathway8Plant J. 11: 1285-1295 (1997)Plant J. 30 :679-689 (2002)!PubMed: 9225468;PubMed: 12061899; ACCGAGADRE2COREZMRAB17S000402 03-Jun-2003 (last modified) kehi�"DRE2" core found in maize (Z.M.) rab17 gene promoter; "DBF1" and"DBF2" bound to "DRE2"; rab17 is expressed during lateembryogenesis, and is induced by ABA; See S000150, S000200 andS000401;rab17ABAdrought responseDBF1DBF2maize (Zea mays)�Busk PK, Jensen AB, Pages MKizis D, Pages MDubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S,Seki M, Shinozaki K, Yamaguchi-Shinozaki K.�yRegulatory elements in vivo in the promoter of the abscisic acidresponsive gene rab17 from maizeMaize DRE-binding proteins DBF1 and DBF2 are involved in rab17regulation through the drought-responsive element in anABA-dependent pathwayOsDREB genes in rice, Oryza sativa L., encode transcriptionactivators that function in drought-, high-salt- andcold-responsive gene expression.SPlant J. 11: 1285-1295 (1997)Plant J. 30 :679-689 (2002)Plant J. 33: 751-763 (2003)2PubMed: 9225468;PubMed: 12061899;PubMed: 12609047; ACCGACDREDR1ATRD29ABS000152!23-June-2006 (last modified) kehi��Related to responsiveness to drought, low-temperature orhigh-salt stress; See S000153, S000157; Binding site of DREB1 andDREB2: Binding site of Arabidopsis CBF1(C-repeat/DRE bindingfactor); Overexpression of DREB1A activated the expression ofstress tolerance genes; CBF1 overexpression induces COR genes andenhances freezing tolerance; Heterologous CBF1 expressionenhances oxidative stresses tolerance; DRE and ABRE areinterdependent in the ABA-responsive expression of the rd29A inArabidopsis;DREdrought water stressoxidative stresslow temperature high saltstressLREDREBC-repeatCBF1AP2cold dehydrationCRTleafshoot#Arabidopsis thaliana; Populus spp.;��Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki KSuzuki M, Ketterling MG, McCarty DR.Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, AbeH, Narusaka M, Shinozaki K, Yamaguchi-Shinozaki K.Benedict C, Skinner JS, Meng R, Chang Y, Bhalerao R, Huner NPA,Finn CE, Chen THH, Hurry VPandey GK, Grant JJ, Cheong YH, Kim BG, Li L, Luan S.Nakashima K, Shinwari ZK, Sakuma Y, Seki M, Miura S, Shinozaki K,Yamaguchi-Shinozaki KHsieh TH, Lee JT, Yang PT, Chiu LH, Charng YY, Wang YC, Chan MT��Improving plant drought, salt, and freezing tolerance by genetransfer of a single stress-inducible transcription factorQuantitative statistical analysis of cis-regulatory sequences inABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis.Interaction between two cis-acting elements, ABRE and DRE, inABA-dependent expression of Arabidopsis rd29A gene in response todehydration and high-salinity stresses.The CBF1-dependent low temperature signalling pathway, regulonand increase in freeze tolerance are conserved in Populus spp.ABR1, an APETALA2-Domain Transcription Factor That Functions as aRepressor of ABA Response in Arabidopsis.Organization and expression of two Arabidopsis DREB2 genesencoding DRE-binding proteins involved in dehydration- andhigh-salinity-responsive gene expressionHeterology expression of the Arabidopsis C-repeat/dehydrationresponse element binding factor 1 gene confers elevated toleranceto chilling and oxidative stresses in transgenic tomato�Nat Biotechnol 17: 287-291 (1999)Plant Physiol.139: 437-447 (2005)Plant J. 34: 137-148 (2003)Plant, Cell and Environment 29:1259-1272 (2006)Plant Physiol. 139: 1185-1193 (2005)Plant Mol Biol 42: 657-665 (2000)Plant Physiol. 129: 1086-1094 (2002)dPubMed: 10096298;PubMed: 16113229PubMed: 12694590;PubMed: 16227468PubMed: 10809011;PubMed: 12114563; in silico TACCGACAT
E2F1OSPCNAS000396 21-May-2002 (last modified) uchi�"re2f-1" found in the promoter of rice PCNA gene; Located between-142 and -135; "te2f-1" found in the promote of Tobacco PCBAgene; Located between -122 and -115; Binding site of OsE2F1 andOsE2F2; Involved in transcriptional activation in activelydividing cells and tissue;E2FPCNAmeristematic tissue
cell cycle0rice (Oryza sativa); tobacco (Nicotiana tabacum)Kosugi S, Ohashi Y�E2F sites that can interact with E2F proteins cloned from riceare required for meristematic tissue-specific expression of riceand tobacco proliferating cell nuclear antigen promotersPlant J 29: 45-59 (2002)PubMed: 12060226; GCGGGAAA E2FANTRNRS000366!23-June-2006 (last modified) kehi�"E2Fa element" found in the tobacco (N.t.) RNR (Ribonucleotidereductase) gene promoter and in the Arabidopsis thaliana (A.t.)CDC6 gene promoter; Binding site of tobacco and Arabidopsis E2F;Involved in upregulation of the promoter at G1/S transition; SeeS000367;E2FaRNRG1/S transitionCDC6
Cell-division
Cell cycleS-phasecell suspension culture2tobacco (Nicotiana tabacum); Arabidopsis thaliana;�Chaboute ME, Clement B, Sekine M, Philipps G, Chaubet-Gigot Nde Jager SM, Menges M, Bauer UM, Murra JASozzani R, Maggio C, Varotto S, Canova S, Bergounioux C, AlbaniD, Cella R�sCell cycle regulation of the tobacco ribonucleotide reductasesmall subunit gene is mediated by E2F-like elementsArabidopsis E2F1 binds a sequence present in the promoter ofS-phase-regulated gene AtCDC6 and is a member of a multigenefamily with differential activitiesInterplay between Arabidopsis Activating Factors E2Fb and E2Fa inCell Cycle Progression and Development.ePlant Cell 12: 1987-2000 (2000)Plant Mol Biol 47: 555-568 (2001)Plant Physiol. 140: 1355-1366 (2006)"PubMed: 11041892;PubMed: 11669580; TTTCCCGC E2FBNTRNRS000367%29-November-2004 (last modified) kehi�="E2Fb" found in the tobacco (N.t.) RNR (Ribonucleotide reductase)gene promoter; Binding site of tobacco E2F; Involved inupregulation of the promoter at G1/S transition; See S000366;"dE2F (distal reverse E2F element)" important for regulatingspecific RNR1a gene expression in respsonse to UV-C irradiation;See S000455;E2FbRNRG1/S transitiondE2FUV-C
ceel cycletobacco (Nicotiana tabacum)`Chaboute ME, Clement B, Sekine M, Philipps G, Chaubet-Gigot NLincker F, Philipps G, Chaboute ME.� Cell cycle regulation of the tobacco ribonucleotide reductasesmall subunit gene is mediated by E2F-like elementsUV-C response of the ribonucleotide reductase large subunitinvolves both E2F-mediated gene transcriptional regulation andprotein subcellular relocalization in tobacco cells.HPlant Cell 12: 1987-2000 (2000)Nucleic Acids Res. 32: 1430-1438. (2004).!PubMed: 11041892;PubMed: 14990748 GCGGCAAA
EIN3ATERF1S000332 7-Sep-2000 (last modified) seki��EIN3 (Ethylene-insensitive 3) binding site found in the promoterof the Arabidopsis (A.t.) ERF1 (Ethylene-Response-Factor 1); EIN3recognizes its target as a homodimer; EIN3 is necessary andsufficient for ERF1 expression; Consititutive expression of ERF1results in the activation of a variety of ethylene response genesand phenotype; ERF1 is a GCC-box binding site; ERF1 actsdownstream of EIN3;EIN3ERF1EthyleneArabidopsis thaliana'Solano R, Stepanova A, Chao Q, Ecker JR~Nuclear events in ethylene signaling: a transcriptional cascademediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1 Genes Dev. 12: 3703-3714 (1998)-PubMed: 9851977; GenBank: AF076277; AF076278; GGATTCAAGGGGCATGTATCTTGAATCCELEMENT1GMLBC3S000319 7-Sep-2000 (last modified) seki� "Element 1" found in the promoter of soybean (G.m.)leghaemoglobin lbc3 gene; Binding site of nuclear extract fromsoybean nodules; Located at -223 to -246; Element 1 and Element 2(S000320) bind to the same nodule specific factor; Element 1 andElement 2 share a common motif; See S000320;noduleleghaemoglobinlbc3rootSoybean (Glycine max),Jensen EO, Marcker KA, Schell J, de Bruijn J�Interaction of a nodule specific, trans-acting factor withdistinct DNA elements in the soybean leghaemoglobin lbc3 5'upstream regionEMBO J 7:1265-1271 (1988) GATATATTAATATTTTATTTTATAELEMENT2GMLBC3S000320 7-Sep-2000 (last modified) seki�B"Element 2" found in the promoter of soybean (G.m.)leghaemoglobin lbc3 gene; Binding site of nuclear extract fromsoybean nodules; Located at -161 to -176; Element 1(S000319) andElement 2 (S000320) bind to the same nodule specific factor;Element 2 is highly conserved in other soybean lb gene promoterregions; See S000319;noduleleghaemoglobinlbc3rootSoybean (Glycine max),Jensen EO, Marcker KA, Schell J, de Bruijn J�Interaction of a nodule specific, trans-acting factor withdistinct DNA elements in the soybean leghaemoglobin lbc3 5'upstream regionEMBO J 7:1265-1271 (1988) CTTAAATTATTTATTT ELRE1PCPAL1S000306 10-Feb-2000 (last modified) seki�� One of two elicitor (ELRE) and light response elements (LRE)found in the parsley (P.c.) phenylalanine ammonia-lyase (PAL-1)gene promoter; Involved in UV light and elicitor responsiveness;Conserved in several elicitor or light-responsive genes; SeeS000307;!phenylalanine ammonia-lyase (PAL)UVelicitorlightleafshoot parsley (Petroselinum crispum)(Lois R, Dietrich A, Hahlbrok K, Schulz W�A phenylalanine ammonia-lyase gene from parsley: structure,regulation and identification of elicitor and light responsivecis-acting elementsEMBO J 8: 1641-1648 (1989)(PubMed: 2767049; GenBank: X15473, X16772 CTCCAACAAACCCCTTC ELRE2PCPAL1S000307 10-Feb-2000 (last modified) seki�� One of two elicitor (ELRE) and light response elements (LRE)found in the parsley (P.c.) phenylalanine ammonia-lyase (PAL-1)gene promoter; Involved in UV light and elicitor responsiveness;Conserved in several elicitor or light-responsive genes; SeeS000306;!phenylalanine ammonia-lyase (PAL)UVelicitorlightleafshoot parsley (Petroselinum crispum)(Lois R, Dietrich A, Hahlbrok K, Schulz W�A phenylalanine ammonia-lyase gene from parsley: structure,regulation and identification of elicitor and light responsivecis-acting elementsEMBO J 8: 1641-1648 (1989)(PubMed: 2767049; GenBank: X15473, X16772 ATTCTCACCTACCA
ELRECOREPCRP1S000142!22-June-2006 (last modified) kehi��ElRE (Elicitor Responsive Element) core of parsley (P.c.) PR1genes; consensus sequence of elements W1 and W2 of parsley PR1-1and PR1-2 promoters; Box W1 and W2 are the binding site of WRKY1and WRKY2, respectively; ERE; "WA box"; One of the W boxes foundin the Parsley (P.c.) WRKY1 gene promoter; Required for elicitorresponsiveness; See S000310; "WC box" WB box (S000310) and WC boxconstitute a palindrome; WRKY1 protein binding site; W-box foundin thioredoxin h5 gene in Arabidopsis (Laloi et al.);
ElicitorPR1ElREELREEREW boxWRKY1
palindromesalicylic acidTMV<Petroselinum crispum (parsley); Nicotiana tabacum (tobacco);�.Rushton PJ, Torres JT, Parniske M, Wernert P, Hahlbrock K,Somssich IEEulgem T, Rushton PJ, Schmelzer E, Hahlbrock K, Somssich IEEulgem T, Rushton PJ, Robatzek S, Somssich IEChen C, Chen ZRushton PJ, Reinstadler A, Lipka V, Lippok B, Somssich IELaloi C, Mestres-Ortega D, Marco Y, Meyer Y, Reichheld JP.��Interaction of elicitor-induced DNA-binding proteins withelicitor response elements in the promoters of parsley PR1genes.Early nuclear events in plant defence signalling: rapid geneactivation by WRKY transcription factorsThe WRKY superfamily of plant transcription factorsIsolation and characterization of two pathogen- and salicylicacid-induced genes encoding WRKY DNA-binding proteins fromtobaccoSynthetic plant promoters containing defined regulatory elementsprovide novel insights into pathogen- and wound-inducedsignalingThe Arabidopsis cytosolic thioredoxin h5 gene induction byoxidative stress and its W-box-mediated response to pathogenelicitor.�EMBO J 15:5690-5700 (1996)EMBO J 18: 4689-4699 (1999)Trends Plant Sci 5: 199-206 (2000)Plant Mol Biol 42: 387-396 (2000)Plant Cell. 14: 749-762 (2002)Plant Physiol. 134:1006-1016 (2004).}PubMed: 8896462; GenBank: U48862, U48863;PubMed: 10469648;PubMed: 10785665;PubMed: 10794538;PubMed: 11971132;PubMed: 14976236ReviewTTGACC EMBP1TAEMS000119 16-Feb-2001 (last modified) seki�lBinding site of trans-acting factor EMBP-1; wheat (T.a.) Em gene;See S000015; Binding site of ABFs; ABFs (ABRE binding factors)were isolated from Arabidopsis by a yeast one-hybrid screeningsystem; Expression ABFs is induced by ABA and various stresstreatment; ABFs belongs to a distinct subfamily of bZIP proteins;Involved in ABA-mediated stress-signaling pathway;EMBP-1EmABAABFABREbZIPseed0wheat (Triticum aestivum); Arabidopsis thaliana;�Guiltinan MJ, Marcotte WR Jr, Quatrano RSVasil V, Marcotte Jr. WR, Rosenkrans L, Cocciolone SM, Vasil IK,Quatrano RS, McCarty DRChoi H, Hong J, Ha J, Kang J, Kim SY�"A plant leucine zipper protein that recognizes an abscisic acidresponse element.Overlap of viviparous1 (VP1) and abscisic acid response elementsin the EM promoter: G-Box elements are sufficient but notnecessary for VP1 transactivationABFs, a family of ABA-responsive element binding factorsYScience 250:267-270 (1990)Plant Cell 7: 1511-1518 (1995)J Biol Chem 275: 1723-1730 (2000)IPubMed: 2145628; GenBank: M62893, M63999;PubMed: 8589631PubMed: 10636868; CACGTGGC EMHVCHORDS000452%29-November-2004 (last modified) kehi�"Endosperm motif (EM)" found in the promoter of barley (H.v.)c-hordein gene; Involved in the nitrogen response of c-hordeinpromoter;EM endospermhordeinnitrogenHordeum vulgare (barley)Muller M, Knudsen S.�The nitrogen response of a barley C-hordein promoter iscontrolled by positive and negative regulation of the GCN4 andendosperm box.Plant J. 4: 343-355 (1993).PubMed: 8220485 TGTAAAGTEREGCCS000036 03-Jun-2003 (last modified) kehi��"GCC box" in "ERE (ethylene responsive element)";Ethylene-responsive region of tobacco (N.t.) chitinase genecontains two copies of the GCC-box; ERF2 and ERF4 enhanced theGCC box-mediated transcription; ERF3 reduced the transcription ofthe reporter gene in tobacco protoplasts; Binding site of AtEBP;Pti4/5/6 proteins from tomato which belong to the ERF familyactivate the expression of "GCC box"-containing PR genes; ERF3was found to interact with NtUBC2, a ubiquitin-conjugatingenzyme;EthyleneEREBPGCC boxG-boxCHNEREERFxylanaseTvXOBFbZIPEBPpathogenocsleafshootPti4/5/6 ubiquitinUBC22tobacco (Nicotiana tabacum); Arabidopsis thaliana;�Koyama T, Okada T, Kitajima S, Ohme-Takagi M, Shinshi H, Sato F.Gu YQ, Wildermuth MC, Chakravarthy S, Loh YT, Yang C, He X, HanY, Martin GBYamamoto S, Suzuki K, Shinshi HOhta M, Ohme-Takagi M, Shinshi HOhme-Takagi M, Shinshi HButtner M, Singh KBOhme-Takagi M, Suzuki K, Shinshi H�YIsolation of tobacco ubiquitin-conjugating enzyme cDNA in a yeasttwo-hybrid system with tobacco ERF3 as bait and itscharacterization of specific interaction.Tomato transcription factors pti4, pti5, and pti6 activatedefense responses when expressed in ArabidopsisElicitor-responsive, ethylene-independent activation of GCCbox-mediated transcription that is regulated by both proteinphosphorylation and dephosphorylaton in cultured tobacco cellsThree ethylene-responsive transcription factors in tobacco withdistinct transactivation functionsEthylene-inducible DNA binding proteins that interact with anethylene-responsive elementArabidopsis thaliana ethylene-responsive element binding protein(AtEBP), an ethylene-inducible, GCC box DNA-binding proteininteracts with an ocs element binding proteinRegulation of Ethylene-Induced Transcription of Defense Genes�J Exp Bot. 54: 1175-1181 (2003)Plant Cell 14: 817-831 (2002)Plant J 20: 571-579 (1999)Plant J 22:29-38 (2000)Plant Cell 7: 173-182 (1995)Proc Natl Acad Sci USA 94: 5961-5966 (1997)Plant Cell Physiol 41: 1187-1192 (2000)�PubMed: 12654868;PubMed: 11971137;PubMed: 10652129;PubMed: 10792818;PubMed: 7756828;PubMed: 9159183; GenBank: Y09942;PubMed: 11092902; TAAGAGCCGCC ESPASGL01S000509$04-January-2007 (last modified) kehik"ESP (endosperm specificity palindrome)" element found in thepromoter of oat (A.s.) globulin gene (AsGlo1); endospermglobulinAvena sativa (oat) Vickers CE, Xue G, Gresshoff PM.tA novel cis-acting element, ESP, contributes to high-levelendosperm-specific expression in an oat globulin promoter.!Plant Mol Biol. 62:195-214 (2006)PubMed: 16915522 ACATGTCATCATGT EVENINGATS000385$26-October-2005 (last modified) kehi�d"Evening element" found 46 times in the promoters of 31 cyclinggenes in Arabidopsis thaliana (Harmer et al. 2000); Required forcircadian control of gene expression; "EE (evening element)motif"; Also found in the promoter of the Solanum melongena geneencoding cysteine protease, and identified as cis-element for itscircadian regulation (Rawat et al. 2005);evening circadianclockEE(Arabidopsis thaliana; Solanum melongena;sHarmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, WangX, Kreps JA, Kay SARawat R, Xu ZF, Yao KM, Chye ML.�Orchestrated transcription of key pathways in Arabidopsis by thecircadian clockIdentification of cis-elements for ethylene and circadianregulation of the Solanum melongena gene encoding cysteineproteinase.AScience 290: 2110-2113 (2000)Plant Mol Biol. 57: 629-643 (2005).!PubMed: 11118138;PubMed: 15988560 AAAATATCTGADOWNATS000438#01-August-2006 (last modified) kehi�Sequence present in 24 genes in the GA-down regulated d1 cluster(106 genes) found in Arabidopsis seed germination; This motif issimilar to ABRE (Busk and Pages 1998);Gaseed germainationArabidopsis thaliana;�Ogawa M, Hanada A, Yamauchi Y, Kuwahara A, Kamiya Y, YamaguchiS.Nakashima K, Fujita Y, Katsura K, Maruyama K, Narusaka Y, Seki M,Shinozaki K, Yamaguchi-Shinozaki K.�Gibberellin biosynthesis and response during Arabidopsis seedgermination.Transcriptional regulation of ABI3- and ABA-responsive genesincluding RD29B and RD29A in seeds, germinating embryos, andseedlings of Arabidopsis.@Plant Cell 15: 1591-1604 (2003)Plant Mol Biol. 60: 51-68 (2006).!PubMed: 12837949;PubMed: 16463099 ACGTGTC GAGA8HVBKN3S000427 29-Sep-2003 (last modified) kehi�"GA octodinucleotide repeat" found in intron IV of the barley(H.v.) gene Bkn3; Binding site for GAGA-binding factor BBR; SeeS000405 (GAGA element in the soy bean Gsa1 gene);GAGAGBPBBRHordeum vulgare (barley)iSanti L, Wang Y, Stile MR, Berendzen K, Wanke D, Roig C, Pozzi C,Muller K, Muller J, Rohde W, Salamini F.zThe GA octodinucleotide repeat binding factor BBR participates inthe transcriptional regulation of the homeobox gene Bkn3.Plant J. 34:813-826 (2003)PubMed: 12795701; GAGAGAGAGAGAGAGA
GAGAGMGSA1S000405 21-Nov-2002 (last modified) uchi�"GAGA element" found in the promoter of the heme and chlorophyllsynthesis gene Gsa1 in soybean (G.m.); GAGA binding protein (GBP)binds to (GA)n/(CT)n DNA;Dinucleotide repeat GAGA elementGBPGsa1Glycine max (soybean)Sangwan I, O'Brian MR[Identification of a Soybean Protein That Interacts with GAGAElement Dinucleotide Repeat DNA$Plant Physiol. 129: 1788-1794 (2002)PubMed: 12177492; GAGAGAGAGAGAGAGAGA GARE1OSREP1S000419%28-November-2004 (last modified) kehi}"Gibberellin-responsive element (GARE)" found in the promoterregion of a cystein proteinase (REP-1) gene in rice; SeeS000020;aleuroneGARE gibberellinseedOryza sativa (rice)Sutoh K, Yamauchi D.oTwo cis-acting elements necessary and sufficient forgibberellin-upregulated proteinase expression in rice seedsPlant J. 34: 636-645 (2003)PubMed: 12787245; TAACAGA GARE2OSREP1S000420%28-November-2004 (last modified) kehi}"Gibberellin-responsive element (GARE)" found in the promoterregion of a cystein proteinase (REP-1) gene in rice; SeeS000020;aleuroneGARE gibberellinseedOryza sativa (rice)Sutoh K, Yamauchi D.oTwo cis-acting elements necessary and sufficient forgibberellin-upregulated proteinase expression in rice seedsPlant J. 34: 636-645 (2003)PubMed: 12787245; TAACGTA GARE4HVEPB1S000297 10-Feb-2000 (last modified) seki�"GARE-4" found in the barley (H.v.) EPB-1 (cysteine proteinase)gene promoter; Located between -142 to -156; Required for GAinduction; Putative binding site of transcription factor, GAMyB;See S000298;EPBcysteine proteinaseGAABAGAREpyrimidine boxseedaleuronebarley (Hordeum vulgare)!Cercos M, Gomez-Cadenas A, Ho THD�Hormonal regulation of a cysteine proteinase gene, EPB-1, inbarley aleurone layers: cis- and trans-acting elements involvedin the co-ordinated gene expression regulated by gibberellins andabscisic acidPlant J 19: 107-118 (1999)PubMed: 10476058 GTAACAGAATGCTGG
GAREHVAMY1S000038 17-May-1998 (last modified) kehia"GARE (gibberellic acid responsive element)" of barley (H.v.)alpha-amylase gene (Amy 1/6-4); GA3;gibberellic acidGAGA3amylaseAmy1/6-4GAREbarley (Hordeum vulgare)TSkriver K, Olsen FL, Rogers JC, Mundy JGilmartin PM, Sarokin L, Memelink J, Chua N-H{Cis-acting DNA elements responsive to gibberellin and itsantagonist abscisic acid.Molecular light switches for plant genes.EProc Natl Acad Sci USA 88:7266-7270 (1991)Plant Cell 2:369-378 (1990) PubMed: 1831269;PubMed: 2152164; GGCCGATAACAAACTCCGGCCGATABOXS000039#01-August-2006 (last modified) kehi�0"GATA box"; GATA motif in CaMV 35S promoter; Binding with ASF-2;Three GATA box repeats were found in the promoter of Petunia(P.h.) chlorophyll a/b binding protein, Cab22 gene; Required forhigh level, light regulated, and tissue specific expression;Conserved in the promoter of all LHCII type I Cab genes;ASF-2GATA boxCab chlorophyll a/b binding proteinleafshootdCaMV; Cauliflower mosaic virus; Petunia hybrida (petunia);Arabidopsis thaliana; Oryza sativa (rice);�Lam E, Chua NHGilmartin PM, Sarokin L, Memelink J, Chua N-HBenfey PN, Chua NHGidoni D, Brosio P, Bond-Nutter D, Bedbrook J, Dunsmuir PTeakle GR, Manfield IW, Graham JF, Gilmartin PMReyes JC, Muro-Pastor MI, Florencio FJ.Rubio-Somoza I, Martinez M, Abraham Z, Diaz I, Carbonero P.�9ASF-2: A factor that binds to the cauliflower mosaic virus 35Spromoter and a conserved GATA motif in cab promoters.Molecular light switches for plant genes.The cauliflower mosaic virus 35S promoter: combinatorialregulation of transcription in plantsNovel cis-acting elements in Petunia Cab gene promotersArabidopsis thaliana GATA factors: organisation, expression andDNA-binding characteristicsThe GATA family of transcription factors in Arabidopsis andrice.Ternary complex formation between HvMYBS3 and other factorsinvolved in transcriptional control in barley seeds.�Plant Cell 1:1147-1156 (1989)Plant Cell 2:369-378 (1990)Science 250:959-966 (1990)Mol Gen Genet 215: 337-344 (1989)Plant Mol Biol. 50 :43-57 (2002)Plant Physiol. 134: 1718-1732 (2004).Plant J. 47: 269-281 (2006)aPubMed: 2535536;PubMed: 2152164;PubMed: 2651885;PubMed: 12139008;PubMed: 15084732PubMed: 16762033 GATAGBOX10NTS000272 15-Oct-1999 (last modified) kehi�One of 11 G-box sequences in tobacco (N.t.); Required forhigh-level constitutive expression in seed, leaf, root, axillarybud, almost all parts of flower buds and pollen;G-boxG-box 10tetramerseedrootleaf axillary budpollentobacco (Nicotiana tabacum)/Ishige F, Takaichi M, Foster R, Chua NH, Oeda KiA G-box motif (GCCACGTGCC) tetramer confers high-levelconstitutive expression in dicot and monocot plantsPlant J 18:443-448 (1999)
GCCACGTGCCGBOXPCS000324 7-Sep-2000 (last modified) seki�G"G box"; Binding site of parsley (P.c.) cytosolic G-box bindingfactors (cytosolic GBFs); Cytosolic G-Box binding activity ismodulated by light; DNA binding activity of cytosolic GBFs isregulated by cytosolic phosphorylation/dephospholylationactivities; Cytosolic GBFs are translocated to the nucleus in alight-regulated manner;G-boxlightcytosolic GBFsbZIPleafshoot parsley (Petroselinum crispum)=Harter K, Kircher S, Frohnmeyer H, Krenz M, Nagy F, Schafer EcLight-regulated modification and nuclear translocation ofcytosolic G-box binding factors in parsley Plant Cell 6: 545-559 (1994)PubMed: 8205004;
ACCACGTGGC
GBOXRELOSAMY3S000206 29-Sep-1999 (last modified) kehiWG box-related element found in Amy3D (amylase) promoter of rice(O.s.); Similar to ABRE;amylaseG boxG box-like elementrice (Oryza sativa);DHwang YS, Karrer EE, Thomas BR, Chen L, Rodriguez RLBusk PK, Pages M�Three cis-elements required for rice alpha-amylase Amy3Dexpression during sugar starvationRegulation of abscisic acid-induced transcription@Plant Mol Biol 36:331-341 (1998)Plant Mol Biol 37:425-435 (1998) PubMed: 9484474;PubMed: 9617810;Review CTACGTGGCCA GBOXSORBCS1S000380 23-Aug-2001 (last modified) uchi�"G-box" found in the spinach(S.O.) RBCS-1 gene promoter; Locatedbetween -219 and -212; G-box trimer confers relatively high levelexpression in roots;RBCS-1G-boxrootspinach (Spinacia oleracea)ELubberstedt T, Bolle CE, Sopory S, Flieger K, Herrmann RG,Oelmuller RoPromoters from genes for plastid proteins possess regions withdifferent sensitivities toward red and blue light"Plant Physiol 104: 997-1006 (1994)PubMed: 8165263;
TCCACGTGGTGCAACREPEATZMZEINS000027 17-May-1998 (last modified) kehi�"GCAAC repeat" found in the 22bp recognition site for beta-1factor in the promoter of beta-zein (prolamin type) gene of maize(Z.m.); GCAAC is the core recognition sequence of the proteinencoded by the retroviral oncogene myb (Biedenkapp et al. Nature335:835-837 (1988)); beta-zeinGCAACrepeatmybseed endospermmaize (Zea mays)So J-S, Larkins BAwBinding of an endosperm-specific nuclear protein to a maizebeta-zein gene correlates with zein transcriptional activity Plant Mol Biol 17:309-319 (1991)PubMed: 1883992;
GCAACGCAAC GCBP2ZMGAPC4S000351 16-Feb-2001 (last modified) seki�Binding site of tobacco nuclear factor (GCBP-2) found in themaize (Z.m.) GapC4 (Glyceraldehyde-3-phosphate dehydrogenase 4)gene promoter; Located between -293 and -285; See S000350; anaerobicGapC4GCBP-2maize (Zea mays)Geffers R, Cerff R, Hehl RuAnaerobiosis-specific interaction of tobacco nuclear factors withcis-regulatory sequences in the maize GapC4 promoter Plant Mol Biol 43: 11-21 (2000)PubMed: 10949370; GTGGGCCCGGCCCORES000430 28-Jan-2004 (last modified) kehi��Core of GCC-box found in many pathogen-responsive genes such asPDF1.2, Thi2.1, and PR4; Has been shown to function asethylene-responsive element; See S000036, S000232, S000332;Appears to play important roles in regulatingjasmonate-responsive gene expression; Tomato Pti4 (ERF) regulatesdefence-related gene expression via GCC box and non-GCC box ciselements (Myb1 (GTTAGTT) and G-box(CACGTG));GCCGCC-boxEREJAPti4ERFPR7Arabidopsis thaliana; Lycopersicon esculentum (tomato);{Brown RL, Kazan K, McGrath KC, Maclean DJ, Manners JM.Chakravarthy S, Tuori RP, DAscenzo MD, Fobert PR, Despres C,Martin GB�A role for the GCC-box in jasmonate-mediated activation of thePDF1.2 gene of Arabidopsis.The tomato transcription factor Pti4 regulates defence-relatedgene expression via GCC box and non-GCC box cis elementsBPlant Physiol. 132:1020-1032 (2003)Plant Cell 15: 3033-3050 (2003)"PubMed: 12805630;PubMed: 14630974; GCCGCC GCN4OSGLUB1S000277 21-May-2002 (last modified) uchi��"GCN4 motif" found in GluB-1 gene in rice (O.s.); Required forendosperm-specific expression; See S000276; AACA and ACGT motifswas found sufficient to confer a detectable level of endospermexpression; See S000353, S000354; This motif is the recognitionsite for a basic leucine zipper transcription factor that belongsto the group of maize Opaque-2 (O2)-like proteins; Although allthe RISBZ proteins are able to interact with the GCN4 motif, onlyRISBZ1 is capable of activating the gene expression;GluB-1glutelin endospermseedstorage protein
GCN4 motifRISBZ proteinsO2rice (Oryza sativa)�Washida H, Wu CY, Suzuki A, Yamanouchi U, Akihama T, Harada K,Takaiwa FWu C, Washida H, Onodera Y, Harada K, Takaiwa FOnodera Y, Suzuki A, Wu CY, Washida H, Takaiwa F��Identification of cis-regulatory elements required for endospermexpression of the rice storage protein glutelin gene GluB-1Quantitative nature of the Prolamin-box, ACGT and AACA motifs ina rice glutelin gene promoter: minimal cis-element requirementsfor endosperm-specific gene expressionA rice functional transcriptional activator, RISBZ1, responsiblefor endosperm-specific expression of storage protein genesthrough GCN4 motifYPlant Mol Biol 40:1-12 (1999)Plant J 23: 415-421 (2000)J Biol Chem 27: 14139-14152 (2001)3PubMed: 10394940;PubMed: 10929134;PubMed: 11133985; TGAGTCAGGTCCCATGMSAURS000360 16-Feb-2001 (last modified) seki�Sequence found in NDE element in Soybean (G.m.) SAUR (SmallAuxin-Up RNA) 15A gene promoter; Involved in auxinresponsiveness; See S000270, S000359;SAURNDEAuxinSoybean (Glycine max)Xu N, Hagen G, Guilfoyle T@Multiple auxin response modules in the soybean SAUR 15A promoter Plant Sci 126: 193-201 (1997) GGTCCCAT
GLUTAACAOSS000045 17-May-1998 (last modified) kehib"glutelin common motif"; "AACA motif"; Conserved in all member ofrice (0.s.) glutelin; -74 to -64;AACAglutelinseed endospermrice (Oryza sativa)Takaiwa F, Oono KpInteraction of an immature seed-specific trans-acting factor withthe 5' upstream region of a rice glutelin gene. Mol Gen Genet 224:289-293 (1990)PubMed: 2277646; AACAAACTCTATGLUTEBOX1OSGT2S000046 17-May-1998 (last modified) kehi]"Box 1" of rice (O.s.) glutelin Gt2 gene family promoter regions;nuclear factor binding site;glutelinBox 1Gt2seed endospermrice (Oryza sativa) Kim SY, Wu R@Multiple protein factors bind to a rice glutelin promoterregion.%Nucleic Acids Res 18:6845-6852 (1990)!PubMed: 2263449; GenBank: X52153; ATATCATGAGTCACTTCAGLUTEBOX1OSGT3S000128 17-May-1998 (last modified) kehiW"Box 1" of rice (O.s.) glutelin Gt3 gene family promoter region;See S000128 GLUTEBOX2A;Box 1glutelinGt3seed endospermrice (Oryza sativa);Croissant-Sych Y, Okita TWaIdentification of positive and negative regulatory cis-elementsof the rice glutelin Gt3 promoter. Plant Science 116:27-35 (1996) TATCTAGTGAGTCACTTCAGLUTEBOX2OSGT2S000047 17-May-1998 (last modified) kehiM"Box II" of rice (O.s.) glutelin Gt2 gene family; nuclear factorbinding site;glutelinBox IIGt2seed endospermrice (Oryza sativa) Kim SY, Wu R@Multiple protein factors bind to a rice glutelin promoterregion.%Nucleic Acids Res 18:6845-6852 (1990)!PubMed: 2263449; GenBank: X52153; TCCGTGTACCAGLUTEBOX2OSGT3S000129 17-May-1998 (last modified) kehiW"Box 2" of rice (O.s.) glutelin Gt3 gene family promoter region;See S000128 GLUTEBOX1A;Box 2glutelinGt3seed endospermrice (Oryza sativa);Croissant-Sych Y, Okita TW.aIdentification of positive and negative regulatory cis-elementsof the rice glutelin Gt3 promoter. Plant Science 116:27-35 (1996) CTTTTGTGTACCTTA
GLUTEBP1OSS000048 17-May-1998 (last modified) kehi�"Glutelin BP-1"; Binding site in the promoter region of glutelinGt3 gene family of nuclear factor (PB-1); PB-1 is observed onlyin nuclear extract of developing seeds;glutelinnuclear factorseed endospermBP-1PB-1rice (Oryza sativa)&Zhao, OkitaCroissant-Sych Y, Okita TW.aIdentification of positive and negative regulatory cis-elementsof the rice glutelin Gt3 promoter.S(in press; cited by Croissant-Sych Y, Okita TW, 1996)Plant Science 116:27-35 (1996) AAGCAACACACAAC
GLUTEBP2OSS000049 17-May-1998 (last modified) kehiC"Glutelin BP-2"; Binding with nuclear factors from developingseeds;glutelinnuclear factorseed endospermGt3 gene familyrice (Oryza sativa)&Zhao, OkitaCroissant-Sych Y, Okita TW.aIdentification of positive and negative regulatory cis-elementsof the rice glutelin Gt3 promoter.S(in press; cited by Croissant-Sych Y, Okita TW, 1996)Plant Science 116:27-35 (1996) ATGCTCAATAGATATAAGT GLUTECOREOSS000050 17-May-1998 (last modified) kehi�Core site required for binding of the trans-acting factor in thepromoter region of rice (O.s.) glutelin (type 2 glutelin genefamily);riceglutelintype 2 glutelinseed endospermrice (Oryza sativa)Takaiwa F, Oono KpInteraction of an immature seed-specific trans-acting factor withthe 5' upstream region of a rice glutelin gene. Mol Gen Genet 224:289-293 (1990)PubMed: 2277646; CTTTCGTGTAC GMHDLGMVSPBS000372 31-Jul-2001 (last modified) uchi�Binding site of the soybean homeodomein leucine zipper proteins(GmHdl56, GmHdl57); Found in the phosphate response domain of thesoybean VspB promoter; Located between -536 and -527; VspBencodes vacuolar glycoprotein acid phosphatase that serve asvegetative storage protein;VspBHD-ZIPSphosphate responsehomeotic domainsoybean (Glycine max)(Tang Z, Sadka A, Morishige DT, Mullet JEpHomeodomain leucine zipper proteins bind to the phosphateresponse domain of the soybean VspB tripartite promoter!Plant Physiol 125: 797-809 (2001)PubMed: 11161037;
CATTAATTAG
GRAZMRAB17S000150 29-Sep-1999 (last modified) kehi�"GRA"; GC-rich rab activator; Found in the promoter of ABAresponsive rab17 gene from maize (Z.m.); Important fortranscription in leaves but not in embryos; See S000200, S000401and S000402;GRAABArab17rableafembryoseedmaize (Zea mays)+Busk PK, Jensen AB, Pages MBusk PK, Pages M�Regulatory elements in vivo in the promoter of the abscisic acidresponsive gene rab17 from maize.Regulation of abscisic acid-induced transcription;Plant J 11:1258-1295 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 9225468;PubMed: 9617810;Review CACTGGCCGCCC
GRAZMRAB28S000220 11-May-2006 (last modified) kehi�"GRA"; "GC-rich rab activator"; Found in the promoter of ABAresponsive rab28 gene from maize (Z.m.); Similar (seven of 12bases) to the GRA element from the maize rab17 promoter (S000150;GRAZMRAB17); Found at -138 to -130;GRAABArab28rabseedmaize (Zea mays) Busk PK, Pages MBusk PK, Pages M�Protein binding to the abscisic acid-responsive element isindependent of VIVIPAROUS1 in vivoRegulation of abscisic acid-induced transcription=Plant Cell 9:2261-2270 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 11407411PubMed: 9617810;Review CATGCCGCCGREGIONNTPRB1BS000364 16-Feb-2001 (last modified) seki�$"G region" found in tobacco (N.t.) PRB-1b gene promoter; Locatedat -201 to -178; Binding site of nuclear protein; Required forethylene induction; Contains an 11bp sequence, TAAGAGCCGCC, whichis highly conserved in the promoter of ethylene-induced PR genes;Contains a G box motif; See S000365;PR-1PRB-1bethyleneGG boxTobacco (Nicotiana tabacum)"Meller Y, Sessa G, Eyal Y, Fluhr RNDNA-protein interactions on a cis-DNA element essential forethylene regulation!Plant Mol Biol 23: 453-463 (1993)PubMed: 8219081; TGGCGGCTCTTATCTCACGTGATGGT1CORES000125 15-Oct-1999 (last modified) kehi�Critical for GT-1 binding to box II of rbcS; See S000051GT1MOTIF1; For a compilation of related GT elements and factors,see Villain et al. (1996);rbcSbox IIGT-1rbcS-3leafshootpea (Pisum sativum);�Green PJ, Yong M-H, Cuozzo M, Kano-Murakami Y, Silverstein P,Chua N-HGilmartin PM, Sarokin L, Memelink J, Chua N-HTerzaghi WB, Cashmore ARVillain P, Mache R, Zhou DXZhou DX��Binding site requirements for pea nuclear protein factor GT-1correlate with sequences required for light-dependenttranscriptional activation of the rbcS-3A gene.Molecular light switches for plant genes.Light-regulated transcriptionThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�EMBO J 7:4035-4044 (1988)Plant Cell 2:369-378 (1990)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)0PubMed: 3243271;PubMed: 2152164;PubMed: 8955086;ReviewGGTTAA
GT1GMSCAM4S000453%29-November-2004 (last modified) kehi�"GT-1 motif" found in the promoter of soybean (Glycine max) CaMisoform, SCaM-4; Plays a role in pathogen- and salt-inducedSCaM-4 gene expression; See also S000198 (GT-1 consensus);GT-1 boxGlycine max (soybean)�Park HC, Kim ML, Kang YH, Jeon JM, Yoo JH, Kim MC, Park CY, JeongJC, Moon BC, Lee JH, Yoon HW, Lee SH, Chung WS, Lim CO, Lee SY,Hong JC, Cho MJ.�Pathogen- and NaCl-induced expression of the SCaM-4 promoter ismediated in part by a GT-1 box that interacts with a GT-1-liketranscription factor.%Plant Physiol. 135: 2150-2161 (2004).PubMed: 15310827 GAAAAA GT2OSPHYAS000207 11-May-2006 (last modified) kehi�7GT-2 (a rice nuclear protein) binding site in a rice (O.s.) phyApromoter; phyA gene are transcriptionaly repressed in response tolight; One of GT elements; For a compilation of related GTelements and factors, see Villain et al. (1996); The HMG-1/Yprotein PF1 stimulates binding of the GT-2 to PHYA genepromoter;GT-2phyAGTlightHMG-1/Y proteinPF1leafshoot(rice (Oryza sativa); oat (Avena sativa);ZDehesh K, Bruce WB, Quail PHVillain P, Mache R, Zhou DXMartinez-Garcia JF, Quail PHZhou DX�PA trans-acting factor that binds to a GT-motif in a phytochromegene promoterThe mechanism of GT element-mediated cell type-specifictranscriptional controlThe HMG-I/Y protein PF1 stimulates binding of the transcriptionalactivator GT-2 to the PHYA gene promoterRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�Science 250:1397-1399 (1990)J Biol Chem 271:32593-32598 (1996)Plant J 18:173-183 (1999)Trends in Plant Science 4:210-214 (1999)BPubMed: 2255908;PubMed: 8955086;PubMed: 10363369;PubMed: 10366876Review GCGGTAATT GTGANTG10S000378 23-Aug-2001 (last modified) uchi�"GTGA motif" found in the promoter of the tobacco (N.t.) latepollen gene g10 which shows homology to pectate lyase and is theputative homologue of the tomato gene lat56; Located between -96and -93; See S000280;g10pollen
pectate lyasetabacco(Nicotiana tabacum)ORogers HJ, Bate N, Combe J, Sullivan J, Sweetman J, Swan C,Lonsdale DM, Twell DeFunctional analysis of cis-regulatory elements within thepromoter of the tobacco late pollen gene g10!Plant Mol Biol 45: 577-585 (2001)PubMed: 11414616; GTGA HDMOTIFPCPR2S000233 17-May-1998 (last modified) kehi{HD (homeodomain) protein target site in parsley (P.c.)pathogenesis-related protein 2 (PR2); A potential in vivo targetsite;HD homeodomainPR2 parsley (Petroselinum crispum):Korfhage U, Trezzini GF, Meier I, Hahlbrock K, Somssich IEbPlant homeodomain protein involved in transcriptional regulationof a pathogen defense-related genePlant Cell 6:695-708 (1994)PubMed: 7913642; CTAATTGTTTA HEXAMERATH4S000146 10-May-1998 (last modified) kehi@hexamer motif of Arabidopsis thaliana (A.t.) histone H4promoter;hexamerhistoneH4meristemArabidopsis thaliana;2Chaubet N, Flenet M, Clement B, Brignon P, Gigot CZIdentification of cis-elements regulating the expression of anArabidopsis histone H4 gene.Plant J 10:425-435 (1996)PubMed: 8811858; CCGTCGHEXATS000334 7-Sep-2000 (last modified) seki�"Hex motif"; Binding site of Arabidopsis (A.t.) bZIP protein TGA1and G box binding factor GBF1; TGA1 and members of the GBF familydiffer in their DNA binding properties; G-Box-like element;TGA1GBFG-boxbZIP Hex motifArabidopsis thaliana$Schindler U, Beckmann H, Cashmore AR�TGA1 and G-box binding factors: two distinct classes ofArabidopsis leucine zipper proteins compete for the G-box-likeelement TGACGTGG Plant Cell 4: 1309-1319 (1992) PubMed: 1446171; GenBank: X68053 TGACGTGGHEXMOTIFTAH3H4S000053 11-May-2006 (last modified) kehi��"hexamer motif" found in promoter of wheat (T.a.) histone genesH3 and H4; CaMV35S; NOS; Binding with HBP-1A and HBP-1B; Bindingsite of wheat (T.a.) nuclear protein HBP-1 (histone DNA bindingprotein-1); HBP-1 has a leucine zipper motif; "hexamer motif" intype 1 element may play important roles in regulation ofreplication- dependent but not of replication-independentexpression of the wheat histone H3 gene; See S000076, S000267;Rice OBF1-homodimer-binding site (Shimizu et al.);hexamerHBP-1AHBP-1B
histone H3CaMV35SNOSHBP-1Leucine zipper motifmeristemOBF1bZIPlip19LIP195wheat (Triticum aestivum); CaMV; Oryza sativa (rice);�0Mikami K, Tabata T, Kawata T, Nakayama T, Iwabuchi MMikami K, Nakayama T, Kawata T, Tabata T, Iwabuchi MTabata T, Takase H, Takayama S, Mikami K, Nakatsuka A, Kawata T,Nakayama T, Iwabuchi MTerada R, Nakayama T, Iwabuchi M, Shimamoto KShimizu H, Sato K, Berberich T, Miyazaki A, Ozaki R, Imai R,Kusano T.��Nuclear protein(s) binding to the conserved DNA hexamericsequence postulated to regulate transcription of wheat histonegenes.Specific interaction of nuclear protein HBP-1 with the conservedhexameric sequence ACGTCA in the regulatory region of wheathistone genes.A protein that binds to a cis-acting element of wheat histonegenes has a leucine zipper motifA type I element composed of the hexamer (ACGTCA) and octamer(CGCGGATC) motifs plays a role(s) in meristematic expression of awheat histone H3 gene in transgenic rice plantsLIP19, a Basic Region Leucine Zipper Protein, is a Fos-likeMolecular Switch in the Cold Signaling of Rice Plants.�FEBS Lett 223: 273-278 (1987)Plant Cell Physiol 30:107-119 (1989).Science 245: 965-967 (1989)Plant Mol Biol 27: 17-26 (1995)Plant Cell Physiol. 46 :1623-34. (2005)NPubMed: 2822486;PubMed: 2772648;PubMed: 2772648PubMed: 7865787PubMed: 16051676 ACGTCA
HSELIKENTGLN2S000057 17-May-1998 (last modified) kehi]"HSE-like sequence" in 5' upstream region of beta-1,3-glucanasegene (GLN2) of tobacco (N.t.);tobaccobeta-1,3-glucanase group 2
PR-proteinhsepromoter
heat shocktobacco (Nicotiana tabacum)Ohme-Takagi M, Shinshi H>Structure and expression of a tobacco beta-1,3-glucanase gene. Plant Mol Biol 15:941-946 (1990)!PubMed: 2103484; GenBank: X53600;
AGGAATTCCT
HSRENTHSR203JS000466"24-April-2005 (last modified) kehi�"HSRE(HSR203 responsive element)" in tobacco (N.t.) responsiblefor the marked induction of the HSR203J gene during the HR(hypersensitive response); HSR203J is specifically activatedduring the early steps of incompatible plant/pathogeninteractions;HRNicotiana tabacum (tobacco)HPontier D, Balague C, Bezombes-Marion I, Tronchet M, Deslandes L,Roby D.�Identification of a novel pathogen-responsive element in thepromoter of the tobacco gene HSR203J, a molecular marker of thehypersensitive response. Plant J. 26: 495-507 (2001).PubMed: 11439136 CAAAATTTTGTAHY5ATS000345 16-Feb-2001 (last modified) seki��"G box"; Binding site of Arabidopsis bZIP protein HY5; HY5 isconstitutively nuclear localized and is involved in lightregulation of transcriptional activity of the promoterscontaining the G-box; See S000041, S000042, S000229; HY5abundance peaks in early seedling development, consistent withits role in promoting photomorphogenesis; HY5 stability andactivity is regulated by phosphorylation in its COP1 bindingdomain; HY5 regulates stimulus-induced development of root andhypocotyl; bZIPHY5LREG boxCOP1bZIPstimulus-responseroot hypocotylleafshootArabidopsis thaliana�Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei NHardtke CS, Gohda K, Osterlund MT, Oyama T, Okada K, Deng XWOyama T, Shimura Y, Okada K�NArabidopsis bZIP protein HY5 directly interacts withlight-responsive promoters in mediating light control of geneexpressionHY5 stability and activity in arabidopsis is regulated byphosphorylation in its COP1 binding domainThe Arabidopsis HY5 gene encodes a bZIP protein that regulatesstimulus-induced development of root and hypocotylUPlant Cell 10:673-683 (1998)EMBO J 19: 4997-5006 (2000)Genes Dev (1997) 11: 2983-29951PubMed: 9596629;PubMed: 10990463;PubMed: 9367981; TGACACGTGGCAIBOXS000124 7-Sep-2000 (last modified) seki�&"I box"; "I-box"; Conserved sequence upstream of light-regulatedgenes; Sequence found in the promoter region of rbcS of tomatoand Arabidopsis; I box (Giuliano et al. 1988); Binding site ofLeMYB1, that is a member of a novel class of myb-like proteins;LeMYBI act as a transcriptional activator; I boxI-boxrbcSlight regulationlightLeMYB1, Myb-likeproteinleafshoot7tomato (Lycopersicon esculentum); Arabidopsis thaliana;tGiuliano G, Pichersky E, Malik VS, Timko MP, Scolnik PA, CashmoreARDonald RGK, Cashmore ARRose A, Meier I, Wienand U�#An evolutionarily conserved protein binding sequence upstream ofa plant light-regulated gene.Mutation of either G box or l box sequences profoundly affectsexpression from the Arabidopsis rbcS-1A promoter.The tamato I-box binding factor LeMYBI is a member of a novelclass of Myb-like proteins]Proc Natl Acad Sci USA 85:7089-7093 (1988)EMBO J 9:1717-1726 (1990)Plant J 20: 641-652 (1999)1PubMed: 2902624;PubMed: 2347304;PubMed: 10652136; GATAAGIBOXCORES000199 2-May-1998 (last modified) kehi�"I box"; "I-box"; Conserved sequence upstream of light-regulatedgenes; Conserved sequence upstream of light-regulated genes ofboth monocots and dicots; See IBOX (S000124);I boxI-boxrbcSlight regulationlightleafshoot Terzaghi WB, Cashmore AR Light-regulated transcription7Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995) ReviewGATAAIBOXLSCMCUCUMISINS000423 29-Sep-2003 (last modified) kehi�"I-box-like sequence" found in the region (from -254 to -215) ofcucumisin (a subtilisin-like serine protease) in the fruit ofmelon (Cucumis melo L.); I-box-like sequence functions as anegative regulatory element; See S000199 (I-box, GATAA), S000124(I-box, GATAAG); cucumisinfruitCucumis melo L. (melon))Yamagata H, Yonesu K, Hirata A, Aizono Y.tTGTCACA motif is a novel cis-regulatory enhancer element involvedin fruit-specific expression of the cucumisin gene.#J Biol Chem. 277:11582-11590 (2002)PubMed: 11782472;
AGATATGATAAAA
IDE1HVIDS2S000463"24-April-2005 (last modified) kehi�IDE1 (iron-deficiency-responsive element 1) found at -153/-136 ofbarley IDS2 (iron deficiency specific clone 2) gene promoter; Seealso S000464;ironrootHordeum vulgare (barley)�Kobayashi T, Nakayama Y, Itai RN, Nakanishi H, Yoshihara T, MoriS, Nishizawa NK.Kobayashi T, Suzuki M, Inoue H, Itai RN, Takahashi M, NakanishiH, Mori S, Nishizawa NK.�OIdentification of novel cis-acting elements, IDE1 and IDE2, ofthe barley IDS2 gene promoter conferringiron-deficiency-inducible, root-specific expression inheterogeneous tobacco plants.Expression of iron-acquisition-related genes in iron-deficientrice is co-ordinately induced by partially conservediron-deficiency-responsive elements.<Plant J. 36: 780-793 (2003).J Exp Bot. 56: 1305-1316. (2005) PubMed: 14675444PubMed: 15781441 ATCAAGCATGCTTCTTGC
IDE2HVIDS2S000464"24-April-2005 (last modified) kehi�IDE2 (iron-deficiency-responsive element 2) found at -262/-236 ofbarley IDS2 (iron deficiency specific clone 2) gene promoter; Seealso S000463;ironrootHordeum vulgare (barley)�Kobayashi T, Nakayama Y, Itai RN, Nakanishi H, Yoshihara T, MoriS, Nishizawa NK.Kobayashi T, Suzuki M, Inoue H, Itai RN, Takahashi M, NakanishiH, Mori S, Nishizawa NK.�OIdentification of novel cis-acting elements, IDE1 and IDE2, ofthe barley IDS2 gene promoter conferringiron-deficiency-inducible, root-specific expression inheterogeneous tobacco plants.Expression of iron-acquisition-related genes in iron-deficientrice is co-ordinately induced by partially conservediron-deficiency-responsive elements.<Plant J. 36: 780-793 (2003).J Exp Bot. 56: 1305-1316. (2005) PubMed: 14675444PubMed: 15781441 TTGAACGGCAAGTTTCACGCTGTCACT INTRONLOWERS000086 17-May-1998 (last modified) kehid"3' intron-exon splice junctions"; Plant intron lower sequence;Consensus sequence for plant introns;intronsplice junctionmaize (Zea mays) Brown JWSSA catalog of splice junction and putative branch point sequencesfrom plant introns.%Nucleic Acids Res 14:9549-9559 (1986)PubMed: 3808952;ReviewTGCAGGIRO2OSS000505&15-September-2006 (last modified) kehiqOsIRO2-binding core sequence; "G-box plus G"; Transcriptionfactor OsIRO2 is induced exclusively by Fe deficiency;rootshootFeironOryza sativa (rice)^Ogo Y, Itai RN, Nakanishi H, Inoue H, Kobayashi T, Suzuki M,Takahashi M, Mori S, Nishizawa NK.oIsolation and characterization of IRO2, a novel iron-regulatedbHLH transcription factor in graminaceous plants. J Exp Bot. 57:2867-2878. (2006)PubMed: 16887895 CACGTGG JASE1ATOPR1S000388 20-Feb-2002 (last modified) uchi�"JASE1"found in promoter of Arabidopsis thaliana12-oxo-phytodienoic acid-10,11-reductase (OPR1) gene; Locatedbetween -179 and -170; Involved in up-regulation by bothsenescence and JA;OPR1
senescence
Jasmonic acidJASE1JASE2leafArabidopsis thaliana He Y, Gan SuIdentical promoter elements are involved in regulation of theOPR1 gene by senescence and jasmonic acid in Arabidopsis"Plant Mol Biol 47: 595-605 (2001)PubMed: 11725945;
CGTCAATGAA JASE2ATOPR1S000389 20-Feb-2002 (last modified) uchi�"JASE2"found in promoter of Arabidopsis thaliana12-oxo-phytodienoic acid-10,11-reductase (OPR1) gene; Locatedbetween -112 and -100; Involved in up-regulation by bothsenescence and JA; JASE2 contains a mixed A/C box-like motif;OPR1
senescence
Jasmonic acidJASE1JASE2leafArabidopsis thaliana He Y, Gan SuIdentical promoter elements are involved in regulation of theOPR1 gene by senescence and jasmonic acid in Arabidopsis"Plant Mol Biol 47: 595-605 (2001)PubMed: 11725945;
CATACGTCGTCAA JERECRSTRS000384 21-Nov-2002 (last modified) uchi�e"JERE" (jasmonate- and elicitor-responsive element) found in theperiwinkle(C.R.) strictosidine synthase(Str) gene promoter;Located between -100 and -58; ORCA1, ORCA2 and ORCA3 bindspecifically to the JERE of the Str promoter; Elicitor and MeJArapidly induce Orca2, but not Orca1 mRNA levels; ORCA3 mRNAaccumulation was rapidly induced by the metyljasmonate; JEREJA jasmonateelicitorstrictosidine synthase(Str)ORCA1ORCA2ORCA3
AP2 domain periwinkle(Catharanthus roseus)}Menke FL, Champion A, Kijne JW, Memelink Jvan der Fits L, Memelink JRushton PJ, Reinstadler A, Lipka V, Lippok B, Somssich IE��A novel jasmonate- and elicitor-responsive element in theperiwinkle secondary metabolite biosynthetic gene Str interactswith a jasmonate- and elicitor-inducible AP2-domain transcriptionfactor, ORCA2The jasmonate-inducible AP2/ERF-domain transcription factor ORCA3activates gene expression via interaction with ajasmonate-responsive promoter elementSynthetic plant promoters containing defined regulatory elementsprovide novel insights into pathogen- and wound-inducedsignalingQEMBO J 18: 4455-4463 (1999)Plant J 25: 43-53 (2001)Plant Cell. 14: 749-762 (2002)3PubMed: 10449411;PubMed: 11169181;PubMed: 11971132; CTCTTAGACCGCCTTCTTTGAAAGL1DCPAL1S000504&15-September-2006 (last modified) kehi�"L1" element, found in PAL1 promoter in carrot (Daucus carota),is a protoplastization (dilution) responsive element; L1 containsBox L-like sequence (ACCTACCC); see also S000492 (BOXL CORE of DCPAL1);L1Daucus carota (carrot)"Takeda J, Ito Y, Maeda K, Ozeki Y.�Assignment of UVB-responsive cis-element andprotoplastization-(dilution-) and elicitor-responsive ones in thepromoter region of a carrot phenylalanine ammonia-lyase gene(gDcPAL1).'Photochem Photobiol. 76:232-238 (2002).PubMed: 12194222 ATTCACCTACCCL4DCPAL1S000503&15-September-2006 (last modified) kehi�"L4" element, found in PAL1 promoter in carrot (Daucus carota),is a UV-B responsive element; L4 contains Box L-like sequence(TCCAACCA); see also S000492 (BoxL core of DC PAL);L4PALDaucus carota (carrot)"Takeda J, Ito Y, Maeda K, Ozeki Y.�Assignment of UVB-responsive cis-element andprotoplastization-(dilution-) and elicitor-responsive ones in thepromoter region of a carrot phenylalanine ammonia-lyase gene(gDcPAL1).'Photochem Photobiol. 76:232-238 (2002).PubMed: 12194222 AATCTCCAACCA
LBOXLERBCSS000126 17-May-1998 (last modified) kehi^"L box"; Conserved sequence found in rbcS upstream sequences ofboth tomato (L.e.) and tobacco;L boxrbcSleafshoot>tomato (Lycopersicon esculentum); tobacco (Nicotiana tabacum);ZGiuliano G, Pichersky E, Malik VS, Timko MP, Scolnik PA, CashmoreARDonald RGK, Cashmore AR�An evolutionarily conserved protein binding sequence upstream ofa plant light-regulated gene.Mutation of either G box or l box sequences profoundly affectsexpression from the Arabidopsis rbcS-1A promoter.CProc Natl Acad Sci USA 85:7089-7093 (1988)EMBO J 9:1717-1726 (1990) PubMed: 2902624;PubMed: 2347304; AAATTAACCAA LEAFYATAGS000432 27-Jan-2004 (last modified) kehiqTarget sequence of LEAFY in the intron of AGAMOUS gene inArabidopsis; See Lohmann et al. Cell 105:793-803 (2003);LEAFYAGAMOUS*Oryza sativa (rice); Arabidopsis thaliana;5Kamiya N, Nagasaki H, Morikami A, Sato Y, Matsuoka M.�Isolation and characterization of a rice WUSCHEL-tyope homoeboxgene that is specifically expressed in the central cells of aquiescent center in the root apical meristem.Plant J. 35: 429-441 (2003)PubMed: 12904206; CCAATGT
LECPLEACS2S000465"24-April-2005 (last modified) kehiaCore element in LeCp (tomato Cys protease) binding cis-element(from -715 to -675) in LeAcs2 gene;cysteine proteaseethylenexylanaseACS Lycopersicon esculentum (tomato) Matarasso N, Schuster S, Avni A.�A novel plant cysteine protease has a dual function as aregulator of 1-aminocyclopropane-1-carboxylic Acid synthase geneexpression.!Plant Cell. 17: 1205-1216. (2005)PubMed: 15749766 TAAAATATLREBOX2PSRBCS3S000061 11-May-2006 (last modified) kehi�R"LRE (light-responsive element) Box II" of pea (P.s.) rbcS-3Agene; GT-1 binding; "GT-motif"; "GT1 motif"; Some similarity toSV40 enhancer core sequence; For a compilation of related GTelements and factors, see Villain et al. (1996); "BoxII" Bindingsite of transcriptional factor GTI; Located at -152 to -138;Confers light responsiveness; lightrbcSGT-1GT1enhancercoreBox IILRE
GT elementleafshoot*pea (Pisum sativum); Arabidopsis thaliana;�Green PJ, Kay SA, Chua N-HKuhlemeier C, Green PJ, Chua N-HVillain P, Mache R, Zhou DXChattopadhyay S, Puente P, Deng X-W, Wei NZhou DXLam E, Chua NH�'Sequence-specific interactions of a pea nuclear factor withlight-responsive elements upstream of the rbcS-3A gene.Regulation of gene expression in higher plantsThe mechanism of GT element-mediated cell type-specifictranscriptional controlCombinatorial interaction of ligth-responsive elements plays acritical role in determining the response characteristics ofligth-regulated promoters in ArabidopsisRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorsGT-1 binding site confers light responsive expression intransgenic tobacco�EMBO J 6:2543-2549 (1987)Ann Rev Plant Physiol 38:221-257 (1987)J Biol Chem 271:32593-32598 (1996)Plant J 15:69-77 (1998)Trends in Plant Science 4:210-214 (1999)Science 248: 471-474 (1990)@PubMed: 3678200;PubMed: 8955086;PubMed: 9744096;PubMed: 2330508 ReviewReviewTGTGTGGTTAATATGLREBOX3PSRBCS3S000062 17-May-1998 (last modified) kehi�"LRE (light-responsive element) Box III" of pea (P.s.) rbcS-3Agene; GT-1 binding; For a compilation of related GT elements andfactors, see Villain et al. (1996);lightrbcSGT-1leafshootpea (Pisum sativum)5Green PJ, Kay SA, Chua N-HVillain P, Mache R, Zhou DX�Sequence-specific interactions of a pea nuclear factor withlight-responsive elements upstream of the rbcS-3A gene.The mechanism of GT element-mediated cell type-specifictranscriptional control;EMBO J 6:2543-2549 (1987)J Biol Chem 271:32593-32598 (1996) PubMed: 3678200;PubMed: 8955086; ACTATTTTCACTATCLREBOXIIPCCHS1S000303 10-Feb-2000 (last modified) seki�"BoxII"; Light responsive element (LRE) found in the parsley(P.c.) CHS-1 (chalcone synthase-1) gene promoter; Required forlight responsiveness; nuclear protein binding site; Highlyconserved in various light inducible gene promoters; SeeS000302;chalcone synthaseCHSlightBox IILREleafshoot parsley (Petroselinum crispum)@Schulze-Lefert P, Dangl JL, Becker-Andre M, Hahlbrock K, SchulzWvInducible in vivo DNA footprints define sequences necessary forUV light activation of the parsley chalcon sythase geneEMBO J 8: 651-656 (1989)PubMed: 2566481
TCCACGTGGC
LREBOXIPCCHS1S000302 16-Feb-2001 (last modified) seki�N"BoxI"; Light responsive element (LRE) found in the parsley(P.c.) CHS-1 (chalcone synthase-1) gene promoter; Required forlight responsiveness; nuclear protein binding site; See S000303;"MRECHS" (MRE=Myb Recognition Element)Recognition site of MYB305and a novel factor PcMYB1 (Myb1 from P. crispum); PcMYB1 containsonly one MYB repeat;
chalcone synthaseCHSlightBox ILREPcMYB1MRECHSMYBleafshoot parsley (Petroselinum crispum)rSchulze-Lefert P, Dangl JL, Becker-Andre M, Hahlbrock K, SchulzWFeldbrugge M, Sprenger M, Hahlbrock K, Weisshaar B� Inducible in vivo DNA footprints define sequences necessary forUV light activation of the parsley chalcone synthase genePcMYB1, a novel plant protein containing a DNA-binding domainwith one MYB repeat, interacts in vivo with a light-regulatorypromoter unit4EMBO J 8: 651-656 (1989)Plant J (1997) 11: 1079-1093 PubMed: 2566481PubMed: 9193077;
AACCTAACCT LRENPCABES000231 17-May-1998 (last modified) kehi^"LRE"; A positive light regulatory element in tobacco (N.p.) CAB(cab-E) gene; Located at -241;CABcabcab-ECABElightleafshoot#tobacco (Nicotiana plumbaginifolia)=Castresana C, Garcia-Luque I, Alonso E, Malik VS, Cashmore AR|Both positive and negative regulatory elements mediate expressionof a photoregulated CAB gene from Nicotiana plumbaginifoliaEMBO J 7:1929-1936 (1988)!PubMed: 2901343; GenBank: X12512; ACGTGGCALS5ATPR1S000323$04-January-2007 (last modified) kehi��"LS5"; A negative regulatory element found in the Arabidopsis(A.t.) PR-1 gene promoter; Binding site of TGA2; NPR1 increasedthe binding of TGA2 to the element; NPR1 is essential inactivating systemic, inducible plant defense response; SeeS000322; TGA6 expressed in roots in young seedlings; TGA2.1 is adirect transcriptional activator; TGA2.2 stabilizes TGA2.1binding; NOTE: The motif sequence previously shown was that ofLS7. The correction was made. TGA2LS5LS7SANPR1TGA6auxinsalicylic acidroot2Arabidopsis thaliana; tobacco (Nicotiana tabacum);�Despres C, DeLong C, Glaze S, Liu E, Fobert PRXiang C, Miao Z, Lam ENiggeweg R, Thurow C, Weigel R, Pfitzner U, Gatz CThurow C, Schiermeyer A, Krawczyk S, Butterbrodt T, Nickolov K,Gatz C.�The Arabidopsis NPR1/NIM1 protein enhances the DNA bindingactivity of a subgroup of the TGA family of bZIP transcriptionfactorsDNA-binding properties, genomic organization and expressionpattern of TGA6,a new member of the TGA family of bZIPtranscription factors in Arabidopsis thalianaTobacco TGA factors differ with respect to interaction with NPR1,activation potential and DNA-binding properties.Tobacco bZIP transcription factor TGA2.2 and related factorTGA2.1 have distinct roles in plant defense responses and plantdevelopment.yPlant Cell 12: 279-290 (2000)Plant Mol Biol 34: 403-415 (1997)Plant Mol Biol 42: 775-788 (2000)Plant J. 44:100-113 (2005)APubMed: 10662863;PubMed: 9225852PubMed: 10809449;PubMed: 16167899
TCTACGTCACLS7ATPR1S000322$04-January-2007 (last modified) kehi��"LS7"; A positive salicylic acid-inducible element found in theArabidopsis (A.t.) PR-1 gene promoter; Binding site of TGA1; NPR1increased the binding of TGA2 to the element; NPR1 is essentialin activating systemic, inducible plant defense responses; SeeS000323; TGA6 expressed in roots in young seedlings; TGA2.1 is adirect transcriptional activator; TGA2.2 stabilizes TGA2.1binding; NOTE: The motif sequence previously shown was that ofLS5. The correction was made. We are very sorry. TGA2LS5LS7SANPR1TGA6auxinsalicylic acidroot2Arabidopsis thaliana; tobacco (Nicotiana tabacum);�Despres C, DeLong C, Glaze S, Liu E, Fobert PRXiang C, Miao Z, Lam ENiggeweg R, Thurow C, Weigel R, Pfitzner U, Gatz CJohnson C, Boden E, Arias J.Thurow C, Schiermeyer A, Krawczyk S, Butterbrodt T, Nickolov K,Gatz C.��The Arabidopsis NPR1/NIM1 protein enhances the DNA bindingactivity of a subgroup of the TGA family of bZIP transcriptionfactorsDNA-binding properties, genomic organization and expressionpattern of TGA6,a new member of the TGA family of bZIPtranscription factors in Arabidopsis thalianaTobacco TGA factors differ with respect to interaction with NPR1,activation potential and DNA-binding propertiesSalicylic acid and NPR1 induce the recruitment oftrans-activating TGA factors to a defense gene promoter inArabidopsis.Tobacco bZIP transcription factor TGA2.2 and related factorTGA2.1 have distinct roles in plant defense responses and plantdevelopment.�Plant Cell 12: 279-290 (2000)Plant Mol Biol 34: 403-415 (1997)Plant Mol Biol 42: 775-788 (2000)Plant Cell. 15:1846-1858 (2003)Plant J. 44:100-113 (2005)QPubMed: 10662863;PubMed: 9225852PubMed: 10809449;PubMed: 12897257PubMed: 16167899
ACGTCATAGA LTRE1HVBLT49S000250 11-Oct-1999 (last modified) kehi�"LTRE-1" (low-temperature-responsive element) in barley (H.v.)blt4.9 gene promoter; A new LTRE; A previously known LTRE isCCGAC;low temperatureLTREbarley (Hordeum vulgare)%Dunn MA, White AJ, Vural S, Hughes MApIdentification of promoter elements in alow-temperature-responsive gene (blt4.9) from barley (Hordeumvulgare L.)!Plant Mol Biol 38:551-564 (1998)PubMed: 9747801; CCGAAA LTREATLTI78S000157 17-May-1998 (last modified) kehi��Putative low temperature responsive element (LTRE); Found inArabidopsis thaliana (A.t.) low-temperature-induced (lti) genes,lti78 and lti65; Repeated four times in lti78 which is alsoknown as cor78 and rd29A (see S000152)(Baker et al., Plant MolBiol 24:701(1994)); Found also in barley low temperatureresponsive genes, blt4.2, blt4.6, blt4.9 (lipid transfer genes);cold inducible; See LTRECORE (S000153); Also present in rab18,kin1, and kin2 (Nordin et al., 1993);"low temperature responsive elementLTREcoldleafshoot/Arabidopsis thaliana; barley (Hordeum vulgare);ANordin K, Vahala T, Palva ETWhite AJ, Dunn MA, Brown K, Hughes MA�Differential expression of two related, low-temperature-inducedgenes in Arabidopsis thaliana (L.) Heynh.Comparative analysis of genomic sequence and expression of alipid transfer protein gene family in winter barley.=Plant Mol Biol 21:641-653 (1993)J Exp Bot 45:1885-1892 (1994))PubMed: 8448363; GenBank: X67670, X67671;!Consensus sequence among 2 genes;ACCGACALTRECOREATCOR15S000153$8-February-2006 (last modified) kehi��Core of low temperature responsive element (LTRE) of cor15a genein Arabidopsis (A.t.); A portion of repeat-C (C-repeat),TGGCCGAC, which is repeated twice in cor15a promoter (Baker etal., 1994); ABA responsiveness; Involved in cold induction ofBN115 gene from winter Brassica napus; LTRE; See S000157,S000152; Light signaling mediated by phytochrome is necessary forcold- or drought- induced gene expression through the C/DRE inArabidopsis; See S000152;
low temperaturecoldLTREdroughtABAcor15aBN115leafshoot phytochrome$Arabidopsis thaliana; Brassica napusfBaker SS, Wilhelm KS, Thomashow MFJiang C, Iu B, Singh JBusk PK, Pages MKim HJ, Kim YK, Park JY, Kim J��The 5'-region of Arabidopsis thaliana cor15a has cis-actingelements that confer cold-, drought- and ABA-regulated geneexpression.Requirement of a CCGAC cis-acting element for cold induction ofthe BN115 gene from winter Brassica napusRegulation of abscisic acid-induced transcriptionLight signalling mediated by phytochrome plays an important rolein cold-induced gene expression through the C-repeat/dehydrationresponsive element (C/DRE) in Arabidopsis thalianazPlant Mol Biol 24:701-713 (1994)Plant Mol Biol 30:679-684 (1996)Plant Mol Biol 37:425-435 (1998)Plant J 29: 693-704 (2002)RPubMed: 8193295; GenBank: U01377;PubMed: 8605318;PubMed: 9617810;PubMed: 12148528;ReviewCCGAC
MNF1ZMPPC1S000251 11-Oct-1999 (last modified) kehiu"MNF1" binding site in maize (Z.m.) Ppc1 (phosphoenolpyruvatecarboxylase) gene promoter; Involved in light induction;MNF1Ppc1lightleafshootmaize (Zea mays) Morishima A�Identification of preferred binding sites of a light-inducibleDNA-binding factor (MNF1) within 5'-upstream sequence of C4-typephosphoenolpyruvate carboxylase gene in maize!Plant Mol Biol 38:633-646 (1998)PubMed: 9747808; GTGCCCTTMREATCHSS000356#02-August-2006 (last modified) kehi�"MREAtCHS (MRE = Myb Recognition Element)" found in the LRU(light-responsive unit) in Arabidopsis (A.t.) chalcone synthase(CHS) gene promoter; Required for UV-B and UV-A/blue lightresponsiveness; See S000355; CHSACEMYBlightUV-AUV-BleafshootMREArabidopsis thaliana�Hartmann U, Valentine WJ, Christie JM, Hays J, Jenkins GI,Weisshaar BHartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B.�iIdentification of UV/blue light-response elements in theArabidopsis thaliana chalcone synthase promoter using ahomologous protoplast transient expression systemDifferential combinatorial interactions of cis-acting elementsrecognized by R2R3-MYB, BZIP, and BHLH factors controllight-responsive and tissue-specific activation ofphenylpropanoid biosynthesis genes.DPlant Mol Biol (1998) 36: 741-754Plant Mol Biol. 57: 155-171 (2005). PubMed: 9526507;PubMed: 15821875 TCTAACCTACCA MRNA3ENDTAH3S000069 17-May-1998 (last modified) kehi�Cis element in 3' end region of wheat (T.a.) histone H3 mRNA; 3'end formation; Also found in histone genes of other plants,yeast, etc;
histone H3mRNA3' end formationmeristem!wheat (Triticum aestivum); yeast;Ohtsubo N, Iwabuchi M�The conserved 3'-flanking sequence, AATGGAAATG, of the wheathistone H3 gene is necessary for the accurate 3'-end formation ofmRNA.%Nucleic Acids Res 22:1052-1058 (1994)PubMed: 8152910;
AATGGAAATGMSACRCYMS000236 17-May-1998 (last modified) kehi�"MSA (M-specific activator)" motif in Catharanthus roseus (C.r.)B-type cyclin (CYM) promoter; Essential for M phase-specificexpression; Found at -66 to -58;M phasecyclinCYMmeristemCatharanthus roseusRIto M, Iwase M, Kodama H, Lavisse P, Komamine A, Nishihama R,Machida Y, Watanabe AlA novel cis-acting element in promoters of plant B-type cyclingenes activates M phase-specific transcription Plant Cell 10:331-341 (1998)PubMed: 9501108; AGACCGTTGMYB1LEPRS000443 28-Jan-2004 (last modified) kehi�Tomato Pti4(ERF) regulates defence-related gene expression viaGCC box and non-GCC box cis elements (Myb1(GTTAGTT), G box(CACGTG));Pti4ERFPRMYB7Arabidopsis thaliana; Lycopersicon esculentum (tomato);EChakravarthy S, Tuori RP, DAscenzo MD, Fobert PR, Despres C,Martin GBvThe tomato transcription factor Pti4 regulates defence-relatedgene expression via GCC box and non-GCC box cis elements Plant Cell 15: 3033-3050 (2003)PubMed: 14630974; GTTAGTTMYB26PSS000182 17-May-1998 (last modified) kehi�Myb26 binding site; Myb26 recognizes the c-Myb and P-box-likebinding sites representing cis-elements in the promoter regionsof several phenylpropanoid biosynthetic genes; Identical to P-boxin maize, and to Myb305 binding site in snapdragon;MYBmybMybmyb26P-boxP boxflowerpea (Pisum sativum)Uimari A, Strommer J\Myb26: a MYB-like protein of pea flowers with affinity forpromoters of phenylpropanoid genesPlant J 12:1273-1284 (1997)PubMed: 9450341; GTTAGGTTMYB2ATS000177 16-May-2001 (last modified) uchi�`Binding site for ATMYB2, an Arabidopsis MYB homolog; ATMYB2binds oligonucleotides that contained a consensus MYB recognitionsequence (TAACTG), such as is in the SV40 enhancer and the maizebronze-1 promoter (Urao et al., Plant Cell 5:1529 (1993)); ATMYB2is involved in regulation of genes that are responsive to waterstress in Arabidopsis; See S000355;MYBmybSV40enhancerbronzebronze-1leafshootArabidopsis thaliana;2Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki KAn Arabidopsis myb homolog is induced by dehydration stress andits gene product binds to the conserved MYB recognition sequence Plant Cell 5:1529-1539 (1993)!PubMed: 8312738; GenBank: D14712; TAACTG MYBATRD22S000175 16-May-2001 (last modified) uchi�Binding site for MYB (ATMYB2) in dehydration-responsive gene,rd22; MYB binding site in rd22 gene of Arabidopsis thaliana;ABA-induction; Located at ca. -141 of rd22 gene; Also MYC at ca.-200 of rd22 gene; See S000174 (MYCATRD22); See S000355; Dehydration Water stressABAMYCleafshootArabidopsis thalianaWAbe H, Yamaguchi-Shinozaki k, Urao T, Iwasaki T, Hosokawa D,Shinozaki KBusk PK, Pages M�Role of Arabidopsis MYC and MYB homologs in drought- and abscisicacid-regulated gene expression.Regulation of abscisic acid-induced transcription=Plant Cell 9:1859-1868 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 9368419;PubMed: 9617810;ReviewCTAACCAMYBCOREATCYCB1S000502&15-September-2006 (last modified) kehi�7"Myb core" in the 18 bp sequence which is able to activatereporter gene without leading to M-phase-specific expression,found in the promoter of Arabidopsis thaliana cyclin B1:1 gene;the 18 bp sequence share homology with a sequence found in the N.sylvestris cyclin B1 promoter (Trehin et al., 1999; seeS000283):CycM phaseMybArabidopsis thalianaAPlanchais S, Perennes C, Glab N, Mironov V, Inze D, BergouniouxC.�Characterization of cis-acting element involved in cell cyclephase-independent activation of Arath;CycB1;1 transcription andidentification of putative regulatory proteins."Plant Mol Biol. 50:111-127 (2002).PubMed: 12139003 AACGGMYBGAHVS000181&15-September-2006 (last modified) kehi��Central element of gibberellin (GA) response complex (GARC) inhigh-pI alpha-amylase gene in barley (H.v.); Similar to c-myb andv-myb consensus binding site; GAmyb binds specifically to theTAACAAA box in vitro; GAmyb is the sole GA-regulatedtranscriptional factor required for transcriptional activation ofthe high-pI alpha-amylase; GARC consist of the pyrimidine,TAACAAA and TATCCAC boxes; GARE in RAmy1A gene; GARE andpyrimidine box in RAmy1A are partially involved in sugarrepression; mybMybGAmybGA gibberellinGARC alph-amylaseamylasealeuroneGAREseed.barley (Hordeum vulgare); rice (Oryza sativa);�Gubler F, Kalla R, Roberts JK, Jacobsen JVMorita A, Umemura T, Kuroyanagi M, Futsuhara Y, Perata P,Yamaguchi JGubler F, Raventos D, Keys M, Watts R, Mundy J, Jacobsen JV.�KGibberellin-regulated expression of a myb gene in barley aleuronecells: evidence for Myb transactivation of a high-plalpha-amylase gene promoterFunctional dissection of a sugar-repressed alpha-amylase gene(Ramy1A) promoter in rice embryosTarget genes and regulatory domains of the GAMYB transcriptionalactivator in cereal aleurone.MPlant Cell 7:1879-1891 (1995)FEBS Lett 423:81-85 (1998)Plant J. 17:1-9(1999).0PubMed: 8535141;PubMed: 9506846;PubMed: 10069063 TAACAAAMYBST1S000180 17-Apr-1998 (last modified) kehi�Core motif of MybSt1 (a potato MYB homolog) binding site; MybSt1cDNA clone was isolated by using CaMV 35S promoter domain A as aprobe (Baranowskij et al. 1994); The Myb motif of the MybSt1protein is distinct from the plant Myb DNA binding domaindescribed so far;MYBmybMybpotato (Solanum tuberosum);/Baranowskij N, Frohberg C, Prat S, Willmitzer L�A novel DNA binding protein with homology to Myb oncoproteinscontaining only one repeat can function as a transcriptionalactivatorEMBO J 13:5383-5392 (1994)PubMed: 7957104; GGATA MYCATERD1S000413%29-November-2004 (last modified) kehi�MYC recognition sequence (from -466 to -461) necessary forexpression of erd1 (early responsive to dehydration) indehydrated Arabidopsis; NAC protein bound specifically to theCATGTG motif (Tran et al., 2004)); NAC protein bound specificallyto the CATGTG motif (Tran et al., 2004); water-stresserdArabidopsis thaliana�Simpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K,Yamaguchi-Shinozaki K.Tran LS, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K,Fujita M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K.�ZTwo different novel cis-acting elements of erd1, a clpAhomologous Arabidopsis gene function in induction by dehydrationstress and dark-induced senescence.Isolation and functional analysis of arabidopsis stress-inducibleNAC transcription factors that bind to a drought-responsivecis-element in the early responsive to dehydration stress 1promoter.<Plant J. 33: 259-270 (2003)Plant Cell. 16: 2481-2498 (2004).!PubMed: 12535340;PubMed: 15319476 CATGTG MYCATRD22S000174 29-Sep-1999 (last modified) kehi�� Binding site for MYC (rd22BP1) in Arabidopsis (A.t.)dehydration-resposive gene, rd22; MYC binding site in rd22 geneof Arabidopsis thaliana; ABA-induction; Located at ca. -200 ofrd22 gene; Also MYB at ca. -141 of rd22 gene; See also S000175(MYBATRD22); Dehydration Water stressABAMYCmycleafshootArabidopsis thalianaWAbe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D,Shinozaki KBusk PK, Pages M�Role of Arabidopsis MYC and MYB homologs in drought- and abscisicacid-regulated gene expression.Regulation of abscisic acid-induced transcription=Plant Cell 9:1859-1868 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 9368419;PubMed: 9617810;ReviewCACATG NAPINMOTIFBNS000070 17-May-1998 (last modified) kehi�Sequence found in 5' upstream region (-6, -95, -188) of napin (2Salbumin) gene in Brassica napus (B.n.); Interact with a proteinpresent in crude nuclear extracts from developing B. napusseeds;napin
2S albuminseedstorage proteinrape (Brassica napus):Ericson ML, Muren E, Gustavsson H-O, Josefsson L-G, Rask L�Analysis of the promoter region of napin genes from Brassicanapus demonstrates binding of nuclear protein in vitro to aconserved sequence motif. Eur J Biochem 197:741-746 (1991)!PubMed: 2029903; GenBank: X58142; TACACAT NDEGMSAURS000359 16-Feb-2001 (last modified) seki�"NDE" found in Soybean (G.m.) SAUR (Small Auxin-Up RNA) 15A genepromoter; Required for auxin responsiveness; Contains twoadjacent sequences, TGTCTC (see S000270) and GGTCCCAT, which havebeen previously identified as putative auxin-responsive elements;See S000360;NDESAURAuxinSoybean (Glycine max)*Li Y, Liu ZB, Shi X, Hagen G, Guilfoyle TJ4An auxin-inducible element in soybean SAUR promoters Plant Physiol 106:37-43 (1994)PubMed: 7972520; CCATATGCCATGTCTCTCAATTGGTCCCAT NODCON1GMS000461"24-April-2005 (last modified) kehiMOne of two putative nodulin consensus sequences; See also S000462(NODCON2GM);nodulinGlycine max (soybean)^Sandal NN, Bojsen K, Marcker KA.Stougaard J, Jorgensen JE, Christensen T, Kuhle A, Marcker KA.�A small family of nodule specific genes from soybean.Interdependence and nodule specificity of cis-acting regulatoryelements in the soybean leghemoglobin lbc3 and N23 genepromoters.JNucleic Acids Res. 15:1507-1519 (1987).Mol Gen Genet. 220: 353-360 (1990). PubMed: 3822835PubMed: 2338938consesus; in silico;AAAGAT NODCON2GMS000462"24-April-2005 (last modified) kehiMOne of two putative nodulin consensus sequences; See also S000461(NODCON1GM);nodulinGlycine max (soybean)^Sandal NN, Bojsen K, Marcker KA.Stougaard J, Jorgensen JE, Christensen T, Kuhle A, Marcker KA.�A small family of nodule specific genes from soybean.Interdependence and nodule specificity of cis-acting regulatoryelements in the soybean leghemoglobin lbc3 and N23 genepromoters.JNucleic Acids Res. 15:1507-1519 (1987).Mol Gen Genet. 220: 353-360 (1990). PubMed: 3822835PubMed: 2338938consesus; in silico;CTCTT NONAMERATH4S000147 10-May-1998 (last modified) kehi@Nonamer motif of Arabidopsis thaliana (A.t.) histone H4promoter;nonamerhistoneH4meristemArabidopsis thaliana;2Chaubet N, Flenet M, Clement B, Brignon P, Gigot CZIdentification of cis-elements regulating the expression of anArabidopsis histone H4 gene.Plant J 10:425-435 (1996)PubMed: 8811858; AGATCGACGNONAMERMOTIFTAH3H4S000071 17-May-1998 (last modified) kehiI"Nonamer motif" found in promoter of wheat (T.a.) histone genesH3 and H4;HBP-1AHBP-1B
wheat histoneCaMV 35SNOSmeristem wheat (Triticum aestivum); CaMV;FNakayama T, Sakamoto A, Yang P, Minami M, Fujimoto Y, Ito T,Iwabuchi MvHighly conserved hexamer, octamer and nonamer motifs are positivecis-regulatory elements of the wheat histone H3 gene. FEBS Lett 300:167-170 (1992)!PubMed: 1563517; GenBank: S95162; CATCCAACG NRRBNEXTAS000242 11-0ct-1999 (last modified) kehi�"NRR (negative regulatory region)" in promoter region of Brassicanapus (B.n.) extA extensin gene; Removal of this region leads toexpression in all tissues within the stem internode, petiole androot;extextensinstem internodepetiolerootBrassica napusElliott KA , Shirsat AH{Promoter regions of the extA extensin gene from Brassica napuscontrol activation in response to wounding and tensile stress!Plant Mol Biol 37:675-687 (1998)PubMed: 9687071; TAGTGGAT NTBBF1ARROLBS000273 15-Oct-1999 (last modified) kehi�NtBBF1(Dof protein from tobacco) binding site in Agrobacteriumrhizogenes (A.r.) rolB gene; Found in regulatory domain B (-341to -306); Required for tissue-specific expression and auxininduction;rolBDofauxindomain BrootshootmeristemvascularAgrobacterium rhizogenes1Baumann K, De Paolis A, Costantino P, Gualberti G�The DNA binding site of the Dof protein NtBBF1 is essential fortissue-specific and auxin-regulated expression of the rolBoncogene in plants Plant Cell 11:323-333 (1999)%PubMed: 10072394; GenBank: AJ009594; ACTTTA O2F1BE2S1S000162 17-May-1998 (last modified) kehi�opaque-2 recognition site F1 in Bertholletia excelsa (Brazil nuttree) 2S storage protein gene (be2S1); O2 protein binds to F1, F2and F3 sequences of be2S1 promoter; F1 is hybrid C/G box;O2opaque-2be2S1F1seed'Brazil nut tree (Bertholletia excelsa);~Vincentz M, Leite A, Neshich G, Vriend G, Mattar C, Barros L,Weinberg D, de Almeida ER, Paes de Carvalho M, Aragao F, GanderES�ACGT and vicilin core sequences in a promoter domain required forseed-specific expression of a 2S storage protein gene arerecognized by the opaque-2 regulatory protein. Plant Mol Biol 34:879-889 (1997)!PubMed: 9290640; GenBank: X78287;
TCCACGTCGA O2F2BE2S1S000163 17-May-1998 (last modified) kehi�.opaque-2 recognition site F2 in Bertholletia excelsa (Brazil nuttree) 2S storage protein gene (be2S1); O2 protein binds to F1, F2and F3 sequences of be2S1 promoter; F2 is a new O2-bindingsequence related to the O2 target sites of the Coix alpha-coxin,the maize b-32 genes and the AP-1 pseudopalindrome;O2opaque-2be2S1seed&Brazil nut tree (Bertholletia excelsa)~Vincentz M, Leite A, Neshich G, Vriend G, Mattar C, Barros L,Weinberg D, de Almeida ER, Paes de Carvalho M, Aragao F, GanderES�ACGT and vicilin core sequences in a promoter domain required forseed-specific expression of a 2S storage protein gene arerecognized by the opaque-2 regulatory protein. Plant Mol Biol 34:879-889 (1997)!PubMed: 9290640; GenBank: X78287;
GCCACCTCAT O2F3BE2S1S000164 17-May-1998 (last modified) kehi�opaque-2 recognition site F3 in Bertholletia excelsa (Brazil nuttree) 2S storage protein gene (be2S1); O2 protein binds to F1, F2and F3 sequences of be2S1 promoter; F3 is hybrid of A/G box;O2opaque-2be2S1seed&Brazil nut tree (Bertholletia excelsa)~Vincentz M, Leite A, Neshich G, Vriend G, Mattar C, Barros L,Weinberg D, de Almeida ER, Paes de Carvalho M, Aragao F, GanderES�ACGT and vicilin core sequences in a promoter domain required forseed-specific expression of a 2S storage protein gene arerecognized by the opaque-2 regulatory protein. Plant Mol Biol 34:879-889 (1997)!PubMed: 9290640; GenBank: X78287;
TCCACGTACT
OBF5ATGST6S000304 29-Sep-2003 (last modified) kehi��"OBF5 (ocs element binding factor 5)" binding site found in theArabidopsis (A.t.) GST6 gene promoter; Similar to Ocs sequence;Located between -426 and -401; See S000305; Overexpression ofOBP3 lead to severe growth defect with altered root developmentand yellowish leaves; All OBP proteins contain transcriptionalactivation domains in their C-terminal region; Dof protein playimportant roles in plant growth and development; Binding site ofOBF4 and OBF5; See S000305, S000346; GSTOcsOBFOBPauxinSAcycloheximide, DofTGApathogenrootleafshoot"Arabidopsis (Arabidopsis thaliana)rChen W, Chao G, Singh KBKang HG, Singh KBZhang B, Foley RC, Singh KBZhang B, Chen W, Foley RC, Buttner M, Singh KB��The promoter of a H202-inducible, Arabidopsis glutathioneS-transferase gene contains closely linked OBF- and OBP1-bindingsitesCharacterization of salicylic acid-responsive, Arabidopsis Dofdomain proteins: Overexpression of OBP3 leads to growth defectsIsolation and characterization of two related Arabidopsisocs-element bZIP binding proteinsInteractions between distinct types of DNA binding proteinsenhance binding to ocs element promoter sequenceskPlant J 10: 955-966 (1996)Plant J 21: 329-339 (2000)Plant J (1993) 4: 711-716Plant Cell 7: 2241-2252 (1995)kPubMed: 9011080;PubMed: 10758484;PubMed: 8252072; GenBank: X69899; X69900;PubMed: 8718629; GenBank: X89192; ATCTTATGTCATTGATGACGACCTCC
OBP1ATGST6S000305 29-Sep-2003 (last modified) kehi��OBP1, 4, and 5 (OBF binding protein) binding site found in theArabidopsis (A.t.) GST6 gene promoter; Located between -398 and-388; OBP1 is able to stimulate the binding of OBF proteins tothe GST6 promoter; See S000304; Overexpression of OBP3 lead tosevere growth defect with altered root development and yellowishleaves; All OBP proteins contain transcriptional activationdomains in their C-term. region; Dof protein play important rolesin plant growth and development; See S000304;
GSTOcsOBFOBPauxinSAcycloheximide, Dofrootleafshoot"Arabidopsis (Arabidopsis thaliana)rChen W, Chao G, Singh KBKang HG, Singh KBZhang B, Foley RC, Singh KBZhang B, Chen W, Foley RC, Buttner M, Singh KB��The promoter of a H202-inducible, Arabidopsis glutathioneS-transferase gene contains closely linked OBF- and OBP1-bindingsitesCharacterization of salicylic acid-responsive, Arabidopsis Dofdomain proteins: Overexpression of OBP3 leads to growth defectsIsolation and characterization of two related Arabidopsisocs-element bZIP binding proteinsInteractions between distinct types of DNA binding proteinsenhance binding to ocs element promoter sequenceskPlant J 10: 955-966 (1996)Plant J 21: 329-339 (2000)Plant J (1993) 4: 711-716Plant Cell 7: 2241-2252 (1995)kPubMed: 9011080;PubMed: 10758484;PubMed: 8252072; GenBank: X69899; X69900;PubMed: 8718629; GenBank: X89192; TACACTTTTGGOCETYPEIINTHISTONES000268 15-Oct-1999 (last modified) kehi�"Type II element"; Oct-containing composite element Type II foundin tobacco (N.t.) histone gene promoter; Oct (octomer) motif ispaired with TCA motif to form Type II element; Required forS-phase specific and meristematic tissue-specific expression;histoneOctOCE TCA-motifType IIS-phasemeristemtobacco (Nicotiana tabacum)9Taoka K, Kaya H, Nakayama T, Araki T, Meshi T, Iwabuchi MzIdentification of three Kinds of mutually related compositeelements conferring S phase-specific transcriptional activationPlant J 18:611-623 (1999)PubMed: 10417712; TCACGCGGATCOCSENHANMOTIFATS000074 16-Feb-2001 (last modified) seki��"OCS enhancer element" in octopine synthase gene (OCS) ofTi-plasmid of Agrobacterium tumefaciens (A.t.); Binding withnuclear protein isolated from tobacco and maize; See S000346;Tandem OCSTF binding-sites are essential for the activity of theOcs-element; The Ocs-element occures rarely in plant genepromoters; See S000357; "OCS palindrome" found in tobacco (N.t.)OCS (Octopine synthase gene) promoter; Located at -193 to -178;Binding site of ASF-1; Confers expression of the gene;octopine synthaseocsenhancerASF-1HAgrobacterium tumefaciens; tobacco (Nicotiana tabacum); maize(Zea mays);�Singh K, Tokuhisa JG, Dennis ES, Peacock WJEllis JG, Tokuhisa JG, Llewellyn DJ, Bouchez D, Singh K, DennisES, Peacock WJFromm H, Katagiri F, Chua NHTokuhisa JG, Singh K, Dennis ES, Peacock WJ��Saturation mutagenesis of the octopine synthase enhancer:correlation of mutant phenotypes with binding of a nuclearprotein factor.Does the ocs-element occur as a functional component of thepromoters of plant genes?An octopine synthase enhancer element directs tissue-specificexpression and binds ASF-1, a factor from tobacco nuclearextractsA DNA-binding protein factor recognizes two binding domainswithin the octopine synthase enhancer element{Proc Natl Acad Sci USA 86:3733-3737 (1989)Plant J (1993) 4: 433-443Plant Cell 1: 977-984 (1989)Plant Cell 2: 215-224 (1990)@PubMed: 2726750;PubMed: 8220489;PubMed: 2562557;PubMed: 2152113; ACGTAAGCGCTTACGT OCSGMGH24S000346 16-Feb-2001 (last modified) seki�q"OCS element" found in the soybean (G.m) GH2/4 gene promoter;Required for auxin and salycylic acid responsiveness; Activatedby both active and inactive auxin and salicylic acid analogues;See S000074, S000130, S000158, S000304; Tandem OCSTFbinding-sites are essential for the activity of the Ocs-element;The Ocs-element occurs rarely in plant gene promoters; SeeS000357;OCSauxinsalicylic acidGH2/4Soybean (Glycine max)lUlmasov T, Hagen G, Guilfoyle TEllis JG, Tokuhisa JG, Llewellyn DJ, Bouchez D, Singh K, DennisES, Peacock WJ�The ocs element in the soybean GH2/4 promoter is activated byboth active and inactive auxin and salicylic acid analoguesDoes the ocs-element occur as a functional component of thepromoters of plant genes?<Plant Mol Biol 26: 1055-1064 (1994)Plant J (1993) 4: 433-443 PubMed: 7811965;PubMed: 8220489; CGGTTTACGTAATCTCTTACATCA OCSGMHSP26AS000357 16-Feb-2001 (last modified) seki�Ocs element found in soybean (Glycine max) heat shock gene(Gmhsp26-A) promoter; The element is a functional ocs-element;The element did not affect the promoter's response to heat orwounding;OcsHspSoybean (Glycine max)MEllis JG, Tokuhisa JG, Llewellyn DJ, Bouchez D, Singh K, DennisES, Peacock WJTDoes the ocs-element occur as a functional component of thepromoters of plant genes?Plant J (1993) 4: 433-443PubMed: 8220489; TGATGTAAGAGATTACGTAAOCTAMERMOTIFTAH3H4S000076 11-May-2006 (last modified) kehi�."Octamer motif" found in promoter of wheat (T.a.) histone genesH3 and H4, and corn histone genes H3 and H4; Arabidopsis histoneH4; "histone-specific octamer"; About half of the Oct motifs arepresent together with another element, HexA, TCA or CCAAT-box,forming OCES (Oct-containing composite elements);histoneOctS-phaseCaMV 35SNOSmeristemdwheat (Triticum aestivum); maize (Zea mays); CaMV; Arabidopsisthaliana; tobacco (Nicotiana tabacum);�Chaubet N, Philipps G, Chaboute M-E, Ehling M, Gigot CNakayama T, Sakamoto A, Yang P, Minami M, Fujimoto Y, Ito T,Iwabuchi MChaubet N, Flenet M, Clement B, Brignon P, Gigot CTaoka K, Kaya H, Nakayama T, Araki T, Meshi T, Iwabuchi M��Nucleotide sequences of two corn histone H3 genes. Genomicorganization of the corn histone H3 and H4 genes.Highly conserved hexamer, octamer and nonamer motifs are positivecis-regulatory elements of the wheat histone H3 gene.Identification of cis-elements regulating the expression of anArabidopsis histone H4 gene.Identification of three Kinds of mutually related compositeelements conferring S phase-specific transcriptional activationmPlant Mol Biol 6:253-263 (1986)FEBS Lett 300:167-170 (1992)Plant J 10:425-435 (1996)Plant J 18:611-623 (1999)BPubMed: 1563517; GenBank: S95162;PubMed: 8811858;PubMed: 10417712; CGCGGATC
OCTAMOTIF2S000116 17-May-1998 (last modified) kehi�Octamer motif found in histone-gene-specific consensus sequences;200 base upstream from the initiation codon ATG; Exist in all ofseven plant histone genes;octamerhistonemeristemmaize (Zea mays);6Chaubet N, Philipps G, Chaboute M-E, Ehling M, Gigot ClNucleotide sequences of two corn histone H3 genes. Genomicorganization of the corn histone H3 and H4 genes. Plant Mol Biol 6:253-263 (1986) CGCGGCAT OPAQUE2ZM22ZS000017 17-May-2001 (last modified) uchi�Opaque-2 (O2) target sequence in maize (Z.m.) 22- and 27-kD zeinpromoters; "ACGT motif"; Related to seed expression; "O2 targetsequence"; Gene: maize 22-kD zein; transacting factor: 02;O2opaque
22-kD zeinseedACGTopaque-2maize (Zea mays)�Schmidt RJ, Ketudat M, Aukerman MJ, Hoschek GThomas TLUeda T, Waverczak W, Ward K, Sher N, Ketudat M, Schmidt RJ,Messing JSingh KB�OOpaque-2 is a transcriptional activator that recognizes aspecific target site in 22-kD zein genesGene expression during plant embryogenesis and germination: Anoverview.Mutations of the 22- and 27-kD zein promoters affecttransactivation by the opaque-2 proteinTranscriptional Regulation in Plants: The Importance ofCombinatorial ComtroluPlant Cell 4:689-700 (1992)Plant Cell 5:1401-1410 (1993)Plant Cell 4:701-709 (1992)Plant Pysiol 118: 1111-1120 (1998)PPubMed: 1392590; GenBank: M86591;PubMed: 8281041;PubMed: 1392591;PubMed: 9847085 Reviewreview
TCCACGTAGAOSE1ROOTNODULES000467"24-April-2005 (last modified) kehi�One of the consensus sequence motifs of organ-specific elements(OSE) characteristic of the promoters activated in infected cellsof root nodules; See also S000468;
leghemoglobinLb29rootnodule arbuscule@Vicia faba; Medicago truncatula; Glycine max; Sesbania rostrata;�Vieweg MF, Fruhling M, Quandt HJ, Heim U, Baumlein H, Puhler A,Kuster H, Andreas MP.Fehlberg V, Vieweg MF, Dohmann EM, Hohnjec N, Puhler A, PerlickAM, Kuster H.��The promoter of the Vicia faba L. leghemoglobin gene VfLb29 isspecifically activated in the infected cells of root nodules andin the arbuscule-containing cells of mycorrhizal roots fromdifferent legume and nonlegume plants.The promoter of the leghaemoglobin gene VfLb29: functionalanalysis and identification of modules necessary for itsactivation in the infected cells of root nodules and in thearbuscule-containing cells of mycorrhizal roots.IMol Plant Microbe Interact. 17: 62-69 (2004).J Exp Bot. 56:799-806 (2005) PubMed: 14714869PubMed: 15668224 AAAGATOSE2ROOTNODULES000468"24-April-2005 (last modified) kehi�One of the consensus sequence motifs of organ-specific elements(OSE) characteristic of the promoters activated in infected cellsof root nodules; See also S000467;
leghemoglobinLb29rootnodule arbuscule@Vicia faba; Medicago truncatula; Glycine max; Sesbania rostrata;�Vieweg MF, Fruhling M, Quandt HJ, Heim U, Baumlein H, Puhler A,Kuster H, Andreas MP.Fehlberg V, Vieweg MF, Dohmann EM, Hohnjec N, Puhler A, PerlickAM, Kuster H.��The promoter of the Vicia faba L. leghemoglobin gene VfLb29 isspecifically activated in the infected cells of root nodules andin the arbuscule-containing cells of mycorrhizal roots fromdifferent legume and nonlegume plants.The promoter of the leghaemoglobin gene VfLb29: functionalanalysis and identification of modules necessary for itsactivation in the infected cells of root nodules and in thearbuscule-containing cells of mycorrhizal roots.IMol Plant Microbe Interact. 17: 62-69 (2004).J Exp Bot. 56:799-806 (2005) PubMed: 14714869PubMed: 15668224 CTCTT PALBOXAPCS000137$06-January-2006 (last modified) kehi��Box A; Consensus; One of three putative cis-acting elements(boxes P, A, and L) of phenylalanine ammonia-lyase (PAL; EC4.3.1.5) genes in parsley (P.c.); "None of these elements (boxesP, A, and L) alone, or the promoter region containing all of themtogether, conferred elicitor or light responsiveness. Theseelements appear to be necessary but not sufficient for elicitor-or light-mediated PAL gene activation." (Logemann et al., 1995);See also S000136 (Box P), S000138 (Box L);Box APAL parsley (Petroselinum crispum)#Logemann E, Parniske M, Hahlbrock KuModes of expression and common structural features of thecomplete phenylalanine ammonia-lyase gene family in parsley.*Proc Natl Acad Sci USA 92:5905-5909 (1995)1PubMed: 7597051; GenBank: L37355, L37356, L37357; CCGTCCPALINDROMICCBOXGMS000255!23-June-2006 (last modified) kehi�Palindromic C-box in soybean (G.m.); bZIP factors, STGA1 and STFs(STF1 and STF2) found in soybean apical hypocotyl, bind to thissequence;C-boxbZIPSTGA1STF hypocotylTGASA*Glycine max(soybean); Arabidopsis thaliana�Cheong YH, Yoo CM, Park JM, Ryu GR, Goekjian VH , Nagao RT, KeyJL, Cho MJ, Hong JCThibaud-Nissen F, Wu H, Richmond T, Redman JC, Johnson C, GreenR, Arias J, Town CD�#STF1 is a novel TGACG-binding factor with a zinc-finger motif anda bZIP domain which heterodimerizes with GBF proteinsDevelopment of Arabidopsis whole-genome microarrays and theirapplication to the discovery of binding sites for the TGA2transcription factor in salicylic acid-treated plants.3Plant J 15:199-209 (1998)Plant J 47:152-162 (2006)PubMed: 9721678;>in silico based on whole-genome microarray analysis after ChIPTGACGTCA PASNTPARAS000336 7-Sep-2000 (last modified) seki�"pas"; as-1-related element found in the tobacco (N.t.) parA genepromoter; Involved in Cadmium responsiveness; Not related tocopper responsiveness; Located between -68 and -49;parApascadmiumas-1tobacco (Nicotiana tabacum) Kusaba M, Takahashi Y, Nagata TrA multiple-stimuli-responsive as-1-related element of parA geneconfers responsiveness to cadmium but not to copper#Plant Physiol 111: 1161-1167 (1996)PubMed: 8756498; TTACGCAAGCAATGACATCT
PE1ASPHYA3S000196 17-May-1998 (last modified) kehi�PE1; Positively acting element found at -381 to -348 of oat(A.s.) phyA3 promoter; A general positive element (Terzaghi &Cashmore, 1995); phytochromephyphyAphyA3leafshootoat (Avena sativa);FBruce WB, Quail PHBruce WB, Deng X-W, Quial PHTerzaghi WB, Cashmore AR�cis-Acting elements involved in photoregulation of an oatphytochrome promoter in riceA negatively acting DNA sequence element mediatesphytochrome-directed repression of phyA gene transcription.Light-regulated transcriptionnPlant Cell 2:1081-1089 (1990)EMBO J 10:3015-3024 (1991)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995) PubMed: 2152109;PubMed: 1915276;ReviewGAAATAGCAAATGTTAAAAATA PE2FNTRNR1AS000455%29-November-2004 (last modified) kehi�$"pE2F (proximal E2F elemen)" at -143bp of tobacco (N.t.) RNR1apromoter; E2F factors involved in gene induction at the G1/Stransition of the cell cycle; Important for regulating specificRNR1a (ribonucleotide reductase large subunit) gene expression inresponse to UV-C irradiation; See S000367;E2FRNR1aUV-C
cell cycleG1SNicotiana tabacum (tobacco)#Lincker F, Philipps G, Chaboute ME.�UV-C response of the ribonucleotide reductase large subunitinvolves both E2F-mediated gene transcriptional regulation andprotein subcellular relocalization in tobacco cells.*Nucleic Acids Res. 32: 1430-1438 (2004). .PubMed: 14990748 ATTCGCGC
PE3ASPHYA3S000197 17-May-1998 (last modified) kehiePE3; Positively acting element found at -111 to -81 (Bruce etal., 1991) of oat (A.s.) phyA3 promoter; phytochromephyphyAphyA3leafshootoat (Avena sativa);.Bruce WB, Quail PHBruce WB, Deng X-W, Quial PH�cis-Acting elements involved in photoregulation of an oatphytochrome promoter in riceA negatively acting DNA sequence element mediatesphytochrome-directed repression of phyA gene transcription.7Plant Cell 2:1081-1089 (1990)EMBO J 10:3015-3024 (1991) PubMed: 2152109;PubMed: 1915276; CAGCTCCCATGGCTCTCCCATCCGCGCCGGTPIATGAPBS000381 23-Aug-2001 (last modified) uchi�"PI" found in the Arabidopsis thaliana(A.T.) GAPB gene promoter;Located between -157 and -150; Mutations in the "PI" resulted inreductions of light-activated gene transcription; GAPB encodesthe B subunit of chloroplast glyceraldehyde-3-phosphatedehydrogenase(GADPH) of A.T.;GAPB(glyceraldehyde-3-phosphate dehydrogenaselight-activated
transcriptionArabidopsis thalianaChan CS, Guo L, Shih MC�Promoter analysis of the nuclear gene encoding the chloroplastglyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsisthaliana!Plant Mol Biol 46: 131-141 (2001)PubMed: 11442054; GTGATCAC PIIATGAPBS000382 23-Sep-2001 (last modified) kehi�"PII" found in the Arabidopsis thaliana(A.T.) GAPB gene promoter;Located between -69 and -50; Mutations in the "PII" resulted inreductions of light-activated gene transcription; GAPB encodesthe B subunit of chloroplast glyceraldehyde-3-phosphatedehydrogenase(GADPH) of A.T.;GAPB(glyceraldehyde-3-phosphate dehydrogenaselight-activated
transcriptionArabidopsis thalianaChan CS, Guo L, Shih MC�Promoter analysis of the nuclear gene encoding the chloroplastglyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsisthaliana!Plant Mol Biol 46: 131-141 (2001)PubMed: 11442054; TTGGTTTTGATCAAAACCAAPOLASIG1S000080%18-November-2005 (last modified) kehi�"PolyA signal"; poly A signal found in legA gene of pea, ricealpha-amylase; -10 to -30 in the case of animal genes. Nearupstream elements (NUE) in Arabidopsis (Loke et al. 2005);
poly A signalNUEFUE?pea (Pisum sativum); rice (Oryza sativa); Arabidopsis thaliana;�Heidecker G, Messing JJoshi CPO'Neill SD, Kumagai MH, Majumdar A, Huang N, Sutliff TD,Rodriguez RLLoke JC, Stahlberg EA, Strenski DG, Haas BJ, Wood PC, Li QQ.�oStructural analysis of plant genes.Putative polyadenylation signals in nuclear genes of higherplants: a compilation and analysis.The alpha-amylase genes in Oryza sativa: Characterization of cDNAclones and mRNA expression during seed germination.Compilation of mRNA polyadenylation signals in Arabidopsisrevealed a new signal element and potential secondarystructures.�Ann Rev Plant Physiol 37:439-466 (1986)Nucleic Acids Res 15:9627-9640 (1987)Mol Gen Genet 221:235-244 (1990)Plant Physiol. 138: 1457-1468. (2005)IPubMed: 3697078;PubMed: 2370848; GenBank: M24286, M24287;PubMed: 15965016Reviewin silicoAATAAAPOLASIG2S000081 17-May-1998 (last modified) kehi�"PolyA signal"; poly A signal found in rice alpha-amylase; -10 to-30 in the case of animal genes. AATAAA; AATAAT; AATTAAA;AATAAG;
poly A signal rice (Oryza sativa); animal;DO'Neill SD, Kumagai MH, Majumdar A, Huand N, Sutliff TD,Rodriguez RLtThe alpha-amylase genes in Oryza sativa: Characterization of cDNAclones and mRNA expression during seed germination. Mol Gen Genet 221:235-244 (1990))PubMed: 2370848; GenBank: M24286, M24287; AATTAAAPOLASIG3S000088 11-May-2006 (last modified) kehiI"Plant polyA signal"; Consensus sequence for plantpolyadenylation signal;poly Apolyadenylationmaize (Zea mays) Heidecker G, Messing JJoshi CP�Structural analysis of plant genes.Putative polyadenylation signals in nuclear genes of higherplants: a compilation and analysis.LAnn Rev Plant Physiol 37:439-466 (1986)Nucleic Acids Res 15:9627-9640 (1987)PubMed: 3697078;ReviewAATAATPOLLEN1LELAT52S000245$26-October-2005 (last modified) kehi�XOne of two co-dependent regulatory elements responsible forpollen specific activation of tomato (L.e.) lat52 gene; Found at-72 to -68 region; See S000246 (POLLEN2LELAT52); AGAAA andTCCACCATA (S000246) are required for pollen specific expression;Also found in the promoter of tomato endo-beta-mannanase gene(LeMAN5) gene (Filichkin et al. 2004);pollenlat52endo-beta-mannnanaseMAN Lycopersicon esculentum (tomato)HBate N, Twell DFilichkin SA, Leonard JM, Monteros A, Liu PP, Nonogaki H.� Functional architecture of a late pollen promoter:pollen-specific transcription is developmentally regulated bymultiple stage-specific and co-dependent activator elementsA novel endo-beta-mannanase gene in tomato LeMAN5 is associatedwith anther and pollen development.DPlant Mol Biol 37:859-869 (1998)Plant Physiol. 134 1080-1087 (2004) PubMed: 9678581;PubMed: 14976239 AGAAAPOLLEN2LELAT52S000246 11-Oct-1999 (last modified) kehi�One of two co-dependent regulatory elements responsible forpollen specific activation of tomato (L.e.) lat52 gene; Found at-60 to -52 region; See S000245 (POLLEN1LELAT52); AGAAA (S000245)and TCCACCATA are required for pollen specific expression;pollenlat52 tomato (Lycopersicon esculentum)Bate N, Twell D�Functional architecture of a late pollen promoter:pollen-specific transcription is developmentally regulated bymultiple stage-specific and co-dependent activator elements!Plant Mol Biol 37:859-869 (1998)PubMed: 9678581; TCCACCATA
PREATPRODHS000450#04-August-2006 (last modified) kehi��"PRE (Pro- or hypoosmolarity-responsive element) found in thepromoter region of proline dehydrogenase (ProDH) gene inArabidopsis; Core of 9-bp sequence ACTCATCCT which is necessaryfor the efficient expression of ProDH in response to L-Pro andhypoosmolarity (Satoh et al., 2002); ATB2-binding site; Similarto GCN4 motif (ATGA(C/G)TCAT); ATB2 subgroup of bZIPtranscription factors function as transcriptional activator forhypoosmolarity-inducible ProDH (Satoh et al., 2004);prolineProDHhypoosomolaritybZIPArabidopsis thaliana�Satoh R, Nakashima K, Seki M, Shinozaki K, Yamaguchi-ShinozakiK.Satoh R, Fujita Y, Nakashima K, Shinozaki K, Yamaguchi-ShinozakiK.Weltmeier F, Ehlert A, Mayer CS, Dietrich K, Wang X, Schutze K,Alonso R, Harter K, Vicente-Carbajosa J, Droge-Laser W.��ACTCAT, a novel cis-acting element for proline- andhypoosmolarity-responsive expression of the ProDH gene encodingproline dehydrogenase in Arabidopsis.A novel subgroup of bZIP proteins functions as transcriptionalactivators in hypoosmolarity-responsive expression of the ProDHgene in Arabidopsis.Combinatorial control of Arabidopsis proline dehydrogenasetranscription by specific heterodimerisation of bZIPtranscription factors.ePlant Physiol. 130:709-719 (2002).Plant Cell Physiol. 45: 309-317 (2004).EMBO J. 25:3133-3143. (2006)0PubMed: 12376638PubMed: 15047879PubMed: 16810321 ACTCATPREMOTIFNPCABES000230 17-May-1998 (last modified) kehi�Motif sequence repeated many times in two positive regulatoryelements, PRE1 (-1554 to -1182) and PRE2 (-747 to -516) found farupstream in the tobacco (N.p.) CAB gene (cab-E) promoter; Confermaximum levels of photoregulated expression;PREcabCABphotoregulated geneslight-regulated geneslightleafshoot#tobacco (Nicotiana plumbaginifolia)UCastresana C, Garcia-Luque I, Alonso E, Malik VS, Cashmore ARTerzaghi WB, Cashmore AR�Both positive and negative regulatory elements mediate expressionof a photoregulated CAB gene from Nicotiana plumbaginifolia.Light-regulated transcriptionPEMBO J 7:1929-1936 (1988)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)!PubMed: 2901343; GenBank: X12512;Review ACCGGCCCACTT PROLAMINBOXS000091 15-Oct-1999 (last modified) kehi��"Prolamin Box"; -330 consensus sequence found in all zein genes;prolamin type consensus sequence found in the 5'upstream regionsof seed storage proteins of maize (22 kDa zein); similar sequencefound in 19 kDa zein, B-hordein (barley), gamma-gliadin (wheat),high M.W. glutenin (wheat); ESBF-1 enhanced transcriptionalactivation mediated by SPA (the endosperm-specific wheat bZIPfactor);
prolamin-boxzeinhordeingliadingluteninSPAbZIPEBESBF-1 endospermWPBFDOFseedZrice (Oryza sativa); maize (Zea mays); barley (Hordeum vulgare);wheat (Triticum aestivum);�Brown JWS, Wandelt C, Feix GMaier U-G, Brown JWS, Toloczyki C, Feix GSchmidt RJ, Ketudat M, Aukerman MJ, Hoschek GConlan RS, Hammond-Kosack M, Bevan M��The upstream regions of zein genes: sequence analysis andexpression in the unicellular green alga Acetabularia.Binding of a nuclear factor to a consensus sequence in the 5'flanking region of zein genes from maize.Opaque-2 is a transcriptional activator that recognizes aspecific target site in 22-kD zein genes.Transcription activation mediated by the bZIP factor SPA on theendosperm box is modulated by ESBF-1 in vitrojEur J Cell Biol 42:161-170 (1986)EMBO J 6:17-22 (1987)Plant Cell 4:689-700 (1992)Plant J 19:173-181 (1999)2PubMed: 1392590; GenBank: M86591;PubMed: 10476064; CACATGTGTAAAGGTPROLAMINBOXOSGLUB1S000354 16-Feb-2001 (last modified) seki�"Prolamine box" found in the rice (O.s.) GluB-1 gene promoter;Involved in quantitative regulation of the GluB-1 gene; SeeS000276, S000277, S000278 (for elements in GluB-1); See S000001,S000091, S000265, S000341 (for Prolamin box);
prolamine boxGluB-1seed endospermrice (Oryza sativa)/Wu C, Washida H, Onodera Y, Harada K, Takaiwa F�Quantitative nature of the Prolamin-box, ACGT and AACA motifs ina rice glutelin gene promoter: minimal cis-element requirementsfor endosperm-specific gene expressionPlant J 23: 415-421 (2000)PubMed: 10929134; TGCAAAG PROXBBNNAPAS000263 16-Feb-2001 (last modified) seki��"prox B (proximal portion of B-box) found in napA gene ofBrassica napus (B.n.); CA-rich sequence; Found between -130 and-124; Required for seed specific expression and ABAresponsiveness; See S000262, S000264; dist B ABRE mediatedtransactivation by ABI3 adn ABI3-dependent response to ABA; atetramer of the composite RY/G complex mediated onlyABA-independent transactivation by ABI3; B2 domain of ABI3 isnecessary for ABA-independent and ABA-dependent activationthrough the dist B ABRE;ABREABAprox BB-boxseednapAnapinBrassica napus|Ezcurra I, Ellerstrom M, Wycliffe P, Stalberg K, Rask LBusk PK, Pages MEzcurra I, Wycliffe P, Nehlin L, Ellerstrom M, Rask L��Interaction between composite elements in the napA promoter: boththe B-box ABA-responsive complex and the RY/G complex arenecessary for seed-specific expressionRegulation of abscisic acid-induced transcriptionTransactivation of the Brassica napus napin promoter by ABI3requires interaction of the conserved B2 and B3 domains of ABI3with different cis-elements: B2 mediates activation through anABRE, whereas B3 interacts with an RY/G-boxYPlant Mol Biol 40:699-709 (1999)Plant Mol Biol 37:425-435 (1998)Plant J 24:57-66 (2000)1PubMed: 10480393PubMed: 9617810;PubMed: 11029704; CAAACACCPSREGIONZMZM13S000253 11-Oct-1999 (last modified) kehiSPollen specific (PS) region in maize (Z.m.) ZM13 gene promoter;Found at -84 to -53;pollenZM13maize (Zea mays)'Hamilton DA, Schwarz YH, Mascarenhas JP^A monocot pollen-specific promoter contains separablepollen-specific and quantitative elements!Plant Mol Biol 38:663-669 (1998)PubMed: 9747811; TCGGCCACTATTTCTACGGGCAGCCAGACAAAPYRIMIDINEBOXHVEPB1S000298 10-Feb-2000 (last modified) seki�"Pyrimidine box" found in the barley (H.v.) EPB-1 (cysteineproteinase) gene promoter; Located between -120 to -113; Requiredfor GA induction; See S000297, S000259;EPBcysteine proteinaseGAABAGAREpyrimidine boxseedaleuronebarley (Hordeum vulgare)!Cercos M, Gomez-Cadenas A, Ho THD�Hormonal regulation of a cysteine proteinase gene, EPB-1, inbarley aleurone layers: cis- and trans-acting elements involvedin the co-ordinated gene expression regulated by gibberellins andabscisic acidPlant J 19: 107-118 (1999)PubMed: 10476058 TTTTTTCCPYRIMIDINEBOXOSRAMY1AS000259#19-August-2004 (last modified) kehi�VPyrimidine box found in rice (O.s.) alpha-amylase (RAmy1A) gene;Gibberellin-respons cis-element of GARE and pyrimidine box arepartially involved in sugar repression; Found in the promoter ofbarley alpha-amylase (Amy2/32b) gene which is induced in thealeurone layers in response to GA; BPBF protein bindsspecifically to this site; See S000265;
alpha-amylasesugar repressionGAREpyrimidine box feed-backmetabolic repressionembryoseedDofBPBFpbf.rice (Oryza sativa); barley (Hordeum vulgare);uMorita A, Umemura T, Kuroyanagi M, Futsuhara Y, Perata P,Yamaguchi JMena M, Cejudo FJ, Isabel-Lamoneda I, Carbonero P�Functional dissection of a sugar-repressed alpha-amylase gene(Ramy1A) promoter in rice embryosA Role for the DOF Transcription Factor BPBF in the Regulation ofGibberellin-Responsive Genes in Barley Aleurone<FEBS Lett 423:81-85 (1998)Plant Physiol. 130: 111-119 (2002)!PubMed: 9506846;PubMed: 12226491; CCTTTT QARBNEXTAS000244 11-0ct-1999 (last modified) kehid"QAR (quantitative activator region)" in promoter region ofBrassica napus (B.n.) extA extensin gene;extextensinBrassica napusElliott KA , Shirsat AH{Promoter regions of the extA extensin gene from Brassica napuscontrol activation in response to wounding and tensile stress!Plant Mol Biol 37:675-687 (1998)PubMed: 9687071; AACGTGTQELEMENTZMZM13S000254 11-Oct-1999 (last modified) kehi�"Q(quantitative)-element" in maize (Z.m.) ZM13 gene promoter;Found at -107 to -102; Involved in expression enhancing activity;ZM13 is a maize homolog of tomato LAT52 gene; ZM13 is apollen-specific maize gene; enhancingZM13LAT52pollenmaize (Zea mays)'Hamilton DA, Schwarz YH, Mascarenhas JP^A monocot pollen-specific promoter contains separablepollen-specific and quantitative elements!Plant Mol Biol 38:663-669 (1998)PubMed: 9747811; AGGTCARAV1AATS000314 7-Sep-2000 (last modified) seki��Binding consensus sequence of Arabidopsis (A.t.) transcriptionfactor, RAV1; RAV1 specifically binds to DNA with bipartitesequence motifs of RAV1-A (CAACA) and RAV1-B (CACCTG); RAV1protein contain AP2-like and B3-like domains; The AP2-like andB3-like domains recognize the CAACA and CACCTG motifs,respectively; The expression level of RAV1 were relatively highin rosette leaves and roots; See S000315(CACCTG);RAV1AP2VP1B3rootleafshoot"Arabidopsis (Arabidopsis thaliana) Kagaya Y, Ohmiya K, Hattori T�RAV1, a novel DNA-binding protein, binds to bipartite recognitionsequence through two distinct DNA-binding domains uniquely foundin higher plants$Nucleic Acids Res 27: 470-478 (1999)PubMed: 9862967; CAACARAV1BATS000315 7-Sep-2000 (last modified) seki��Binding consensus sequence of an Arabidopsis (A.t.) transcriptionfactor, RAV1; RAV1 specifically binds to DNA with bipartitesequence motifs of RAV1-A (CAACA) and RAV1-B (CACCTG); RAV1protein contain AP2-like and B3-like domains; The AP2-like andB3-like domains recognize the CAACA and CACCTG motifs,respectively; The expression level of RAV1 were relatively highin rosette leaves and roots; See S000314(CAACA);RAV1AP2VP1B3rootleafshoot"Arabidopsis (Arabidopsis thaliana) Kagaya Y, Ohmiya K, Hattori T�RAV1, a novel DNA-binding protein, binds to bipartite recognitionsequence through two distinct DNA-binding domains uniquely foundin higher plants$Nucleic Acids Res 27: 470-478 (1999)PubMed: 9862967; CACCTG
RBCSBOX2PSS000094 15-Oct-1999 (last modified) kehi�G"rbcS box II"; 5' upstream region (-151) of pea (P.s.) rbcS gene;Binding with trans factor GT-1; one of GT-1 boxes; For acompilation of related GT elements and factors, see Villain etal. (1996); GT-1 may act as a molecular switch modulated bycalcium-dependent phosphorylation and dephosphorylation inresponse to light signals;rbcSbox IIGT-1 boxGT-1lightLREleafshootpea (Pisum sativum)�� Fluhr R, Kuhlemeier C, Nagy F, Chua N-HGreen PJ, Yong M-H, Cuozzo M, Kano-Murakami Y, Silverstein P,Chua N-HGilmartin PM, Sarokin L, Memelink J, Chua N-HVillain P, Mache R, Zhou DXMarechal E, Hiratsuka K, Delgado J, Nairn A, Qin J, Chait BT,Chua NHZhou DX��Organ-specific and light-induced expression of plant genes.Binding site requirements for pea nuclear protein factor GT-1correlate with sequences required for light-dependenttranscriptional activation of the rbcS-3A gene.Molecular light switches for plant genes.The mechanism of GT element-mediated cell type-specifictranscriptional controlModulation of GT-1 DNA-binding activity by calcium-dependentphosphorylationRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�Science 232:1106-1112 (1986)EMBO J 7:4035-4044 (1988)Plant Cell 2:369-378 (1990)J Biol Chem 271:32593-32598 (1996)Plant Mol Biol 40:373-386 (1999)Trends in Plant Science 4:210-214 (1999)APubMed: 3243271;PubMed: 2152164;PubMed: 8955086;PubMed: 10437822;ReviewGTGTGGTTAATATG
RBCSBOX3PSS000095 17-May-1998 (last modified) kehi�"rbcS box III"; 5' upstream region (-114) of pea (P.s.) rbcSgene; binding with trans factor GT-1; one of GT-1 boxes; For acompilation of related GT elements and factors, see Villain etal. (1996);rbcSbox IIIGT-1 boxGT-1leafshootpea (Pisum sativum)�Fluhr R, Kuhlemeier C, Nagy F, Chua N-HGreen PJ, Yong M-H, Cuozzo M, Kano-Murakami Y, Silverstein P,Chua N-HGilmartin PM, Sarokin L, Memelink J, Chua N-HVillain P, Mache R, Zhou DX�SOrgan-specific and light-induced expression of plant genes.Binding site requirements for pea nuclear protein factor GT-1correlate with sequences required for light-dependenttranscriptional activation of the rbcS-3A gene.Molecular light switches for plant genes.The mechanism of GT element-mediated cell type-specifictranscriptional controlrScience 232:1106-1112 (1986)EMBO J 7:4035-4044 (1988)Plant Cell 2:369-378 (1990)J Biol Chem 271:32593-32598 (1996)0PubMed: 3243271;PubMed: 2152164;PubMed: 8955086; ATCATTTTCACT
RBCSCONSENSUSS000127 17-May-1998 (last modified) kehi7"rbcS general consensus sequence"; AATCCAA or AATCCAAC;rbcSG boxI boxleafshoot�tomato (Lycopersicon esculentum); petunia (Petunia hybrida);tobacco (Nicotiana tabacum); pea (Pisum sativum); soybean(Glycine max);,Manzara T, Gruissem WDonald RGK, Cashmore AR�Organization and expression of the genes encodingribulose-1,5-bisphosphate carboxylase in higher plants.Mutation of either G box or l box sequences profoundly affectsexpression from the Arabidopsis rbcS-1A promoter.9Photosynth Res 16:117-139 (1988)EMBO J 9:1717-1726 (1990)PubMed: 2347304; AATCCAA
RBCSGBOXPSS000096 17-May-1998 (last modified) kehis"rbcS G-box"; 5'upstream region (-211) of pea rbcS gene; bindingwith trans factor GBF (CG-1); Light-responsiveness;rbcSG-boxG boxGBFCG-1lightleafshootpea (Pisum sativum);-Gilmartin PM, Sarokin L, Memelink J, Chua N-H)Molecular light switches for plant genes.Plant Cell 2:369-378 (1990)PubMed: 2152164; CACATGGCACTRBENTGA3S000358 16-Feb-2001 (last modified) seki�"rbe (RSG binding element)" found in the tobacco (N.t.) GA3 genepromoter; Binding site of RSG (Repression of shoot growth); RSGis a bZIP transcriptional activator; RSG regulates the morphologyof plants by controlling the endogenous amounts of GAs;RSGrberbeGA3bZIPGA3 gibberellinleafshoottobacco (Nicotiana tabacum)@Fukazawa J, Sakai T, Ishida S, Yamaguchi I, Kamiya Y, TakahashiY~Repression of shoot growth, a bZIP transcriptional activator,regulates cell elongation by controlling the level ofgibberellins Plant Cell 12: 901-915 (2000)PubMed: 10852936; TCCAACTTGGA
RE1ASPHYA3S000195 17-May-1998 (last modified) kehi�RE1 (putative repressor element) responsible for Pfr-directedrepression of oat (A.s.) phyA3 phytochrome gene; Also found inpea AS1 (asparagine synthetase) gene (Ngai, Tsai, Coruzzi: PlantJ 12:1021-1234 (1997));light
repressionphyphyAleafshoot(oat (Avena sativa); pea (Pisum sativum);5Bruce WB, Deng XW, Quail PHNgai N, Tsai FY, Coruzzi G�A negatively acting DNA sequence element mediatesphytochrome-directed repression of phyA gene transcriptionLight-induced transcriptional repression of the pea AS1 gene:identification of cis-elements and transfactors5EMBO J 10:3015-3024 (1991)Plant J 12:1021-1034 (1997) PubMed: 1915276;PubMed: 9418044; CATGGGCGCGGREALPHALGLHCB21S000362 16-Feb-2001 (last modified) seki�"REalpha" found in Lemna gibba Lhcb21 gene promoter; Located at-134 to -129; Binding site of proteins of whole-cell extracts;The DNA binding activity is high in etiolated plants but muchlower in green plants; Required for phytochrome regulation; SeeS000363;REalphaLhcb21 phytochromeREbeta Lemna gibbaDegenhardt J, Tobin EM�A DNA binding activity for one of two closely defined phytochromeregulatory elements in an Lhcb promoter is more abundant inetiolated than in green plantsPlant Cell 8: 31-41 (1996)PubMed: 8597658; AACCAAREBETALGLHCB21S000363 16-Feb-2001 (last modified) seki�"REbeta" found in Lemna gibba Lhcb21 gene promoter; Located at-114 to -109; A GATA sequence created at a position sixnucleotides upstream could replace the function of REbeta;Required for phytochrome regulation; See S000362;REalphaLhcb21 phytochromeREbeta Lemna gibbaDegenhardt J, Tobin EM�A DNA binding activity for one of two closely defined phytochromeregulatory elements in an Lhcb promoter is more abundant inetiolated than in green plantsPlant Cell 8: 31-41 (1996)PubMed: 8597658; CGGATA
REGION1OSOSEMS000300 16-Feb-2001 (last modified) seki�"region 1" ABRE-like sequence found in rice (O.s.) Osem genepromoter; Important for regulation by ABA; See S000102, S000299;TRAB1, bZIP transcription factor, interacts with VP1 and mediatesabscisic acid-induced transcritption;ABREEmOsemABAVP1seedrice (Oryza sativa);Hattori T, Terada t, Hamasuna SHobo T, Kowyama Y, Hattori T�Regulation of the Osem gene by abscisic acid and thetranscriptional activator VP1: analysis of cis-acting promoterelements required for regulation by abscisic acid and VP1A bZIP factor, TRAB1, interacts with VP1 and mediates abscisicacid-induced transcriptionFPlant J 7: 913-925 (1995)Proc Natl Acad Sci USA 96: 15348-15353 (1999)1PubMed: 7599651; GenBank: U22102PubMed: 10611387; CGGCGGCCTCGCCACGRGATAOSS000191 17-May-1998 (last modified) kehi�
R-GATA (GATA motif binding factor) binding site; GATA motif isfound at -143 to -135 of RTBV promoter; GATA motif is requiredfor phloem-specific gene expression of Rice Tungro BacilliformVirus (RTBV); See also RNFG1OS (S000188), RNFG2OS (S000189), andABFOS (S000190);GATAphloemRTBVR-GATAstemphloem9rice (Oryza sativa); RTBV; rice tungro bacilliform virus;Yin Y, Chen L, Beachy R\Promoter elements required for phloem-specific gene expressionfrom the RTBV promoter in ricePlant J 12:1179-1188 (1997)PubMed: 9418055; CAGAAGATARNFG1OSS000188 17-May-1998 (last modified) kehi�RNFG1 binding site; Box I; RNFG1 is one of two Rice NuclearFactors required for phloem-specific gene expression of RiceTungro Bacilliform Virus (RTBV); Box I is found at -3 to +8 ofRTBV promoter; See also RNFG2OS (S000189);RNFG1phloemRTBVstemphloemrice (Oryza sativa);Yin Y, Beachy RN|The regulatory regions of the rice tungro bacilliform viruspromoter and interacting nuclear factors in rice (Oryza sativaL.)Plant J 7:969-980 (1995)PubMed: 7599653; GATCATCGATCRNFG2OSS000189!12-Apri-2004 (last modified) kehi�hRNFG2 binding site; Box II; RNFG2 is one of two Rice NuclearFactors required for phloem-specific gene expression of RiceTungro Bacilliform Virus (RTBV); Box II is found at -53 to -39 ofRTBV promoter; See also RNFG1OS (S000188); "Box II" is thebinding site of bZIP protein RF2a and RF2b; RF2a and RF2b arepredominantly expressed in vascular tissue (Dai et al.);
RNFG1phloemRTBVBox IIstemphloemRF2aRF2bbZIPvascularrice (Oryza sativa);IYin Y, Beachy RNYin Y, Chen L, Beachy RDai S, Zhang Z, Chen S, Beachy RN.�TThe regulatory regions of the rice tungro bacilliform viruspromoter and interacting nuclear factors in rice (Oryza sativaL.)Promoter elements required for phloem-specific gene expressionfrom the RTBV promoter in riceRF2b, a rice bZIP transcription activator, interacts with RF2aand is involved in symptom development of rice tungro disease.^Plant J 7:969-980 (1995)Plant J 12:1179-1188 (1997)Proc Natl Acad Sci U S A. 101:687-92.(2004)1PubMed: 7599653;PubMed: 9418055;PubMed: 14704272; CCAGTGTGCCCCTGGROOTMOTIFTAPOX1S000098 13-Feb-2001 (last modified) kehi&Motif found both in promoters of rolD;rootrolDAgrobacterium rhizogenes;Elmayan T, Tepfer M�Evaluation in tobacco of the organ specificity and strength ofthe rol D promoter, domain A of the 35S promoter and the 35S^2promoter Transgenic Res 4:388-396 (1995)PubMed: 7581519;Sequence similarity;ATATT RSEPVGRP1S000099 13-Feb-2001 (last modified) kehii"RSE (root-specific element)" of bean (P.v.) GRP1.8 gene;consensus sequence;See also S000288 and S000289;rootGRP1.8bean (Phaseolus vulgaris)Elmayan T, Tepfer M�Evaluation in tobacco of the organ specificity and strength ofthe rol D promoter, domain A of the 35S promoter and the 35S^2promoter. Transgenic Res 4:388-396 (1995)PubMed: 7581519; CAACTTTCATAT
RSEPVGRP18S000289 10-Feb-2000 (last modified) seki�"RSE (root-specific element)" found in bean (P.V.) grp1.8 genepromoter; Located at -98 to -73; Required also forvascular-specific expression in stem; See S000288, S000099;RSEgrp1.8vascularrootstemshootbean (Phaseolus vulgaris)Keller B, Heierli D�Vascular expression of the grp1.8 promoter is controlled by threespecific regulatory elements and one unspecific activatingsequence!Plant Mol Biol 26: 747-756 (1994)PubMed: 7948928 CATCCAACTTTCATATCCATGTGCTT RSRBNEXTAS000243 11-0ct-1999 (last modified) kehi["RSR (root specific region)" in promoter region of Brassica napus(B.n.) extA extensin gene;rootBrassica napusElliott KA , Shirsat AH{Promoter regions of the extA extensin gene from Brassica napuscontrol activation in response to wounding and tensile stress!Plant Mol Biol 37:675-687 (1998)PubMed: 9687071; CAAACTCGTATATCCAT RYREPEAT4S000010 16-Feb-2001 (last modified) seki�o"RY repeat motif"; "Sph element"; seed expression; ABA; Gene:maize C1, wheat Em, rice rab16A, maize Rab17; Transacting factor:VP1 (maize C1); See S000105 RYREPEAT2 (CATGCAT); The RY sequencemotif does not play a major role in VP1 or ABA regulation of Emgene in protoplast; VP1 gene is specifically required forexpression of the maturation program in seed development;RY motifC1EmRab17seedABAVP1 Sph element@maize (Zea mays); wheat (Triticum aestivum); rice (Oryza sativa)�Hattori T, Vasil V, Rosenkrans L, Hannah LC, McCarty DR, VasilIKThomas TLBusk PK, Pages MVasil V, Marcotte Jr. WR, Rosenkrans L, Cocciolone SM, Vasil IK,Quatrano RS, McCarty DRMcCarty DR, Hattori T, Carson CB, Vasil V, Lazar M, Vasil IK��The Viviparous-1 gene and abscisic acid activate the C1regulatory gene for anthocyanin biosynthesis during seedmaturation in maize.Gene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcriptionOverlap of viviparous1 (VP1) and abscisic acid response elementsin the EM promoter: G-Box elements are sufficient but notnecessary for VP1 transactivationThe Viviparous-1 developmental gene of maize encodes a noveltranscriptional activator�Genes Dev 6:609-618 (1992)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998)Plant Cell 7: 1511-1518 (1995)Cell 66: 895-905 (1991)NPubMed: 1532784;PubMed: 8281041;PubMed: 9617810PubMed: 8589631PubMed: 1889090; ReviewReview
TCCATGCATGCACRYREPEATBNNAPAS000264 16-Feb-2001 (last modified) seki��"RY repeat" found in RY/G box (the complex containing the two RYrepeats and the G-box) of napA gene in Brassica napus (B.n.);Found between -78 and -50; Required for seed specific expression;See S000262, S000263; dist B ABRE mediated transactivation byABI3 adn ABI3-dependent response to ABA; a tetramer of thecomposite RY/G complex mediated only ABA-independenttransactivation by ABI3; B2 domain of ABI3 is necessary forABA-independent and ABA-dependent activation through the dist BABRE; RY repeatRY/G boxseednapAnapinBrassica napuslEzcurra I, Ellerstrom M, Wycliffe P, Stalberg K, Rask LEzcurra I, Wycliffe P, Nehlin L, Ellerstrom M, Rask L��Interaction between composite elements in the napA promoter: boththe B-box ABA-responsive complex and the RY/G complex arenecessary for seed-specific expressionTransactivation of the Brassica napus napin promoter by ABI3requires interaction of the conserved B2 and B3 domains of ABI3with different cis-elements: B2 mediates activation through anABRE, whereas B3 interacts with an RY/G-box8Plant Mol Biol 40:699-709 (1999)Plant J 24:57-66 (2000)"PubMed: 10480393;PubMed: 11029704; CATGCA
RYREPEATGMGY2S000105 11-May-2006 (last modified) kehi_"RY repeat motif (CATGCAT)"; Present in the 5' region of thesoybean (G.m.) glycinin gene (Gy2);glycininCATGCATGy2seedsoybean (Glycine max);%Lelievre J-M, Oliveira LO, Nielsen NC@5'-CATGCAT-3' elements modulate the expression of glyciningenes. Plant Physiol 98:387-391 (1992)PubMed: 16668640 CATGCATRYREPEATVFLEB4S000102#01-August-2006 (last modified) kehi��"RY repeat motif"; quantitative seed expression; Gene: Vicia fabaLeB4; Soybean glycinin (Gy2); other dicot and monocot seedprotein genes; "Sph box" found in rice (O.s.) Osem gene promoter;See S000010, S000299, S000300; Binding site of ArabidopsisB3-domain-containing transcription factor FUS3; TRAB1, bZIPtranscription factor, interacts with VP1 and mediates abscisicacid-induced transcritption; FUS3 protein physically interactwith two RY elements present in the AtGA3ox promoter (Curaba etal., 2004);RY repeat motifLeB4Gy2seedSphABAVP1OsemEmABREFUS3embryoB3GAubean (Phaseolus vulgaris); soybean (Glycine max); Vicia faba;rice (Oryza sativa); Arabidopsis (Arabidopsis thaliana);�'Nag R, Maity MK, Dasgupta M.Baumlein H, Nagy I, Villarroel R, Inze D, Wobus UThomas TLHattori T, Terada t, Hamasuna SReidt W, Wohlfarth T, Ellerstrom M, Czihal A, Tewes A, Ezcurra I,Rask L, Baumlein HHobo T, Kowyama Y, Hattori TCuraba J, Moritz T, Blervaque R, Parcy F, Raz V, Herzog M, VachonG.�zDual DNA binding property of ABA insensitive 3 like factorstargeted to promoters responsive to ABA and auxin.Cis-analysis of a seed protein gene promoter: the conservative RYrepeat CATGCATG within the legumin box is essential fortissue-specific expression of a legumin gene.Gene expression during plant embryogenesis and germination: Anoverview.Regulation of the Osem gene by abscisic acid and thetranscriptional activator VP1: analysis of cis-acting promoterelements required for regulation by abscisic acid and VP1Gene regulation during late embryogenesis: the RY motif ofmaturation-specific gene promoters is a direct target of the FUS3gene productA bZIP factor, TRAB1, interacts with VP1 and mediates abscisicacid-induced transcriptionAtGA3ox2, a Key Gene Responsible for Bioactive GibberellinBiosynthesis, Is Regulated during Embryogenesis by LEAFYCOTYLEDON2 and FUSCA3 in Arabidopsis.�Plant Mol Biol. 59: 821-838 (2005).Plant J 2:233-239 (1992)Plant Cell 5:1401-1410 (1993)Plant J 7: 913-925 (1995)Plant J 21: 401-408 (2000)Proc Natl Acad Sci USA 96: 15348-15353 (1999)Plant Physiol. 136: 3660-3669. (2004)�PubMed: 16270233PubMed: 1338774;PubMed: 8281041;PubMed: 7599651; GenBank: U22102PubMed: 10758492;PubMed: 10611387;PubMed: 15516508ReviewCATGCATGS1FBOXSORPS1L21S000223 10-May-1998 (last modified) kehi� "S1F box" conserved both in spinach (S.o.) RPS1 and RPL21 genesencoding the plastid ribosomal protein S1 and L21, respectively;Negative element; Might play a role in downregulating RPS1 andRPL21 promoter activity (Lagrange et al., 1993); See S000211(SITE1SORPS1), S000215 (S1FSORPL21); S1FS1F boxS1F-boxS1plastid proteinRPS1RPL21leafnegativespinach (Spinacia oleracea)[Zhou DX, LI YF, Rocipon M, Mache RLagrange T, Franzetti B, Axelos M, Mache R, Lerbs-Mache S�(Sequence specific interaction between S1F, a spinach nuclearfactor, and a negative cis-element conserved in plastid-relatedgenesStructure and expression of the nuclear gene encoding for thechloroplast ribosomal protein L21: Developmental regulation of ahouse-keeping gene by alternative promotersCJ Biol Chem 267:23515-23519 (1992)Mol Cell Biol 13:2614-2622 (1993)1PubMed: 1429696;PubMed: 8455634; GenBank: M64682; ATGGTA
S1FSORPL21S000215#19-August-2004 (last modified) kehi�� "S1F binding site" ("S1 site") in spinach (S.o.) RPL21 geneencoding the plastid ribosomal protein L21; Negative element;Might play a role in downregulating RPL21 promoter activity(Lagrange et al., 1993); See S000211 (SITE1SORPS1), S000166(S2FSORPL21);S1FS1plastid proteinRPL21leafnegativespinach (Spinacia oleracea)�Zhou DX, LI YF, Rocipon M, Mache RLagrange T, Franzetti B, Axelos M, Mache R, Lerbs-Mache SLagrange T, Gauvin S, Yeo HJ, Mache R��Sequence specific interaction between S1F, a spinach nuclearfactor, and a negative cis-element conserved in plastid-relatedgenesStructure and expression of the nuclear gene encoding for thechloroplast ribosomal protein L21: Developmental regulation of ahouse-keeping gene by alternative promotersS2F, a leaf-specific trans-acting factor, binds to a novelcis-acting element and differentially activates the RPL21 gene`J Biol Chem 267:23515-23519 (1992)Mol Cell Biol 13:2614-2622 (1993)Plant Cell 9:1469-1479 (1997)APubMed: 1429696;PubMed: 8455634; GenBank: M64682;PubMed: 9286115; ATGGTATT
S2FSORPL21S000166 17-May-1998 (last modified) kehi��"S2F binding site" ("S2 site") in spinach RPL21 gene encoding theplastid ribosomal protein L21; S2 site (CATACAWW) is conserved inpromoter region of many nuclear genes encoding plastid proteins;Leaf-specific, light-independent regulatory element; S2 site isrelated to but different from the light-responsive GT-1 bindingsite (Lagrange et al., 1997); For a compilation of related GTelements and factors, see Villain et al. (1996);
S2FS2plastid proteinRPL21
leaf-specificlight-independentlight
GT elementleafshoot spinach (Spinacia oleracea);@Lagrange T, Gauvin S, Yeo HJ, Mache RVillain P, Mache R, Zhou DX�S2F, a leaf-specific trans-acting factor, binds to a novelcis-acting element and differentially activates the RPL21 gene.The mechanism of GT element-mediated cell type-specifictranscriptional control?Plant Cell 9:1469-1479 (1997)J Biol Chem 271:32593-32598 (1996) PubMed: 9286115;PubMed: 8955086; CCATACATTSARECAMVS000156 16-Jan-1998 (last modified) kehi�Salicylic acid responsive element found in CaMV 35S promoter;Identical to as-1; Binding with ASF-1 (Activation SequenceFactor-1); See AS1 (S000023);Salicylic acidSAREas-1 CaMV; Cauliflower mosaic virus;\Qin X-F, Holuigue L, Horvath DM, Chua N-HStange C, Ramirez I, Gomez I, Jordana X, Holuigue L�Immediate early transcription activation by salicylic acid viathe cauliflower mosaic virus as-1 element.Phosphorylation of nuclear proteins directs binding to salicylicacid-responsive elements.6Plant Cell 6:863-874 (1994)Plant J 11:1315-1324 (1997) PubMed: 8061520;PubMed: 9225470; CTGACGTAAGGGATGACGCAC SB1NPABC1S000435 27-Jan-2004 (last modified) kehi�Sclareol box1 (SB1) found at -827 of a plasma membrane ATPbinding cassette (ABC) transporter gene (NpABC1) in N.plumbaginifolia; Mutation in SB3 completely abolishedsclareolide-mediated expression; See S ; scalareol diterpeneABC transporter$Nicotiana plumbaginifolia (tobacco);8Grec S, Vanham D, de Ribaucourt J, Purnelle B, Boutry P.�Identification of regulatory sequence elements within thetranscription promoter region of NpABC1, a gene encoding a plantABC transporter induced by diterpenes.Plant J. 35: 237-250 (2003)PubMed: 12848828; CACTAACACAAAGTAA SB3NPABC1S000434 27-Jan-2004 (last modified) kehi�Sclareol box3 (SB3) found at -216 of a plasma membrane ATPbinding cassette (ABC) transporter gene (NpABC1) in N.plumbaginifolia; Mutation in SB3 completely abolishedsclareolide-mediated expression; See S ;sclareolABC transporterSB3$Nicotiana plumbaginifolia (tobacco);8Grec S, Vanham D, de Ribaucourt J, Purnelle B, Boutry P.�Identification of regulatory sequence elements within thetranscription promoter region of NpABC1, a gene encoding a plantABC transporter induced by diterpenes.Plant J. 35: 237-250 (2003)PubMed: 12848828; TTATGAACAGTAATT
SBOXATRBCSS000500#04-August-2006 (last modified) kehi�"S-box" conserved in several rbcS promoters in Arabidopsis; ABI4binding site; "Important for the sugar and ABA responsiveness ofCMA5"(Acevedo-Hernandez et al., 2005);rbcSsugarABAABI4Arabidopsis thaliana2Acevedo-Hernandez GJ, Leon P, Herrera-Estrella LR.jSugar and ABA responsiveness of a minimal RBCS light-responsiveunit is mediated by direct binding of ABI4.Plant J. 43:506-519 (2005).PubMed: 160981050in silico; Electrophoretic mobility shift assay;CACCTCCA
SE1PVGRP18S000288 10-Feb-2000 (last modified) seki�"SE1 (Stem element 1)" found in the bean (P.v.) grp1.8 genepromoter; Located between -121 and -94; Enhances the expressionstrongly but unspecifically; See S000289, S000101 (SE2);SE1grp1.8vascularstemshootbean (Phaseolus vulgaris)Keller B, Heierli D�Vascular expression of the grp1.8 promoter is controlled by threespecific regulatory elements and one unspecific activatingsequence!Plant Mol Biol 26: 747-756 (1994)PubMed: 7948928 ATAATGGGCCACACTGTGGGGCAT SEF3MOTIFGMS000115 17-May-1998 (last modified) kehi�"SEF3 binding site"; Soybean (G.m.) consensus sequence found inthe 5' upstream region of beta-conglycinin (7S globulin) gene;AACCCA(-27bp-)AACCCA; SEF=soybean embryo factor; SEF2; SEF3;SEF4;SEF3beta-conglycinin7Sglobulinseedsoybean (Glycine max);lAllen RD, Bernier F, Lessard PA, Beachy RNLessard PA, Allen RD, Bernier F, Crispino JD, Fujiwara T, BeachyRN�Nuclear factors interact with a soybean beta-conglycininenhancer.Multiple nuclear factors interact with upstream sequences ofdifferentially regulated beta-conglycinin genes.;Plant Cell 1:623-631 (1989)Plant Mol Biol 16:397-413 (1991) PubMed: 2535514;PubMed: 1893110; AACCCA
SGBFGMGMAUX28S000287 10-Feb-2000 (last modified) sekiabZIP proteins SGBF-1 and SGBF-2 binding site in soybean (G.m.)GmAux28 gene promoter; see S000042;Aux28G boxauxinbZIPSGBF-1SGBF-2soybean (Glycine max)5Hong JC, Cheong YH, Nagao RT, Bahk JD, Key JL, Cho MJoIsolation of two soybean G-box binding factors which interactwith a G-box sequences of an auxin-responsive genePlant J 8: 199-211 (1995)0PubMed: 7670504; GenBank: L01447, L01448, L01449
TCCACGTGTC SITE1SORPS1S000211 11-May-2006 (last modified) kehi��Site 1 in the spinach (S.o.) rps1 promoter; S1F binding site;Nuclear genes encoding plastid ribosomal proteins are more highlyexpressed in leaves than in root; Involved in leaf-specificinduction; Seems to be light-independent; Involved in negativeregulation; Related to the light-responsive Box II of the pearbcs-3A promoter; Related to GT elements; For a compilation ofrelated GT elements and factors, see Villain et al. (1996); SeeS000215 (S1FSORPL21); S1 box=ATGGTA;Site 1rps1ribosomal proteinS1Fleaf
leaf-specific
repressionnegative spinach (Spinacia oleracea);kZhou DX, Li YF, Rocipon M, Mache RVillain P, Clabault G, Mache R, Zhou DXVillain P, Mache R, Zhou DXZhou DX��Sequence-specific interaction between S1F, a spinach nuclearfactor, and a negative cis-element conserved in plastid-relatedgenesS1F binding site is related to but different from thelight-responsive GT-1 binding site and differentially repressesthe spinach rps1 promoter in transgenic tobaccoThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�J Biol Chem 267:23515-23519 (1992)J Biol Chem 269:16626-16630 (1994)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)@PubMed: 1429696;PubMed: 8206981;PubMed: 8955086;PubMed: 10366876ReviewTCATGGTAACAATT SITE3SORPS1S000212 11-May-2006 (last modified) kehi�Site 3 of spinach (S.o.) rps1 promoter; S1F binding site; For acompilation of related GT elements and factors, see Villain etal. (1996);Site 3rps1S1Fspinach (Spinacia oleracea)IVillain P, Clabault G, Mache R, Zhou DXVillain P, Mache R, Zhou DXZhou DX�>S1F binding site is related to but different from thelight-responsive GT-1 binding site and differentially repressesthe spinach rps1 promoter in transgenic tobaccoThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorsmJ Biol Chem 269:16626-16630 (1994)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)0PubMed: 8206981;PubMed: 8955086;PubMed: 10366876ReviewAGTTAGTTAAAAGA
SITEIIAOSPCNAS000216 11-May-2006 (last modified) kehi�h"Site IIa" of rice (O.s.) PCNA (proliferating cell nuclearantigen) gene; Found at -197 to -188; Binding site for twonuclear proteins, PCF1 and PCF2 (Kosugi and Ohashi, 1997);Suggested to be involved in meristematic tissue-specificexpression; Resemble the conserved motif (T/GGTCCCAT) found inpromoter regions of auxin-regulated genes; See S000026(AUXREPSIAA4);PCNASite IIameristemtissue-specificrice (Oryza sativa)5Kosugi S, Suzuka I, Ohashi YKosugi S, Ohashi YZhou DX�FTwo of three promoter elements identified in a rice gene forproliferating cell nuclear antigen are essential for meristematictissue-specific expressionPCF1 and PCF2 specifically bind to cis elements in the riceproliferating cell nuclear antigen geneRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors^Plant J 7:877-886 (1995)Plant Cell 9:1607-1619 (1997)Trends in Plant Science 4:210-214 (1999)0PubMed: 7599648;PubMed: 9338963;PubMed: 10366876Review TGGGCCCGT
SITEIIBOSPCNAS000217 10-May-1998 (last modified) kehi�b"Site IIb" of rice PCNA (proliferating cell nuclear antigen)gene; Found at -178 to -169; Binding site for two nuclearproteins, PCF1 and PCF2 (Kosugi and Ohashi, 1997); Suggested tobe involved in meristematic tissue-specific expression; Resemblethe conserved motif (T/GGTCCCAT) found in promoter regions ofauxin-regulated genes; See S000026 (AUXREPSIAA4);PCNASite IIbmeristemtissue-specificrice (Oryza sativa).Kosugi S, Suzuka I, Ohashi YKosugi S, Ohashi Y�Two of three promoter elements identified in a rice gene forproliferating cell nuclear antigen are essential for meristematictissue-specific expressionPCF1 and PCF2 specifically bind to cis elements in the riceproliferating cell nuclear antigen gene5Plant J 7:877-886 (1995)Plant Cell 9:1607-1619 (1997) PubMed: 7599648;PubMed: 9338963; TGGTCCCAC SITEIOSPCNAS000224 10-May-1998 (last modified) kehi�"Site I" of rice (O.s.) PCNA (proliferating cell nuclear antigen)gene; Found at -201 to -194; Resemble G-box; May contribute inpart to transcriptional activation;PCNASite IG-boxmeristemrice (Oryza sativa) Kosugi S, Suzuka I, Ohashi Y�Two of three promoter elements identified in a rice gene forproliferating cell nuclear antigen are essential for meristematictissue-specific expressionPlant J 7:877-886 (1995)PubMed: 7599648; CCAGGTGG SORLIP1ATS000482%18-November-2005 (last modified) kehi��one of "Sequences Over-Represented in Light-Induced Promoters(SORLIPs) in Arabidopsis; Computationally identified phyA-inducedmotifs; SORLIP 1 is most over-represented, and most statisticallysingnificant; See also S000483, S000484, S000485, S000486 (allSORLIPs), and also S000487, S000488, S000489, S000490 (allSORLREPs); Over-represented in light-induced cotyledon and rootcommon genes and root-specific genes (Jiao et al. 2005; seeS000486);phyA phytochromelightArabidopsis thaliana8Hudson ME, Quail PH.Jiao Y, Ma L, Strickland E, Deng XW.� Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.Conservation and Divergence of Light-Regulated Genome ExpressionPatterns during Seedling Development in Rice and Arabidopsis.DPlant Physiol. 133: 1605-1616 (2003)Plant Cell. 17: 3239-3256 (2005) PubMed: 14681527PubMed: 16284311,in silico; over-represented motif;in silico;GCCAC SORLIP2ATS000483%18-November-2005 (last modified) kehi�one of "Sequences Over-Represented in Light-Induced Promoters(SORLIPs) in Arabidopsis; Computationally identified phyA-inducedmotifs; See also S000482, S000484, S000485, S000486 (allSORLIPs), and also S000487, S000488, S000489, S000490 (allSORLREPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif;GGGCC SORLIP3ATS000484%18-November-2005 (last modified) kehi�one of "Sequences Over-Represented in Light-Induced Promoters(SORLIPs) in Arabidopsis; Computationally identified phyA-inducedmotifs; See also S000482, S000483, S000485, S000486 (allSORLIPs), and also S000487, S000488, S000489, S000490 (allSORLREPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif; CTCAAGTGA SORLIP4ATS000485%18-November-2005 (last modified) kehi�one of "Sequences Over-Represented in Light-Induced Promoters(SORLIPs) in Arabidopsis; Computationally identified phyA-inducedmotifs; See also S000482, S000483, S000484, S000486 (allSORLIPs), and also S000487, S000488, S000489, S000490 (allSORLREPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif; GTATGATGG SORLIP5ATS000486%18-November-2005 (last modified) kehi�kone of "Sequences Over-Represented in Light-Induced Promoters(SORLIPs) in Arabidopsis; Computationally identified phyA-inducedmotifs; See also S000482, S000483, S000484, S000485 (allSORLIPs), and also S000487, S000488, S000489, S000490 (allSORLREPs); Over-represented in both light-inducedcotyledon-specific and root-specific genes (Jiao et al. 2005; seeS000482);phyA phytochromelightArabidopsis thaliana8Hudson ME, Quail PH.Jiao Y, Ma L, Strickland E, Deng XW.� Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.Conservation and Divergence of Light-Regulated Genome ExpressionPatterns during Seedling Development in Rice and Arabidopsis.DPlant Physiol. 133: 1605-1616 (2003)Plant Cell. 17: 3239-3256 (2005) PubMed: 14681527PubMed: 16284311,in silico; over-represented motif;in silico;GAGTGAG
SORLREP2ATS000487%18-November-2005 (last modified) kehi�� one of "Sequences Over-Represented in Light-Repressed Promoters(SORLREPs) in Arabidopsis; Computationally identifiedphyA-repressed motifs; See also S000488, S000489, S000490 (allSORLREPs); and also S000482, S000483, S000484, S000485, S000486(all SORLIPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif; ATAAAACGT
SORLREP3ATS000488%18-November-2005 (last modified) kehi�� one of "Sequences Over-Represented in Light-Repressed Promoters(SORLREPs) in Arabidopsis; Computationally identifiedphyA-repressed motifs; See also S000487, S000489, S000490 (allSORLREPs); and also S000482, S000483, S000484, S000485, S000486(all SORLIPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif; TGTATATAT
SORLREP4ATS000489%18-November-2005 (last modified) kehi�(one of "Sequences Over-Represented in Light-Repressed Promoters(SORLREPs) in Arabidopsis; Computationally identifiedphyA-repressed motifs; Common in circadian-regulated promoters;See also S000487, S000488, S000490 (all SORLREPs); and alsoS000482, S000483, S000484, S000485, S000486 (all SORLIPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif; CTCCTAATT
SORLREP5ATS000490%18-November-2005 (last modified) kehi�� one of "Sequences Over-Represented in Light-Repressed Promoters(SORLREPs) in Arabidopsis; Computationally identifiedphyA-repressed motifs; See also S000487, S000488, S000489 (allSORLREPs); and also S000482, S000483, S000484, S000485, S000486(all SORLIPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif;
TTGCATGACT
SP8BFIBSP8AIBS000183 16-Feb-2001 (last modified) seki��One of SPBF binding site (SP8a); Found at -155 of gSPO-A1(sporamin) gene, and also at -880 of gB-Amy (beta-amylase) genein sweet potato (I.b.); SP8BF recognizes both SP8a and SP8bsequences; See also SP8BFIBSP8BIB (S000184); SP8BF activity isalso found in tobacco; "SP8a" found in the 5' upstream region ofthree differnt genes coding for sporamin and beta-amylase;Binding site of SPF1; SPF1 also binds to the SP8b; See S000184;SP8SP8aSP8BFsporamin beta-amylaseamylase
tuberous rootroot sweet potato (Ipomoea batatas);,Ishiguro S, Nakamura KIshiguro S, Nakamura K�FThe nuclear factor SP8BF binds to the 5'-upstream regions ofthree different genes coding for major proteins of sweet potatotuberous rootsCharacterization of a cDNA encoding a novel DNA-binding protein,SPF1, that recognizes SP8 sequences in the 5' upstream regions ofgenes coding for sporamin and beta-amylase from sweet potato@Plant Mol Biol 18:97-108 (1992)Mol Gen Genet 244: 563-571 (1994) PubMed: 1531033;PubMed: 7969025; ACTGTGTA
SP8BFIBSP8BIBS000184 16-Feb-2001 (last modified) seki��One of SPBF binding site (SP8b); Found at -330, -220, and -200 ofgSPO-B1 (sporamin) gene, and also at -80 of gB-Amy (beta-amylase)gene; SP8BF recognizes both SP8a and SP8b sequences; See alsoSP8BFIBSP8AIB (S000183); SP8BF activity is also found in tobacco;"SP8b" found in the 5' upstream region of three differnt genescoding for sporamin and beta-amylase; Binding site of SPF1; SPF1also binds to the SP8b; See S000184; SP8SP8bSP8BFsporamin beta-a,ylaseamylase
tuberous roottuberroot sweet potato (Ipomoea batatas);,Ishiguro S, Nakamura KIshiguro S, Nakamura K�FThe nuclear factor SP8BF binds to the 5'-upstream regions ofthree different genes coding for major proteins of sweet potatotuberous rootsCharacterization of a cDNA encoding a novel DNA-binding protein,SPF1, that recognizes SP8 sequences in the 5' upstream regions ofgenes coding for sporamin and beta-amylase from sweet potato@Plant Mol Biol 18:97-108 (1992)Mol Gen Genet 244: 563-571 (1994) PubMed: 1531033;PubMed: 7969025; TACTATT SPHCOREZMC1S000154 16-Feb-2001 (last modified) seki�nCore of Sph element; Core motif of Sph element in maize (Z.m.) C1gene to which maize VP1 (viviparous 1) protein binds;VP1-responsive element; see RYREPEAT4 (S000010); VP1 gene isspecifically required for expression of the maturation program inseed development; VP1 is a novel transcription factor possiblyinvolved in potentiation of a seed-specific hormone response; Sph motifC1VP1ABAseedmaize (Zea mays);XSuzuki M, Kao CY, McCarty DRMcCarty DR, Hattori T, Carson CB, Vasil V, Lazar M, Vasil IK�The conserved B3 domain of VIVIPAROUS1 has a cooperative DNAbinding activity.The Viviparous-1 developmental gene of maize encodes a noveltranscriptional activator2Plant Cell 9:799-807 (1997)Cell 66: 895-905 (1991) PubMed: 9165754;PubMed: 1889090; TCCATGCATSPHZMC1S000293 16-Feb-2001 (last modified) seki�R"Sph element" found in the maize (Z.m.) C1 gene promoter; Locatedbetween -142 and -132; Essential for VP1 activation; See S000154,S000294; VP1 gene is specifically required for expression of thematuration program in seed development; VP1 is a noveltranscription factor possibly involved in potentiation of aseed-specific hormone response;C1anthocyanin pathwayABAVP1lightSphseedmaize (Zea mays)gKao CY, Cocciolone SM, Vasil IK, McCarty DRMcCarty DR, Hattori T, Carson CB, Vasil V, Lazar M, Vasil IK�Localization and interaction of the cis-acting elements forabscisic acid, VIVIPAROUS1, and light activation of the C1 geneof maizeThe Viviparous-1 developmental gene of maize encodes a noveltranscriptional activator5Plant Cell 8: 1171-1179 (1996)Cell 66: 895-905 (1991) PubMed: 8768375PubMed: 1889090; CGTCCATGCATSREATMSDS000470#13-August-2005 (last modified) kehi�"sugar-repressive element (SRE)" found in 272 of the 1592down-regulated genes after main stem decapitation in Arabidopsis;See also S000471, S000472;Axillary bud outgrowthArabidopsis thaliana3Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E.wIdentification of cis-elements that regulate gene expressionduring initiation of axillary bud outgrowth in Arabidopsis.$Plant Physiology 138: 757-766 (2005)PubMed: 15908603 TTATCC SRENTTTO1S000271 15-Oct-1999 (last modified) kehi� Stress responsive element (SRE) in tobacco (N.t.) retrotransposonTto1; A 13 bp cis-regulatory element in the LTR promoter of thetobacco retrotransposon Tto1; Involved in responsiveness totissue culture, wounding, methyl jasmonate and fungal elicitors;Contains a conserved motif, Box L; retrotransposonLTRTto1woundingstresstissue culturemethyl jasmonatefungal elicitorBox Ltobacco (Nicotiana tabacum)+Takeda S, Sugimoto K, Otsuki H, Hirochika H�A 13-bp cis-regulatory element in the LTR promoter of the tobaccoretrotransposon Tto1 is involved in responsiveness to tissueculture, wounding, methyl jasmonate and fungal elicitorsPlant J 18:383-393 (1999)PubMed: 10406122;
TGGTAGGTGAGAT SURE1STPAT21S000186 17-May-1998 (last modified) kehi�Sucrose Responsive Element (SURE); A motif conserved among genesregulated by sucrose; See also SURE2STPAT21 (S000185); Foundbetween -184 and -156 bp in the patatin (a major tuber protein)gene promoter of potato (S.t.);SURESURE 1patatinsucrosetuberrootpotato (Solanum tuberosum);DGrierson C, Du JS, Zabala MT, Beggs K, Smith C, Holdsworth M,Bevan M|Separate cis sequences and trans factors direct metabolic anddevelopmental regulation of a potato tuber storage protein genePlant J 5:815-826 (1994)PubMed: 8054988; AATAGAAAA SURE2STPAT21S000185 17-May-1998 (last modified) kehi�Sucrose Responsive Element 2 (SURE2); A motif conserved amonggenes regulated by sucrose; See also SURE1ST (S000186); Foundbetween -184 and -156 bp in the patatin (a major tuber protein)gene promoter of potato (S.t.);SURESURE 2patatinsucrosetuberrootpotato (Solanum tuberosum);DGrierson C, Du JS, Zabala MT, Beggs K, Smith C, Holdsworth M,Bevan M|Separate cis sequences and trans factors direct metabolic anddevelopmental regulation of a potato tuber storage protein genePlant J 5:815-826 (1994)PubMed: 8054988; AATACTAAT SUREAHVISO1S000441 28-Jan-2004 (last modified) kehi�"SURE-a"; Sugar-responsive element found in barley (H. vulgare)iso1 (encoding isoamylase1) promoter at -597 to -573; Highlysimilar to SURE of potato class-1 putative promoter; SUSIBA2(WRKY transcription factor) binding site;sugarSUREpatatinWRKY
isoamylaseSUSIBA"Hordeum vulgare (barley)@Sun C, Palmqvist S, Olsson H, Boren M, Ahlandsberg S, Jansson C.�A novel WRKY transcription factor, SUSIBA2, participates in sugarsignaling in barley by binding to the sugar-responsive elementsof the iso1 promoter. Plant Cell 15: 2076-2092 (2003)PubMed: 12953112; AAAACTAAGAAAGACCGATGGAAAASURECOREATSULTR11S000499#02-August-2006 (last modified) kehi��Core of sulfur-responsive element (SURE) found in the promoter ofSULTR1;1 high-affinity sulfate transporter gene in Arabidopsis;SURE contains auxin response factor (ARF) binding sequence(GAGACA)(see S000270 ARF:TGTCTC; its complementary seq isGAGACA), and this core sequence is a part of it; this core seq isinvolved in -S response; Beware of other SURE (sucrose responsiveelement) !!;sulfate uptakesulfate transporterARF-SSArabidopsis thalianaVMaruyama-Nakashita A, Nakamura Y, Watanabe-Takahashi A, Inoue E,Yamaya T, Takahashi H.gIdentification of a novel cis-acting element conferring sulfurdeficiency response in Arabidopsis roots. Plant J. 42: 305-314 (2005).PubMed: 15842617 GAGAC T/GBOXATPIN2S000458%29-November-2004 (last modified) kehi�"T/G-box" found in tomato proteinase inhibitor II (pin2) andleucine aminopeptidase (LAP) genes; Involved in jasmonate (JA)induction of these genes; bHLH-Leu zipper JAMYC2 and JAMYC10proteins specifically recognaize this motif (Boter et al.,2004);T/G-boxJApin2LAPMYCwounding7Lycopersicon esculentum (tomato); Arabidopsis thaliana;)Boter M, Ruiz-Rivero O, Abdeen A, Prat S.iConserved MYC transcription factors play a key role in jasmonatesignaling both in tomato and Arabidopsis. Genes Dev 18: 1577-1591 (2004).PubMed: 15231736 AACGTG TAAAGSTKST1S000387 20-Feb-2002 (last modified) uchi�TAAAG motif found in promoter of Solanum tuberosum (S.t.) KST1gene; Target site for trans-acting StDof1 protein controllingguard cell-specific gene expression; KST1 gene encodes a K+influx channel of guard cells; See S000265;KST1Dof
guard cellSolanum tuberosum (potato)&Plesch G, Ehrhardt T, Mueller-Roeber BqInvolvement of TAAAG elements suggests a role for Doftranscription factors in guard cell-specific gene expressionPlant J 28: 455-464 (2001)PubMed: 11737782; TAAAG TACBBFNTEAS4S000257 14-0ct-1999 (last modified) kehi�'TacBBF (TAC box binding factor) binding site in tobacco (N.t.)5-epi-aristolochene synthase (EAS4) gene; Required forelicitor-inducibility; EAS is involved in sesquiterpenephytoalexin biosynthesis; Found between -245 and -232; Appears tofunction as a silencer or repressor of EAS gene expression;EASelicitorTAC boxTacBBF
sesquiterpene phytoalexinsilencer repressortobacco (Nicotiana tabacum) Newman JD, Yin S, Chappell JiCharacterization of the TAC box, a cis-element within anelicitor-inducible sesquiterpene cyclase promoterPlant J 16:1-12 (1998) ACTCTACAGTACTCTATABOX1S000108"12-April-2004 (last modified) kehi�"TATA box"; TATA box found in the 5'upstream region of ricealpha-amylase; TATA box found in beta-phaseolin promoter (Graceet al.); sequence and spacing of TATA box elements are criticalfor accurate initiation (Grace et al.);amylasericeTATAseed phaseolin/rice (Oryza sativa); bean (Phaseolus vulgaris);0Grace ML, Chandrasekharan MB, Hall TC, Crowe AJ.oSequence and spacing of TATA box elements are critical foraccurate initiation from the beta-phaseolin promoter."J Biol Chem. 279:8102-8110 (2004).PubMed: 14660650
CTATAAATACTATABOX2S000109"12-April-2004 (last modified) kehi�"TATA box"; TATA box found in the 5'upstream region of pea legAgene; sporamin A of sweet potato; TATA box found inbeta-phaseolin promoter (Grace et al.); sequence and spacing ofTATA box elements are critical for accurate initiation (Grace etal.);TATAlegA phaseolinKpea (Pisum sativum); tobacco (Nicotiana tabacum); bean (Phaseolusvulgaris);WShirsat A, Wilford N, Croy R, Boulter DGrace ML, Chandrasekharan MB, Hall TC, Crowe AJ.�Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco.Sequence and spacing of TATA box elements are critical foraccurate initiation from the beta-phaseolin promoter.BMol Gen Genet 215:326-331 (1989)J Biol Chem. 279:8102-8110 (2004). PubMed: 2710102;PubMed: 14660650 TATAAATTATABOX3S000110 17-Jun-1997 (last modified) kehiS"TATA box"; TATA box found in the 5'upstream region of sweetpotato sporamin A gene;TATAsporamin sweet potato (Ipomoea batatas); TATTAATTATABOX4S000111"12-April-2004 (last modified) kehi�"TATA box"; TATA box found in the 5'upstream region of sweetpotato sporamin A gene; TATA box found in beta-phaseolin promoter(Grace et al.); sequence and spacing of TATA box elements arecritical for accurate initiation (Grace et al.);TATAsporamin phaseolin9sweet potato (Ipomoea batatas); bean (Phaseolus vulgaris)0Grace ML, Chandrasekharan MB, Hall TC, Crowe AJ.oSequence and spacing of TATA box elements are critical foraccurate initiation from the beta-phaseolin promoter."J Biol Chem. 279:8102-8110 (2004).PubMed: 14660650 TATATAATATABOX5S000203 17-May-1998 (last modified) kehi�"TATA box"; TATA box found in the 5'upstream region of pea (Pisumsativum) glutamine synthetase gene; a functional TATA element byin vivo analysis;TATA glutamine
synthetasepea (Pisum sativum); Tjaden G, Edwards JW, Coruzzi GM�cis elements and trans-acting factors affecting regulation of anonphotosynthetic light-regulated gene for chloroplast glutaminesynthetase"Plant Physiol 108:1109-1117 (1995)!PubMed: 7630938; GenBank: U22971; TTATTT TATABOXOSPALS000400 27-Aug-2002 (last modified) uchi�Binding site for OsTBP2, found in the promoter of rice pal geneencoding phenylalanine ammonia-lyase; OsTFIIB stimulated the DNAbinding and bending activities of OsTBP2 and synergisticallyenhanced OsTBP2-mediated transcription from the pal promoter;TBPTFIIBpalDNA binding and bendingOryza sativa (rice)*Zhu Q, Ordiz MI, Dabi T, Beachy RN, Lamb C�Rice TATA binding protein interacts functionally withtranscription factor IIB and the RF2a bZIP transcriptionalactivator in an enhanced plant in vitro transcription system Plant Cell 14: 795-803 (2002)PubMed: 11971135; TATTTAA
TATAPVTRNALEUS000340 21-May-2002 (last modified) uchi�"TATA-like motif"; A TATA-like sequence found in Phaseolusvulgaris tRNALeu gene promoter; Frequently observed upstream ofplant tRNA genes; Found in maize glycolyticglyceraldehyde-3-phospate dehydrogenase 4 (GapC4) gene promoter;Binding site of TATA binding protein (TBP);TATAtRNA
re-initiationGapC4MybTATA binding proteinTBP$Phaseolus vulgaris; maize (Zea mays)SYukawa Y, Sugita M, Choisne N, Small I, Sugiura MGeffers R, Sell S, Cerff R, Hehl R�The TATA motif, the CAA motif and the poly(T) transcriptiontermination motif are all important for transcriptionre-initiation on plant tRNA genesThe TATA box and a Myb binding site are essential for anaerobicexpression of a maize GapC4 minimal promoter in tobaccoCPlant J 22: 439-447 (2000)Biochim Biophys Acta 1521: 120-125 (2001)"PubMed: 10849359;PubMed: 11690643; TTTATATA
TATCCACHVAL21S000416 10-May-2006 (last modified) kehi�!"TATCCAC box" is a part of the conserved cis-acting responsecomplex (GARC) that most often contain three sequence motifs, theTAACAAA box (see S000181), or GA-responsive element (GARE); thepyrimidine box, CCTTTT (see S000259); and the TATCCAC box, whichare necessary for a full GA response; gibberellinGAGARCbarley (Hordeum vulgare)}Isabel-LaMoneda I, Diaz I, Martinez M, Mena M, Carbonero P.Martinez M, Rubio-Somoza I, Fuentes R, Lara P, Carbonero P, DiazI.�SAD: a new DOF protein from barley that activates transcriptionof a cathepsin B-like thiol protease gene in the aleurone ofgerminating seeds.The barley cystatin gene (Icy) is regulated by DOF transcriptionfactors in aleurone cells upon germination.8Plant J. 33: 329-340 (2003)J Exp Bot. 56: 547-556 (2005)!PubMed: 12535346;PubMed: 15611149 TATCCAC TATCCAOSAMYS000403&15-September-2006 (last modified) kehi�3"TATCCA" element found in alpha-amylase promoters of rice (O.s.)at positions ca.90 to 150bp upstream of the transcription startsites; Binding sites of OsMYBS1, OsMYBS2 and OsMYBS3 whichmediate sugar and hormone regulation of alpha-amylase geneexpression; See also S000021 (AMYBOX2); S000256 (TATCCAY motif);
alpha-amylase MYB proteins gibberellinGAsugar starvationOryza sativa (rice)SLu CA, Ho THD, Ho SL, Yu SMLu CA, Lim EK, Yu SM.Chen PW, Chiang CM, Tseng TH, Yu SM�fThree Novel MYB Proteins with One DNA Binding Repeat MediateSugar and Hormone Regulation of alpha-Amylase Gene ExpressionSugar response sequence in the promoter of a rice alpha-amylasegene serves as a transcriptional enhancer.Interaction between Rice MYBGA and the Gibberellin ResponseElement Controls Tissue-Specific Sugar Sensitivity ofalpha-Amylase Genes.bPlant Cell 14: 1963-1980 (2002)J Biol Chem. 273:10120-10131(1998).PLANT CELL 18: 2326-2340 (2006).0PubMed: 12172034;PubMed: 9553059PubMed: 16905658 TATCCA
TBOXATGAPBS000383 23-Aug-2001 (last modified) uchi�<"Tbox" found in the Arabidopsis thaliana (A.T.) GAPB genepromoter; Located between -94 and -89 (T1) and also between -84and -79 (T2); Mutations in the "Tbox" resulted in reductions oflight-activated gene transcription; GAPB encodes the B subunit ofchloroplast glyceraldehyde-3-phosphate dehydrogenase(GADPH) ofA.T.;GAPB(glyceraldehyde-3-phosphate dehydrogenaselight-activated
transcriptionArabidopsis thalianaChan CS, Guo L, Shih MC�Promoter analysis of the nuclear gene encoding the chloroplastglyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsisthaliana!Plant Mol Biol 46: 131-141 (2001)PubMed: 11442054; ACTTTG TCA1MOTIFS000159 17-May-1998 (last modified) kehi�STCA-1 (tobacco nuclear protein 1) binding site; Related tosalicylic acid-inducible expression of many genes; Found inbarley beta-1,3-glucanase and over 30 different plant genes whichare known to be induced by one or more forms of stress; A similarsequence (TCATTTCTT) was found in tobacco Tnt1 retrotransposonpromoter (Mhiri et al., 1997);SAsalicylic acidstressTCA-16barley (Hordeum vulgare); tobacco (Nicotiana tabacum);pGoldsbrough AP, Albrecht H, Stratford RMhiri C, Morel JB, Verbhettes S, Casacuberta JM, Lucas H,Graandbastien MA�Salicylic acid-inducible binding of a tobacco nuclear protein toa 10 bp sequence which is highly conserved amongststress-inducible genes.The promoter of the tobacco Tnt1 retrotransposon is induced bywounding and by abiotic stress8Plant J 3:563-571 (1993)Plant Mol Biol 33:257-266 (1997) PubMed: 8220463;PubMed: 9037144;
TCATCTTCTT
TDBA12NTCHN50S000266!22-June-2006 (last modified) kehi�TDBA12 binding site found in tobacco (N.t.) basic class Ichitinase gene (CHN50); Elicitor response element; TDBA12 belongsto WRKY proteins that appear to be unique to plants; TDBA12 isactivated by TMV infection in resistant tobacco plant and byplant defense signal molecule SA;TDBA12 chitinaseCHN50WRKYHRTMVSARelicitortobacco (Nicotiana tabacum)RYang P, Chen C, Wang Z, Fan B, Chen ZEulgem T, Rushton PJ, Robatzek S, Somssich IE�A pathogen- and salicylic acid-induced WRKY DNA-binding activityrecognizes the elicitor response element of the tobacco class Ichitinase gene promoterThe WRKY superfamily of plant transcription factors;Plant J 18:141-149 (1999)Trends Plant Sci 5: 199-206 (2000)PubMed: 10785665;Review TGACTTTCTGAC TE2F2NTPCNAS000397%05-November-2005 (last modified) kehi�"te2f-2" found in the promoter of tobacco PCNA gene; Locatedbetween -84 and -77; Binding site of OsE2F1 and OsE2F2; Involvedin transcriptional activation in actively dividing cells andtissue;E2FPCNAmeristematic tissue
cell cycletobacco (Nicotiana tabacum)Kosugi S, Ohashi Y�E2F sites that can interact with E2F proteins cloned from riceare required for meristematic tissue-specific expression of riceand tobacco proliferating cell nuclear antigen promotersPlant J 29: 45-59 (2002)PubMed: 12060226; ATTCCCGC TEF1BOXATA1S000311 7-Sep-2000 (last modified) seki�^"tef1 box" found in the Arabidopsis (A.t.) EF-1 alpha A1 genepromoter; Conserved in the A.t. EF-1 alpha gene promoters;Involved in the activation of EF-1 alpha gene; Involved in thetranscriptional activation of plant genes that are overexpressedin cycling cells; Conserved in the promoters of genes forproducts related to the translational apparatus; EF-1alphaA1tef1 box"Arabidopsis (Arabidopsis thaliana)�Curie C, Liboz T, Bardet C, Gander E, Medale C, Axelos M, LescureBRegad F, Herve C, Marinx O, Bergounioux C, Tremousaygue D, LescueB� Cis and Trans-acting elements involved in the activation ofArabidopsis thaliana A1 gene encoding the translation elongationfactor EF-1alphaThe tef1 box, a ubiquitous cis-acting element involved in theactivation of plant genes that are highly expressed in cyclingcellsONucleic Acids Research 19: 1305-1310 (1991)Mol. Gen. Genet. 248: 703-711 (1995) PubMed: 1840652;PubMed: 7476873; ACAGGGGCATAATGGTAATTTAAATEFBOXATEEF1AA1S000309 7-Sep-2000 (last modified) seki�"tef-box" found in the Arabidopsis (A.t.) eEF1AA1 gene promoter;An activating sequence associated with telo-box (S000308);Required for the gene expression in root primordia; Actsco-operatively with telo-box; See S000308;tef-boxtelomere motifl eEF1Aroot primordiatelo-box"Arabidopsis (Arabidopsis thaliana):Tremousayque D, Manevski A, Bardet C, Lescure N, Lescure BaPlant interstitial telomere mitifs participate in the control ofgene expression in root meristemsPlant J 20: 553-561 (1999)PubMed: 10652127; AGGGGCATAATGGTAATELOBOXATEEF1AA1S000308%05-November-2005 (last modified) kehi�p"telo-box" (telomere motif) found in the Arabidopsis (A.t.)eEF1AA1 gene promoter; Conserved in all known plant eEF1A genepromoters; Found in the 5' region of numerous genes encodingcomponents of the translational apparatus; Required for theactivation of expression in root primordia; Acts co-operativelywith tef-box; Binding site of AtPur alpha-1; See S000309,S000474;telo-boxtelomere motifeEF1Aroot primordiatef-boxPuralpha-1"Arabidopsis (Arabidopsis thaliana)�Tremousayque D, Manevski A, Bardet C, Lescure N, Lescure BAxelos M, Bardet C, Liboz T, Va Thai AL, Curie C, Lescure BWelchen E, Gonzalez DH.��Plant interstitial telomere mitifs participate in the control ofgene expression in root meristemsThe gene family encoding the Arabidopsis thaliana translationelongation factor EF-1alpha: Molecular clonig, characterizationand expression.Differential expression of the Arabidopsis cytochrome c genesCytc-1 and Cytc-2. Evidence for the involvement of TCP-domainprotein-binding elements in anther- and meristem-specificexpression of the Cytc-1 gene.[Plant J 20: 553-561 (1999)Mol Gen Genet 219: 106-112 (1989)Plant Physiol.139: 88-100 (2005)0PubMed: 10652127;PubMed: 2615757PubMed: 16113211 AAACCCTAA TGA1ANTPR1AS000247 16-Feb-2001 (last modified) seki�;TGA1a binding site in tobacco (N.t.) PR1a gene; as-1-likesequence; Contains two TGACG elements reminiscent of activationsequence-1 (as-1); See other as-1-like sequences; TGA1a ispreferentially expressed in root tip meristems; TGA1a maycontribute to the expression of GST isoenzymes, especially inroot tip meristems;TGA1aas-1PR1axenobiotic stressroottipmeristemtobacco (Nicotiana tabacum)�Strompen G, Gruner R, Pfitzner UMKlinedinst S, Pascuzzi P, Redman J, Desai M, Arias JGruner R, Strompen G, Pfitzner AJ, Pfitzner UM.��An as-1-like motif controls the level of expression of the genefor the pathogenesis-related protein 1a from tobaccoA xenobiotic-stress-activated transcription factor and itscognate target genes are preferentially expressed in root tipmeristemsSalicylic acid and the hypersensitive response initiate distinctsignal transduction pathways in tobacco that converge on theas-1-like element of the PR-1a promoter.fPlant Mol Biol 37:871-883 (1998)Plant Mol Biol 42: 679-688 (2000)Eur J Biochem. 270: 4876-4886 (2003)1PubMed: 9678582;PubMed: 10809441;PubMed: 14653814 CGTCATCGAGATGACG TGACGTVMAMYS000377 23-Aug-2001 (last modified) uchi�"TGACGT motif" found in the Vigna mungo (V.m.) alpha-Amylase(Amy) gene promoter; Located between -128 and -123; Required forhigh level expression of alpha-Amylase in the cotyledons of thegerminated seeds; See S000234;
alpha-Amylase cotyledonseed germinationseed Vigna mungo
Yamauchi D�A TGACGT Motif in the 5'-Upstream Region of alpha-Amylase Genefrom Vigna mungo is a cis-Element for Expression in Cotyledons ofGerminated Seeds%Plant Cell Physiol 42: 635-641 (2001)PubMed: 11427683; TGACGTTGTCACACMCUCUMISINS000422 29-Sep-2003 (last modified) kehi�"TGTCACA motif" found in the region (from -254 to -215) ofcucumisin (a subtilisin-like serine protease) in the fruit ofmelon (Cucumis melo L.); A novel enhancer element necessary forfruit-specific expression of the cucumisin gene; cucumisinfruitCucumis melo L. (melon))Yamagata H, Yonesu K, Hirata A, Aizono Y.tTGTCACA motif is a novel cis-regulatory enhancer element involvedin fruit-specific expression of the cucumisin gene.#J Biol Chem. 277:11582-11590 (2002)PubMed: 11782472; TGTCACATL1ATSARS000473#13-August-2005 (last modified) kehi�"TL1", a consensus sequence overrepresented in the promoterregions of all 13 NPR1-responsive ER-resident genes surveyed;NPR1 is "Nonexpressor of pathogenesis-related genes 1", alsoknown as NIM1;SARERPRNIM1Arabidopsis thaliana'Wang D, Weaver ND, Kesarwani M, Dong X.SInduction of protein secretory pathway is required for systemicacquired resistance. Science 308: 1036-1040 (2005)PubMed: 15890886 in silico CTGAAGAAGAA TRANSTARTS000113 17-May-1998 (last modified) kehi4plant consensus sequence for translation start site; translationrice (Oryza sativa);1Joshi CPde Pater S, Hensgens LAM, Schilperoort RA�An inspection of the domain between putative TATA box andtranslation start site in 79 plant genes.Structure and expression of a light-inducible shoot-specific ricegene.ENucleic Acids Res 15:6643-6653 (1987)Plant Mol Biol 15:399-406 (1990)1PubMed: 3628002;PubMed: 2103460; GenBank: X51911; TAAACAATGGCTUP2ATMSDS000472#13-August-2005 (last modified) kehi�"Up2" motif found in 193 of the 1184 up-regulated genes aftermain stem decapitation in Arabidopsis; W=A/T; See also S000470,S000471;Axillary bud outgrowthArabidopsis thaliana3Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E.wIdentification of cis-elements that regulate gene expressionduring initiation of axillary bud outgrowth in Arabidopsis.$Plant Physiology 138: 757-766 (2005)PubMed: 15908603 AAACCCTAUPRE1ATS000428$04-January-2007 (last modified) kehi�"ERSEII-like sequence" found in the plant UPRE (unfolded proteinresponse element) in A.t.; See S000429; Either of ERSEII or XBP1binding sites is essential and sufficient for the UPR; SeeS000425, S000426;UPRUPREunfolded protein responseERSEIIERSEArabidopsis thaliananOh DH, Kwon CS, Sano H, Chung WI, Koizumi N.Martinez IM, Chrispeels MJ.Iwata Y, Koizumi N.Tajima H, Koizumi N.��Conservation between animals and plants of the cis-acting elementinvolved in the unfolded protein response.Genomic analysis of the unfolded protein response in Arabidopsisshows its connection to important cellular processes.An Arabidopsis transcription factor, AtbZIP60, regulates theendoplasmic reticulum stress response in a manner unique toplants.Induction of BiP by sugar independent of a cis-element for theunfolded protein response in Arabidopsis thaliana.�Biochem Biophys Res Commun. 301:225-230 (2003)Plant Cell. 15:561-576 (2003)Proc Natl Acad Sci U S A. 102: 5280-5285. (2005)Biochem Biophys Res Commun. 346:926-930 (2006)BPubMed: 12535667;PubMed: 12566592;PubMed: 15781873PubMed: 16781668 ATTGGTCCACGUPRE2ATS000429$04-January-2007 (last modified) kehi�"XBP1 binding site-like sequence" found in the plant UPRE(unfolded protein response element) in A.t.; See S000428; Eitherof ERSEII or XBP1 binding sites is essential and sufficient forthe UPR; See S000425 (CCACGTCA), S000426;UPRUPREunfolded protein responseERSEIIERSEArabidopsis thaliananOh DH, Kwon CS, Sano H, Chung WI, Koizumi N.Martinez IM, Chrispeels MJ.Iwata Y, Koizumi N.Tajima H, Koizumi N.��Conservation between animals and plants of the cis-acting elementinvolved in the unfolded protein response.Genomic analysis of the unfolded protein response in Arabidopsisshows its connection to important cellular processes.An Arabidopsis transcription factor, AtbZIP60, regulates theendoplasmic reticulum stress response in a manner unique toplants.Induction of BiP by sugar independent of a cis-element for theunfolded protein response in Arabidopsis thaliana.�Biochem Biophys Res Commun. 301:225-230 (2003)Plant Cell. 15:561-576 (2003)Proc Natl Acad Sci U S A. 102: 5280-5285. (2005)Biochem Biophys Res Commun. 346:926-930 (2006)@PubMed: 12535667PubMed: 12566592PubMed: 15781873PubMed: 16781668
CCACGTCATC UPRMOTIFIATS000425 29-Sep-2003 (last modified) kehi�"Motif I" in the conserved UPR (unfolded protein response)cis-acting element in Arabidopsis genes coding for SAR1B, HSP-90,SBR-like, Ca-ATPase 4, CNX1, PDI, etc.; See S000429 (CCACGTCATC);See also S000426, S000428, S000429;UPRunfolded protein responseArabidopsis thalianaGMartinez IM, Chrispeels MJ.Oh DH, Kwon CS, Sano H, Chung WI, Koizumi N.�Genomic analysis of the unfolded protein response in Arabidopsisshows its connection to important cellular processes.Conservation between animals and plants of the cis-acting elementinvolved in the unfolded protein response.KPlant Cell. 15:561-576 (2003)Biochem Biophys Res Commun. 301:225-230 (2003)"PubMed: 12566592;PubMed: 12535667; CCACGTCA VSF1PVGRP18S000249#19-August-2004 (last modified) kehi�jVSF-1 binding site in French bean (P.v.) grp1.8 gene promoter;VSF-1 is a tomato bZIP transcription factor; VSF-1 binding siteis found in 28 bp vs-1 element; This sequence controls vasculargene expression in transgenic tobacco; "VS-1" found in beangrp1.8 gene promoter; Located between -203 and -176; Partiallyoverlaps with NRE; Confers xylem-specific expression;VSF-1vasculargrp1.8VS-1bZIPXylem_French bean (Phaseolus vulgaris); tomato (Lycopersiconesculentum); tobacco (Nicotiana tabacum);NRingli C, Keller BTorres-Schumann S, Ringli C, Heierli D, Amrhein N, Keller B.�Specific interaction of the tomato bZIP transcription factorVSF-1 with a non-palindromic DNA sequence that controls vasculargene expressionIn vitro binding of the tomato bZIP transcriptional activatorVSF-1 to a regulatory element that controls xylem-specific geneexpression9Plant Mol Biol 37:977-988 (1998)Plant J 9:283-296 (1996) PubMed: 9700070;PubMed: 8919907; GCTCCGTTG WARBNEXTAS000241 11-0ct-1999 (last modified) kehiN"WAR (wounding activating region)" in Brassica napus (B.n.) extAextensin gene;woundingextextensinBrassica napusElliott KA , Shirsat AH{Promoter regions of the extA extensin gene from Brassica napuscontrol activation in response to wounding and tensile stress!Plant Mol Biol 37:675-687 (1998)PubMed: 9687071; GTACGTGTTATAAAACGTGT
WBOXATNPR1S000390!23-June-2006 (last modified) kehi��"W-box" found in promoter of Arabidopsis thaliana (A.t.) NPR1gene; Located between +70 and +79 in tandem; They were recognizedspecifically by salicylic acid (SA)-induced WRKY DNA bindingproteins; See S000142 (SQ=TTGACC); See S000310 (SQ=TTTGACY); Acluster of WRKY binding sites act as negative regulatory elementsfor the inducible expression of AtWRKY18 (Chena and Chen, 2002);See also S000142;NPR1WRKYWRKY18disease resistanceSAW boxArabidopsis thaliana�:Yu D, Chen C, Chen ZChen W, Provart NJ, Glazebrook J, Katagiri F, Chang HS, Eulgem T,Mauch F, Luan S, Zou G, Whitham SA, Budworth PR, Tao Y, XieEulgem T, Rushton PJ, Robatzek S, Somssich IE.Chen C, Chen Z.Maleck K, Levine A, Eulgem T, Morgan A, Schmid J, Lawton KA,Dangl JL, Dietrich RA.Xu X, Chen C, Fan B, Chen Z�hEvidence for an important role of WRKY DNA binding proteins inthe regulation of NPR1 gene expressionExpression profile matrix of Arabidopsis transcription factorgenes suggests their putative functions in response toenvironmental stressesThe WRKY superfamily of plant transcription factors.Potentiation of developmentally regulated plant defense responseby AtWRKY18, a pathogen-induced Arabidopsis transcriptionfactor.The transcriptome of Arabidopsis thaliana during systemicacquired resistance.Physical and Functional Interactions between Pathogen-InducedArabidopsis WRKY18, WRKY40, and WRKY60 Transcription Factors.�Plant Cell 13: 1527-1540 (2001)Plant Cell 14: 559-574 (2002)Trends Plant Sci. 5:199-206. (2000)Plant Physiol. 129:706-716 (2002)Nat Genet. 26:403-410 (2000)Plant Cell 18:1310-1326 (2006)RPubMed: 11449049;PubMed: 11910004;PubMed: 10785665PubMed: 12068113PubMed: 11101835Review.TTGAC WBOXGACAD1AS000448#19-August-2004 (last modified) kehi�W-box found in the promoter region of the CAD1-A (cotton (+)delta-cadinene synthase-A) gene (located in the region -340 to-327) of cotton (G.a); Binding site of GaWRKY1; GaWRKY1 regulatessesquiterpene biosynthesis in cotton; See S000390 (TTGAC),S000142 (TTGACC);W-boxTGACCADWRKYGossypium arboreum (cotton))Xu YH, Wang JW, Wang S, Wang JY, Chen XY.�Characterization of GaWRKY1, a cotton transcription factor thatregulates the sesquiterpene synthase gene (+)-delta-cadinenesynthase-A. Plant Physiol. 135:507-515(2004)PubMed: 15133151 AGTCAAAATTGACC
WBOXHVISO1S000442 28-Jan-2004 (last modified) kehiLSUSIBA2 bind to W-box element in barley iso1 (encodingisoamylase1) promoter;sugarSUREpatatinWRKY
isoamylaseSUSIBA2Hordeum vulgare (barley)@Sun C, Palmqvist S, Olsson H, Boren M, Ahlandsberg S, Jansson C.�A novel WRKY transcription factor, SUSIBA2, participates in sugarsignaling in barley by binding to the sugar-responsive elementsof the iso1 promoter. Plant Cell 15: 2076-2092 (2003)PubMed: 12953112; TGACT WINPSTPIIIKS000495 10-May-2006 (last modified) kehi�Binding site of wound-inducible nuclear protein from woundedtomato leaves; Found in the promoter region of a proteaseinhibitor IIK gene from potato (S.t.);woundwoundingSolanum tuberosum (potato)!Palm CJ, Costa MA, An G, Ryan CA.lWound-inducible nuclear protein binds DNA fragments that regulatea proteinase inhibitor II gene from potato.,Proc Natl Acad Sci U S A. 87: 603-607 (1990)PubMed: 2405385
AAGCGTAAGTWRKY71OSS000447!22-June-2006 (last modified) kehi�S"A core of TGAC-containing W-box" of, e.g., Amy32b promoter;Binding site of rice WRKY71, a transcriptional repressor of thegibberellin signaling pathway; Parsley WRKY proteins bindspecifically to TGAC-containing W box elements within thePathogenesis-Related Class10 (PR-10) genes (Eulgem et al., 1999);See S000390 (TTGAC), S000442 (TGACT);WRKYGAMYBW boxTGAC PR proteins4Oryza sativa (rice); Petroselinum crispum (parsley);�Zhang ZL, Xie Z, Zou X, Casaretto J, Ho TH, Shen QJ.Xie Z, Zhang ZL, Zou X, Huang J, Ruas P, Thompson D, Shen QJ.Eulgem T, Rushton PJ, Schmelzer E, Hahlbrock K, Somssich IE.Eulgem T, Rushton PJ, Robatzek S, Somssich IE.��A rice WRKY gene encodes a transcriptional repressor of thegibberellin signaling pathway in aleurone cells.Annotations and functional analyses of the rice WRKY genesuperfamily reveal positive and negative regulators of abscisicacid signaling in aleurone cells.Early nuclear events in plant defence signalling: rapid geneactivation by WRKY transcription factors.The WRKY superfamily of plant transcription factors.�Plant Physiol. 134:1500-1513(2004)Plant Physiol. 137:176-189 (2005)EMBO J. 18:4689-4699 (1999)Trends Plant Sci. 5:199-206. (2000)@PubMed: 15047897PubMed: 15618416PubMed: 10469648PubMed: 10785665Review.TGACWUSATAgS000433 27-Jan-2004 (last modified) kehioTarget sequence of WUS in the intron of AGAMOUS gene inArabidopsis; See Lohmann et al. Cell 105:793-803 (2003); Oryza sativa (rice)5Kamiya N, Nagasaki H, Morikami A, Sato Y, Matsuoka M.�Isolation and characterization of arice WUSCHEL-tyope homoeboxgene that is specifically expressed in the central cells of aquiescent center in the root apical meristem.Plant J. 35: 429-441 (2003)PubMed: 12904206; TTAATGGXYLATS000510$04-January-2007 (last modified) kehiGcis-element identified among the promoters of the "core xylemgene set";secondary xylemwood formationArabidopsis thalianaKo JH, Beers EP, Han KH.�Global comparative transcriptome analysis identifies gene networkregulating secondary xylem development in Arabidopsis thaliana.&Mol Genet Genomics. 276:517-531 (2006)PubMed: 16969662in silico; consensus;ACAAAGAAYREGIONNTPRB1BS000365 16-Feb-2001 (last modified) seki�"Y region" found in tobacco (N.t.) PRB-1b gene promoter; Locatedat -179 to -154; Binding site of nuclear protein; Required forethylene induction; See S000364;PR-1PRB-1bethyleneYTobacco (Nicotiana tabacum)"Meller Y, Sessa G, Eyal Y, Fluhr RNDNA-protein interactions on a cis-DNA element essential forethylene regulation!Plant Mol Biol 23: 453-463 (1993)PubMed: 8219081; TGTGACATTGAAATTCTTTGACTTTAZDNAFORMINGATCAB1S000321#13-August-2005 (last modified) kehi�~"Z-DNA-forming sequence" found in the Arabidopsis (A.t.)chlorophyll a/b binding protein gene (cab1) promoter; Involved inlight-dependent developmental expression of the gene; "Z-box";Activation of Z-box containing promoters is regulated bydownstream regulatory components, COP1 and HY5; phyB and CRY1photoreceptors act redundantly to induce Z-box containingpromoters in white light; cab1lightZ-DNAleafshootHY5COP1LREZ-boxZBF1Z-box binding factorArabidopsis thaliana�Ha SB, An GYadav V, Kundu S, Chattopadhyay D, Negi P, Wei N, Deng XW,Chattopadhyay SYadav V, Mallappa C, Gangappa SN, Bhatia S, Chattopadhyay S.��Identification of upstream regulatory elements involved in thedevelopmental expression of the Arabidopsis thaliana cab1 gene.Light regulated modulation of Z-box containing promoters byphotoreceptors and downstream regulatory components, COP1 andHY5, in ArabidopsisA Basic Helix-Loop-Helix Transcription Factor in Arabidopsis,MYC2, Acts as a Repressor of Blue Light-Mediated PhotomorphogenicGrowth.eProc Natl Acad Sci USA 85: 8017-8021 (1988)Plant J. 31: 741-753 (2002)Plant Cell 17: 1953-1966 (2005)0PubMed: 3054877PubMed: 12220265;PubMed: 15923349 ATACGTGTf -300ELEMENTS000122 11-May-2006 (last modified) kehi�Present upstream of the promoter from the B-hordein gene ofbarley and the alpha-gliadin, gamma-gliadin, and low molecularweight glutenin genes of wheat; See S000001 -300CORE; See S000002-300MOTIF; -300 elementhordeingliadingluteninseedwheat (Triticum aestivum)�Kreis M, Williamson MS, Forde J, Schmitz D, Clark J, Buxton B,Pywell J, Marris C, Henderson J, Harris N, Shewry PR, Forde BG,Miflin BJColot V, Robert LS, Kavanagh TA, Bevan MW, Thompson RDThomas MS, Flavell RB�Differential gene expression in the developing barley endosperm.Localization of sequences in wheat endosperm protein genes whichconfer tissue-specific expression in tobacco.Identification of an enhancer element for the endosperm-specificexpression of high molecular weight glutenin.aPhilos Trans R Soc Lond B314:355-365 (1986)EMBO J 6:3559-3564 (1987)Plant Cell 2:1171-1180 (1990) PubMed: 15467781PubMed: 2152160; TGHAAARK-300MOTIFZMZEINS000002 17-May-1998 (last modified) kehi�Motif in -300 elements of alpha-zein genes of maize (Z.m.);homologous to the sequence to which transacting factors of AP-1,fos, jun or yeast hisS bind;zein
core motifmaize -300 elementseed endospermmaize (Zea mays)Thomas MS, Flavell RBmIdentification of an enhancer element for the endosperm-specificexpression of high molecular weight glutenin. Plant Cell 2:1171-1180 (1990)PubMed: 2152160; RTGAGTCAT27BPDRCONSENSUSPS25SS000286 10-Feb-2000 (last modified) seki�The consensus sequence of 27 bp imperfect repeats found in theuntrascribed spacer close to the 3'end of the pea (P.s.) 25Sgene; Involved in the rDNA replication fork barrier; Nuclearprotein(s) specifically bound to this repeat; W=T/A; M=A/C;rDNA25S
tandem repeat fork barrierpea (Pisum sativum)8Lopez-Estrano C, Schivartzman JB, Krimer DB, Hernandez PfCharacterization of the pea rDNA replication fork barrier:putative cis-acting and trans-acting factors!Plant Mol Biol 40: 99-110 (1999)PubMed: 10394949 TCCGCCWCTTGTATTCGTTGCGTTGMA5659BOXLELAT5659S000280 29-Sep-2003 (last modified) kehi�"56/59 box"; A sequence motif shared between the tomato (L.e.)LAT(Late Anther Tomato)56 and LAT59 promoters; Found in -103 to-94 in LAT56 and in -114 to -105 in LAT59; Involved in modulatingthe activity of the LAT gene promoters in pollen; W=A/T;56/59latlat56lat59GT-1pollenanther tomato (Lycopersicon esculentum)rTwell D, Yamaguchi J, Wing RA, Ushiba J, McCormick SEyal Y, Curie C, McCormick SVillain P, Mache R, Zhou DXZhou DX��Promoter analysis of genes that are coordinately expressed duringpollen development reveals pollen-specific enhancer sequences andshared regulatory elementsPollen specificity elements reside in 30 bp of the proximalpromoters of two pollen-expressed genesThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�Genes Dev 5:496-507 (1991)Plant Cell 7:373-384 (1995)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)RPubMed: 1840556; GenBank: X56488;PubMed: 7734969;PubMed: 8955086;PubMed: 10366876Review
GAAWTTGTGAABADESI1S000007 10-Feb-2000 (last modified) seki�Responsive to ABA and desiccation; "Motif I" of rice rab16A-D(initially called rab-21); Expressed in seeds late duringembryogenesis; Induced by ABA and osmotic stress in vegetativetissues; Contains ACGT motif; transacting factor: TAF-1;rab16ABAABRETAF-1ACGTMotif iseedembryorice (Oryza sativa)nMundy J, Yamaguchi-Shinozaki K, Chua N-HOeda K, Salinas J, Chua N-HThomas TLBusk PK, Pages MSkriver K, Mundy J�~Nuclear proteins bind conserved elements in the abscisicacid-responsive promoter of a rice rab gene.A tobacco bZip transcription activator (TAF-1) binds to aG-box-like motif conserved in plant genes.Gene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcriptionGene expression in response to abscisic acid and osmotic stress�Proc Natl Acad Sci USA 87:1406-1410 (1990)EMBO J 10:1793-1802 (1991)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998)Plant Cell 2: 503-512 (1990)`PubMed: 2137613;PubMed: 2050116; GenBank: X60363;PubMed: 8281041;PubMed: 9617810;PubMed: 2152172?Gel retardation; DNase I cleavage inhibition;ReviewReviewreview
RTACGTGGCRABREATCONSENSUSS000406$06-January-2006 (last modified) kehi�ABA-responsive elements (ABREs) found in the promoter of ABAand/or stress-regulated genes; ABFs, a family of ABRE bindingfactors; ABF3 and ABF4 function in ABA signaling; Y=C/T;ABAABF bZIP factorsArabidopsis thaliana�Choi H, Hong J, Ha J, Kang J, Kim SYKang JY, Choi HI, Im MY, Kim SYOh SJ, Song SI, Kim YS, Jang HJ, Kim SY, Kim M, Kim YK, Nahm BH,Kim JK.Choi HI, Park HJ, Park JH, Kim S, Im MY, Seo HH, Kim YW, Hwang I,Kim SY.��ABFs, a family of ABA-responsive element binding factorsArabidopsis basic leucine zipper proteins that mediatestress-responsive abscisic acid signalingArabidopsis CBF3/DREB1A and ABF3 in transgenic rice increasedtolerance to abiotic stress without stunting growth.Arabidopsis Calcium-Dependent Protein Kinase AtCPK32 Interactswith ABF4, a Transcriptional Regulator of AbscisicAcid-Responsive Gene Expression, and Modulates Its Activity.�J Biol Chem. 275: 1723-1730 (2000)Plant Cell. 14: 343-357 (2002)Plant Physiology 138: 341-351 (2005)Plant Physiol. 139: 1750-1761(2005)BPubMed: 10636868;PubMed: 11884679;PubMed: 15834008PubMed: 16299177 YACGTGGC
ABREATRD22S000013 29-Sep-1999 (last modified) kehid"ABRE (ABA responsive element)" in Arabidopsis (A.t.)dehydration-responsive gene rd22; R=A/G; Y=C/T;ABAresponsive elementABRErd22RD22 dehydrationshootArabidopsis thalianaCIwasaki T, Yamaguchi-Shinozaki K,Shinozaki KBray EABusk PK, Pages M�Identification of a cis-regulatory region of a gene inArabidopsis thaliana whose induction by dehydration is mediatedby abscisic acid and requires protein synthesis.Plant responses to water deficitRegulation of abscisic acid-induced transcriptionfMol Gen Genet 247:391-398 (1995)Trends in Plant Science 2:48-54 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 7770045;PubMed: 9617810;Review
RYACGTGGYR ABREOSRAB21S000012 10-Feb-2000 (last modified) seki�"ABA responsive element (ABRE)" of wheat Em and rice (O.s.) rab21genes; Proposed consensus sequence for the repeated motif (Em1aand Em1b) of wheat Em gene; S=C/G;ABAABREEmrabEm1aEm1bseed.rice (Oryza sativa); wheat (Triticum aestivum)IMarcotte WR Jr, Russell SH, Quatrano RSBusk PK, Pages MSkriver K, Mundy J�Abscisic acid-responsive sequences from the Em gene of wheat.Regulation of abscisic acid-induced transcriptionGene expression in response to abscisic acid and osmotic stressWPlant Cell 1:969-976 (1989)Plant Mol Biol 37:425-435 (1998)Plant Cell 2: 503-512 (1990)/PubMed: 2562556;PubMed: 9617810;PubMed: 2152172 reviewreviewACGTSSSC
ABRERATCALS000507$04-January-2007 (last modified) kehi�"ABRE-related sequence" or "Repeated sequence motifs" identifiedin the upstream regions of 162 Ca(2+)-responsive upregulatedgenes; see also ABRE; M=C/A; Y=T/C; B=T/C/G;ABREcalciumArabidopsis thalianaCKaplan B, Davydov O, Knight H, Galon Y, Knight MR, Fluhr R, FrommH.�Rapid Transcriptome Changes Induced by Cytosolic Ca2+ TransientsReveal ABRE-Related Sequences as Ca2+-Responsive cis Elements inArabidopsis. Plant Cell. 18:2733-2748 (2006)PubMed: 16980540 MACGYGBACGTABREMOTIFA2OSEMS000394$06-January-2006 (last modified) kehi�Experimentally determined sequence requirement of ACGT-core ofmotif A in ABRE of the rice gene, OSEM; See S000281; DRE and ABREare interdependent in the ABA-responsive expression of the rd29Ain Arabidopsis; K=G/T;ABAABREmotif ADRE*rice (Oryza sativa); Arabidopsis thaliana;�Hattori T, Totsuka M, Hobo T, Kagaya Y, Yamamoto-Toyoda ANarusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, AbeH, Narusaka M, Shinozaki K, Yamaguchi-Shinozaki K.�Experimentally Determined Sequence Requirement of ACGT-ContainingAbscisic Acid Response ElementInteraction between two cis-acting elements, ABRE and DRE, inABA-dependent expression of Arabidopsis rd29A gene in response todehydration and high-salinity stresses.@Plant Cell Physiol 43: 136-140 (2002)Plant J. 34: 137-148 (2003)"PubMed: 11828032;PubMed: 12694590; ACGTGKCAGAMOUSATCONSENSUSS000342 16-May-2001 (last modified) uchi��Binding consensus sequence of Arabidopsis (A.t.) AGAMOUS MADSdomain; MCM1 binding-sites in a-mating-type-specific promoters ofSaccharomyces cerevisiae show similarities with the binding-sitesequence of the AGAMOUS MADS domain; See S000316; MADS domain andI region of AGAMOUS are sufficient and necessary for DNA binding;Both the K domain and C region are indispensable for AG functionin flower development; See S000338;AGAMOUS MADS domainflowerArabidopsis thalianaGShiraishi H, Okada K, Shimura YMizukami Y, Huang H, Tudor M, Hu Y, Ma H�Nucleotide sequences recognized by the AGAMOUS MADS domain ofArabidopsis thaliana in vitroFunctional domains of the floral regulator AGAMOUS:characterization of the DNA binding domain and analysis ofdominant negative mutations4Plant J 4: 385-398 (1993)Plant Cell 8:831-845 (1996) PubMed: 8106084;PubMed: 8672883; TTDCCWWWWWWGGHAA
AGATCONSENSUSS000316 16-May-2001 (last modified) uchi��Binding consensus sequence for the product of the Arabidopsis(A.t.) floral homeotic gene AGAMOUS (AG); AG protein contains aregion similar to the DNA binding domain of SRF and MCM1; Theconsensus sequence contains a CArG box; AG protein is a putativetranscription factor for floral genes; H=A/T/C; W=A/T; SeeS000342; MADS domain and I region of AGAMOUS are sufficient andnecessary for DNA binding; Both the K domain and C region areindispensable for AG function in flower development; SeeS000338;floral homeotic geneAGAMOUSAGMCM1SRFGArG boxAPETALA2flower"Arabidopsis (Arabidopsis thaliana)iHuang H, Mizukami Y, Hu Y, Ma HMizukami Y, Huang H, Tudor M, Hu Y, Ma HDrews GN, Bowman JL, Meyerowitz EM�QIsolation and characterization of the binding sequences for theproduct of the Arabidopsis floral homeotic gene AGAMOUSFunctional domains of the floral regulator AGAMOUS:characterization of the DNA binding domain and analysis ofdominant negative mutationsNegative regulation of the Arabidopsis homeotic gene AGAMOUS bythe APETALA2 productZNucleic Acids Res. 21: 4769-4776 (1993)Plant Cell 8:831-845 (1996)Cell 65 :991-1002 (1991)0PubMed: 7901838;PubMed: 8672883;PubMed: 1675158; TTWCCWWWWNNGGWWAGL1ATCONSENSUSS000338 16-May-2001 (last modified) uchi��Binding consensus sequence of Arabidopsis (A.t.) AGL1(AGAMOUS-like 1); AGL1 contains MADS domain; See S000339; AGL20is a MADS domain gene from Arabidopsis that is activated in shootapical meristem during the transition to flowering; AGL20 is alsoregulated by the Gibberellin pathway; Complex regulatory networks involving several MADS-genes underlie development ofvegetative structures;
MADSAGL1AGAMOUSAGL20floral induction photoperiod endosperm
gurd cellsroottrichomeleafshootflowerArabidopsis thaliana�Huang H, Tudor M, Su T, Zhang Y, Hu Y, Ma HBorner R, Kampmann G, Chandler J, Gleissner R, Wisman E, Apel K,Melzer SAlvarez-Buylla ER, Liljegren SJ, Pelaz S, Gold SE, Burgeff C,Ditta GS, Vergara-Silva F, Yanofsky MF�DNA binding properties of two Arabidopsis MADS domain proteins:binding consensus and dimer formationA MADS domain gene involved in the transition to flowering inArabidopsisMADS-box gene evolution beyond flowers: expression in pollen,endosperm, guard cells, roots and trichomesNPlant Cell 8: 81-94 (1996)Plant J 24: 591-599 (2000)Plant J 24: 457-466 (2000)1PubMed: 8597661;PubMed: 11123798;PubMed: 11115127 NTTDCCWWWWNNGGWAANAGL2ATCONSENSUSS000339 16-May-2001 (last modified) uchi�Binding consensus sequence of Arabidopsis (A.t.) AGL2(AGAMOUS-like 2); AGL2 contains MADS domain; AGL2 binds DNA as adimer; See S000338;MADSAGL1AGAMOUSflowerArabidopsis thaliana+Huang H, Tudor M, Su T, Zhang Y, Hu Y, Ma HdDNA binding properties of two Arabidopsis MADS domain proteins:binding consensus and dimer formationPlant Cell 8: 81-94 (1996)PubMed: 8597661; NNWNCCAWWWWTRGWWANAGL3ATCONSENSUSS000343 7-Sep-2000 (last modified) seki�Binding consensus sequence of Arabidopsis(A.t.) AGL3; AGL3 isMADS-box domain protein; AGL3 is expressed in all above-groundvegetative organs; AGL3 may be involved the transcriptionalregulation of genes;MADS-boxAGL3CArGstemleafflowershootArabidopsis thaliana&Huang H, Tudor M, Weiss CA, Hu Y, Ma HiThe Arabidopsis MADS-box gene AGL3 is widely expressed andencodes a sequence-specific DNA-binding protein Plant Mol Biol 28:549-567 (1995)1PubMed: 7632923; GenBank: U81368; U81369; U81370; TTWCYAWWWWTRGWAAAMMORESIIUDCRNIA1S000374 31-Jul-2001 (last modified) uchi�Motifs (IIU and IID) found in the Chlamydomonas (C.R.) Nia1 genepromoter; Involved in ammonium-response; Located between -231 and-219 and also between -76 and -65; Involved in Nia1 transcriptionactivation; W=T/A;nitrate reductaseammonium responseChlamydomonas reinhardtiiLoppes R, Radoux M�Identification of short promoter regions involved in thetranscriptional expression of the nitrate reductase gene inChlamydomonas reinhardtii!Plant Mol Biol 45: 215-227 (2001)PubMed: 11289512; GGWAGGGTAMYBOX1S000020 17-May-1998 (last modified) kehij"amylase box"; Conserved sequence found in 5'-upstream region ofalpha-amylase gene of rice, wheat, barley;amylaseseedGbarley (Hordeum vulgare); rice (Oryza sativa); wheat (Triticumaestivum)+Huang N, Sutliff TD, Litts JC, Rodriguez RLOClassification and characterization of the rice alpha-amylasemultigene family. Plant Mol Biol 14:655-668 (1990)!PubMed: 2102847; GenBank: X16509; TAACARAANAERO4CONSENSUSS000480%05-November-2005 (last modified) kehi�� One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway (anaerobic set1)(Mohanty et al., 2005); Arbitrary named ANAERO4CONSENSUS by thePLACEdb curator; See also S000477, S000478, S000479, S000481;H=A/T/C; anaerobic�Zea mays (maize); Arabidopsis thaliana; Pisum sativum (pea);Hordeum vulgare (barley); Oryza sativa (rice); Petunia hybrida(petunia); Lycopersicon esculentum (tomato);+Mohanty B, Krishnan SP, Swarup S, Bajic VB.sDetection and preliminary analysis of motifs in promoters ofanaerobically induced genes of different plant species.!Ann Bot (Lond).96: 669-681 (2005)PubMed: 16027132 in silico GTTTHGCAAARE1S000022 16-Jan-1998 (last modified) kehi�"ARE (antioxidant response element)"; antioxidant responseelement of rat glutathione S-transferase Ya subunit, and ratNAD(P)H:quinone reductase genes; antioxidant response elementAREoxidative stressactiveoxygenrat"Rushmore TH, Morton MR, Pickett CB�The antioxidant responsive element. Activation by oxidativestress and identification of the DNA consensus sequence requiredfor functional activity."J Biol Chem 266:11632-11639 (1991)PubMed: 1646813; RGTGACNNNGCARR1ATS000454"27-March-2004 (last modified) kehi�"ARR1-binding element" found in Arabidopsis; ARR1 is a responseregulator; N=G/A/C/T; AGATT is found in the promoter of ricenon-symbiotic haemoglobin-2 (NSHB) gene (Ross et al., 2004);ARR1Response regulatorArabidopsis thaliana^Sakai H, Aoyama T, Oka A.Ross EJ, Stone JM, Elowsky CG, Arredondo-Peter R, Klucas RV,Sarath G.�Arabidopsis ARR1 and ARR2 response regulators operate astranscriptional activators.Activation of the Oryza sativa non-symbiotic haemoglobin-2promoter by the cytokinin-regulated transcription factor, ARR1.<Plant J. 24: 703-711 (2000).J Exp Bot. 55: 1721-1731 (2004). PubMed: 11135105PubMed: 15258171 NGATTATHB1ATCONSENSUSS000317 7-Sep-2000 (last modified) seki�Recognition sequence of Arabidopsis Athb-1 protein; Athb-1protein has a HD-Zip motif (homeodomain (HD) with a closelylinked leucine zipper motif (Zip)); HD-Zip domain binds to DNA asa dimer; See S000318; W=A/T;Athb-1 homeodomainZip HD-Zip motifArabidopsis thaliana Sessa G, Morelli G, Ruberti IeThe Athb-1 and -2 HD-Zip domains homodimerize forming complexesof different DNA binding specificitiesEMBO J 12:3507-3517 (1993)PubMed: 8253077; CAATWATTGATHB2ATCONSENSUSS000318 7-Sep-2000 (last modified) seki�Recognition sequence of Arabidopsis Athb-2 protein; Athb-2protein has a HD-Zip motif (homeodomain (HD) with a closelylinked leucine zipper motif (Zip)); See S000317; S=C/G;Athb-2 homeodomainZip HD-Zip motifArabidopsis thaliana Sessa G, Morelli G, Ruberti IeThe Athb-1 and -2 HD-Zip domains homodimerize forming complexesof different DNA binding specificitiesEMBO J 12:3507-3517 (1993)PubMed: 8253077; CAATSATTG ATHB5ATCORES000371%05-November-2005 (last modified) kehi�Consensus binding sequence for Arabidopsis (A.T.) class I HDzip(Homeodomein-leucine zipper) protein, ATHB5; ATHB5 protein formsdimers in solution; ATHB5 and ATHB6 exhibit identical DNA bindingspecificities; ATHB5 forms heterodimers with other class I HDzipproteins; See also S000475;Homeodomein-leucine zipperHDzipATHB5class IHDZip IArabidopsis thalianavJohannesson H, Wang Y, Engstrom PHenriksson E, Olsson AS, Johannesson H, Johansson H, Hanson J,Engstrom P, Soderman E.�DNA-binding and dimerization preferences of Arabidopsishomeodomain-leucine zipper transcription factors in vitroHomeodomain leucine zipper class I genes in Arabidopsis.Expression patterns and phylogenetic relationships.BPlant Mol Biol 45: 63-73 (2001)Plant Physiol. 139: 509-518. (2005)!PubMed: 11247607;PubMed: 16055682 CAATNATTG AUXREPSIAA4S000026 16-Feb-2001 (last modified) seki� "AuxRE (Auxine responsive element )" of pea (P.s.) PS-IAA4/5gene; Indoleacetic acid-inducible genes; domain A; TGA1a ispreferentially expressed in root tip meristems; TGA1a maycontribute to the expression of GST isoenzymes, especially inroot tip meristems;AuxinAuxRErootmeristempea (Pisum sativum)|Ballas N, Wong LM, Theologis AGuilfoyle T, Hagen G, Ulmasov T, Murfett JKlinedinst S, Pascuzzi P, Redman J, Desai M, Arias J�%Identification of the auxin-responsive element, AuxRE, in theprimary indoleacetic acid-inducible gene, PS-IAA4/5, of pea(Pisum sativum).How does auxin turn on genes?A xenobiotic-stress-activated transcription factor and itscognate target genes are preferentially expressed in root tipmeristems_J Mol Biol 233:580-596 (1993)Plant Physiol 118: 341-347 (1998)Plant Mol Biol 42: 679-688 (2000)BPubMed: 8411166; GenBank: X68216;PubMed: 9765520;PubMed: 10809441;ReviewKGTCCCATBOXICHSS000228 16-May-1998 (last modified) kehi�"Box I consensus sequence in the promoters of mustard and parsleychs genes; Essential for light regulation (Terzaghi & Cashmore,1995); M=A/C;Box IBox 1Unit 1CHSchslight regulation7parsley (Petroselinum crispum); mustard (Sinapis alba);{Block A, Dangl JL, Hahlbrock K, Schulze-Lefert PRocholl M, Talke-Messerer C, Kaiser T, Batschauer ATerzaghi WB, Cashmore AR�0Functional borders, genetic fine structure, and distancerequirements of cis elements mediating light responsiveness ofthe parsley chalcone synthase promoterUnit 1 of the mustard chalcone synthase promoter is sufficient tomediate light responses from different photoreceptors.Light-regulated transcriptionzProc Natl Acad Sci USA 87:5387-5391(1990)Plant Sci 97:189-198(1994)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)PubMed: 2371277ReviewGTCCMTCMAACCTAMC
BOXLCOREDCPALS000492$06-January-2006 (last modified) kehi�Consensus of the putative "core" sequences of box-L-likesequences in carrot (D.c.) PAL1 promoter region; DCMYB1 bound tothese sequences in vitro; See also S000136 (Box P), S000137 (BoxA), S000138 (Box L); W=A/T;MYB R2R3 type
PAL: ElicitorUV-BDilutionDaucus carota (carrot)/Maeda K, Kimura S, Demura T, Takeda J, Ozeki Y.�DcMYB1 acts as a transcriptional activator of the carrotphenylalanine ammonia-lyase gene (DcPAL1) in response to elicitortreatment, UV-B irradiation and the dilution effect."Plant Mol Biol. 59: 739-752.(2005)PubMed: 16270227 ACCWWCC C1MOTIFZMBZ2S000237 23-Sep-1999 (last modified) kehi�"C1-motif"; Similar to Myb-box; Found in the promoter region ofmaize (Z.m.) Bronze2 ( glutathione S-transferase) gene; C1binding; C1-motif and R-motif were shown to be important for fullR and C1 activation of the Bz2 promoter; S=C or G;C1-motifBronze2Myb-boxglutathione S-transferaseC1seedmaize (Zea mays)Bodeau JP, Walbot V6Structure and regulation of the maize Bronze2 promoter Plant Mol Biol 32:599-609 (1996)PubMed: 8980512; TAACTSAGTTA CACTFTPPCA1S000449#19-August-2004 (last modified) kehi�Tetranucleotide (CACT) is a key component of Mem1 (mesophyllexpression module 1) found in the cis-regulatory element in thedistal region of the phosphoenolpyruvate carboxylase (ppcA1) ofthe C4 dicot F. trinervia; Y=T/C; mesohpyllCACTFlaveria trinerviaMGowik U, Burscheidt J, Akyildiz M, Schlue U, Koczor M, StreubelM, Westhoff P.�cis-Regulatory elements for mesophyll-specific gene expression inthe C4 plant Flaveria trinervia, the promoter of the C4phosphoenolpyruvate carboxylase gene. Plant Cell. 16:1077-1090(2004)PubMed: 15100398 YACT CANBNNAPAS000148 10-May-1998 (last modified) kehi�Core of "(CA)n element" in storage protein genes in Brasica napus(B.n.); embryo- and endosperm-specific transcription of napin(storage protein) gene, napA; seed specificity; activator andrepressor;
(CA)n elementnapAnapinseedstorage proteinBrassica napus;+Ellerstrom M, Stalberg K, Ezcurra I, Rask L�Functional dissection of a napin gene promoter: identification ofpromoter elements required for embryo and endosperm-specifictranscription."Plant Mol Biol 32:1019-1027 (1996)PubMed: 9002600; CNAACACCARGATCONSENSUSS000404 31-May-2006 (last modified) kehi�<"CArG consensus" sequence found in the promoter of Arabidopsis(A.t.) SOC1 which is the MADS-box flowering-time gene; FLC is acomponent of the vernalization (low-temperature) pathway bindsdirectly to this site and blocks transcriptional activation ofSOC1 by CONSTANS (CO); See also S000342 (AGAMOUSATCONSENSUS);W=A/T;SOC1Flowering timeCONSTANSFLCArabidopsis thaliana�Hepworth SR, Valverde F, Ravenscroft D, Mouradov A, Coupland GMichaels SD, Ditta G, Gustafson-Brown C, Pelaz S, Yanofsky M,Amasino RM.Hong RL, Hamaguchi L, Busch MA, Weigel D.Folter S, Angenent GC.�QAntagonistic regulation of flowering-time gene SOC1 by CONSTANSand FLC via separate promoter motifsAGL24 acts as a promoter of flowering in Arabidopsis and ispositively regulated by vernalization.Regulatory elements of the floral homeotic gene AGAMOUSidentified by phylogenetic footprinting and shadowing.trans meets cis in MADS science.wEMBO J. 21: 4327-4337 (2002)Plant J. 33: 867-874 (2003)Plant Cell 15:1296-1309 (2003)Trends Plant Sci. 11:224-231(2006)BPubMed: 12169635;PubMed: 12609028;PubMed: 12782724PubMed: 16616581Review
CCWWWWWWGG
CARGCW8GATS000431 31-May-2006 (last modified) kehisA variant of CArG motif (see S000404), with a longer A/T-richcore; Binding site for AGL15 (AGAMOUS-like 15); W=A/T;CArGAGL15AGAMOUSMADSArabidopsis thaliana'Tang W, Perry SE.Folter S, Angenent GC.}Binding site selection for the plant MADS domain protein AGL15:an in vitro and in vivo study.trans meets cis in MADS science.EJ Biol Chem.278:28154-28159 (2003)Trends Plant Sci. 11:224-231 (2006)!PubMed: 12743119;PubMed: 16616581review
CWWWWWWWWGCARGNCATS000446 31-May-2006 (last modified) kehi�Noncanonical CArG motif (CC-Wx8-GG) found in the promoter regionof DTA1 (AtGA2ox6); A relevant cis element for the response toAGL15 (AGAMOUS-like 15) in vivo; W=A/T; See S000431 (C-Wx8-G),S000404 (CArG consensus; CC-Wx6-GG);MADSAGAMOUSAGLembryoArabidopsis thaliana;=Wang H, Caruso LV, Downie AB, Perry SE.Folter S, Angenent GC.�The embryo MADS domain protein AGAMOUS-Like 15 directly regulatesexpression of a gene encoding an enzyme involved in gibberellinmetabolism.trans meets cis in MADS science.BPlant Cell 16:1206-1219 (2004)Trends Plant Sci. 11:224-231 (2006) PubMed: 15084721PubMed: 16616581review CCWWWWWWWWGGCBFHVS000497!22-June-2006 (last modified) kehi�Binding site of barley (H.v.) CBF1, and also of barley CBF2; CBF= C-repeat (CRT) binding factors; CBFs are also known asdehydration-responsive element (DRE) binding proteins (DREBs);See also S000411 (SQ=GTCGAC); R=A/G; Y=C/T;CBF
AP2 domainCRT/DRElow temperatureHordeum vulgare (barley)TXue GPSvensson JT, Crosatti C, Campoli C, Bassi R, Stanca AM, Close TJ,Cattivelli L.�Characterisation of the DNA-binding profile of barley HvCBF1using an enzymatic method for rapid, quantitative andhigh-throughput analysis of the DNA-binding activity.Transcriptome analysis of cold acclimation in barley albina andxantha mutants.CNucleic Acids Res. 30: e77 (2002)Plant Physiol. 141:257-270. (2006) PubMed: 12140339PubMed: 16603669 RYCGAC CCA1ATLHCB1S000149 10-May-1998 (last modified) kehi�CCA1 binding site; CCA1 protein (myb-related transcriptionfactor) interact with two imperfect repeats of AAMAATCT inLhcb1*3 gene of Arabidopsis thaliana (A.t.); Related toregulation by phytochrome;CCA1LhcbshootleafArabidopsis thaliana;8Wang Z-Y, Kenigsbuch D, Sun L, Harel E, Ong MS, Tobin EMhA myb-related transcription factor is involved in the phytochromeregulation of an Arabidopsis Lhcb gene.Plant cell 9:491-507 (1997)PubMed: 9144958; AAMAATCT CGCGBOXATS000501#04-August-2006 (last modified) kehi�"CGCG box" recognized by AtSR1-6 (Arabidopsis thalianasignal-responsive genes); Multiple CGCG elements are found inpromoters of many genes; Ca++/calmodulin binds to all AtSRs;V=A/C/G; B=G/T/C;
calmodulinArabidopsis thalianaYang T, Poovaiah BW.jA calmodulin-binding/CGCG box DNA-binding protein family involvedin multiple signaling pathways in plants.$J Biol Chem. 277:45049-45058. (2002)PubMed: 12218065 VCGCGBCIACADIANLELHCS000252 11-Oct-1999 (last modified) kehiCRegion necessary for circadian expression of tomato (L.e.) Lhcgene; circadianlightLhcleafshoot tomato (Lycopersicon esculentum)"Piechulla B, Merforth N, Rudolph BOIdentification of tomato Lhc promoter regions necessary forcircadian expression!Plant Mol Biol 38:655-662 (1998)PubMed: 9747810;
CAANNNNATCCOREOSS000469"24-April-2005 (last modified) kehi�CORE (coordinate regulatory element for antioxidant defense)conserved on the promoter regions of three antioxidant defensegenes in rice: cytosolic superoxide dismutase, cytosolicthioredoxin, and glutaredoxin; K=T/G; W=T/A; Y=T/C; R=A/G;M=C/A;oxidative stress antioxidantOryza sativa (rice)?Tsukamoto S, Morita S, Hirano E, Yokoi H, Masumura T, Tanaka K.lA novel cis-element that is responsive to oxidative stressregulates three antioxidant defense genes in rice."Plant Physiol. 137: 317-327.(2005)PubMed: 15618434 AAKAATWYRTAWATAAAAMTTTTATWTA
DPBFCOREDCDC3S000292 7-Sep-2000 (last modified) seki��A novel class of bZIP transcription factors, DPBF-1 and 2 (Dc3promoter-binding factor-1 and 2) binding core sequence; Found inthe carrot (D.c.) Dc3 gene promoter; Dc3 expression is normallyembryo-specific, and also can be induced by ABA; The Arabidopsisabscisic acid response gene ABI5 encodes a bZIP transcriptionfactor; abi5 mutant have a pleiotropic defects in ABA response;ABI5 regulates a subset of late embryogenesis-abundant genes;GIA1 (growth-insensitivity to ABA) is identical to ABI5; Dc3lea class geneembryoABADPBF-1, DPBF-2bZIPGIA1ABI5seed-carrot (Daucus carota); Arabidopsis thaliana;JKim SY, Chung HJ, Thomas TLFinkelstein RR, Lynch TJLopez-Molina L, Chua NH�kIsolation of a novel class of bZIP transcription factors thatinteract with ABA-responsive and embryo-specification elements inthe Dc3 promoter using a modified yeast one-hybrid systemThe Arabidopsis abscisic acid response gene ABI5 encodes a basicleucine zipper transcription factorA null mutation in a bZIP factor confers ABA-insensitivity inArabidopsis thaliana^Plant J 11: 1237-1251 (1997)Plant Cell 12: 599-609 (2000)Plant Cell Physiol 41: 541-547 (2000)WPubMed: 9225465 GenBank: AF061870, AF001454, AF001453PubMed: 10760247;PubMed: 10929936; ACACNNG DRECRTCOREATS000418$30-January-2006 (last modified) kehi��Core motif of DRE/CRT (dehydration-responsive element/C-repeat)cis-acting element found in many genes in Arabidopsis and inrice; R=G/A; Os DREB1A bound to GCCGAC more preferentially thanto ACCGAC whereas At DREB1A bound to both GCCGAC and ACCGACefficiently; See S000402 (ACCGAC); Maize ZmDREB1A bound to DRE(Qin et al. 2004); HaDREB2 in Helianthus annuus(sunflower)(Diaz-Martin et al. 2005); HaDREB2 physically interactwith HaHSFA9 in vitro (Diaz-Martin et al. 2005);DRE/CRTdrought
high-lightcoldDREBDREB1DREB2CBFDOryza sativa (rice); Zea mays (maize); Helianthus annuus(sunflower);��Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S,Seki M, Shinozaki K, Yamaguchi-Shinozaki K.Qin F, Sakuma Y, Li J, Liu Q, Li YQ, Shinozaki K,Yamaguchi-Shinozaki K.Diaz-Martin J, Almoguera C, Prieto-Dapena P, Espinosa JM, JordanoJSuzuki M, Ketterling MG, McCarty DR.Skinner JS, von Zitzewitz J, Szucs P, Marquez-Cedillo L,Filichkin T, Amundsen K, Stockinger EJ, Thomashow MF, Chen TH,Hayes PM.�qOsDREB genes in rice, Oryza sativa L., encode transcriptionactivators that function in drought-, high-salt- andcold-responsive gene expression.Cloning and functional analysis of a novel DREB1/CBFtranscription factor involved in cold-responsive gene expressionin Zea mays L.Functional Interaction between Two Transcription Factors Involvedin the Developmental Regulation of a Small Heat Stress ProteinGene PromoterQuantitative statistical analysis of cis-regulatory sequences inABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis.Structural, functional, and phylogenetic characterization of alarge CBF gene family in barley.�Plant J. 33: 751-763 (2003)Plant Cell Physiol. 45: 1042-1052 (2004).Plant Physiology, 139: 1483-1494 (2005)Plant Physiol.139: 437-447 (2005)Plant Mol Biol. 59: 533-551 (2005)QPubMed: 12609047;PubMed: 15356330PubMed: 16244139PubMed: 16113229PubMed: 16244905 in silicoRCCGACE2FATS000417 03-Jun-2003 (last modified) kehi�"E2F-binding site" found in many potential E2F target genes; mostpotential E2F targets identified in silico show a cellcycle-regulated expression; Y=T/C; see S000366;E2F
cell cycleArabidopsis thaliana'Ramirez-Parra E, Frundt C, Gutierrez C.BA genome-wide identification of E2F-regulated genes inArabidopsis.Plant J. 33: 801-811 (2003)PubMed: 12609051; TYTCCCGCC E2FCONSENSUSS000476%05-November-2005 (last modified) kehi�"E2F consensus sequence" of all different E2F-DP-binding motifsthat were experimentally verified in plants (Vandepoele et al.,2005); See also S000417, S000397, S000396, S000367, S000366;W=A/T; S=C/G;E2F]Arabidopsis thaliana; Nicotiana tabacum (tobacco); Oryza sativa(rice); Nicotiana benthamiana;kVandepoele K, Vlieghe K, Florquin K, Hennig L, Beemster GT,Gruissem W, Van de Peer Y, Inze D, De Veylder L.?Genome-wide identification of potential plant E2F target genes."Plant Physiol.139: 316-328. (2005)PubMed: 16126853 WTTSSCSS
EBOXBNNAPAS000144#02-August-2006 (last modified) kehi�E-box of napA storage-protein gene of Brassica napus (B.n.); SeeS000042 (CACGTGMOTIF); see S000407 (Myc consensus: CANNTG); Thissequence is also known as RRE (R response element)(Hartmann etal., 2005);napAstorage proteinABREE-boxseedBrassica napus;nStalberg K, Ellerstom M, Ezcurra I, Ablov S, Rask LHartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B.�ZDisruption of an overlapping E-box/ABRE motif abolished hightranscription of the napA storage-protein promoter in transgenicBrassica napus seeds.Differential combinatorial interactions of cis-acting elementsrecognized by R2R3-MYB, BZIP, and BHLH factors controllight-responsive and tissue-specific activation ofphenylpropanoid biosynthesis genes.<Planta 199:515-519 (1996)Plant Mol Biol. 57: 155-171 (2005). PubMed: 8818291;PubMed: 15821875 CANNTG EECCRCAH1S000494"24-April-2006 (last modified) kehi�� "EEC"; Consensus motif of the two enhancer elements, EE-1 andEE-2, both found in the promoter region of the Chlamydomonas Cah1(encoding a periplasmic carbonic anhydrase); Binding site of Mybtranscription factor LCR1 (see Yoshioka et al, 2004); N=A/G/C/T;low-CO2Chlamydomonas reinhardtiiwKucho K, Yoshioka S, Taniguchi F, Ohyama K, Fukuzawa H.Yoshioka S, Taniguchi F, Miura K, Inoue T, Yamano T, Fukuzawa H.�ECis-acting elements and DNA-binding proteins involved inCO2-responsive transcriptional activation of Cah1 encoding aperiplasmic carbonic anhydrase in Chlamydomonas reinhardtii.The novel Myb transcription factor LCR1 regulates theCO2-responsive gene Cah1, encoding a periplasmic carbonicanhydrase in Chlamydomonas reinhardtii.CPlant Physiol. 133: 783-793 (2003).Plant Cell. 16: 1466-1477.(2004) PubMed: 14555782PubMed: 15155888 GANTTNC ELRENTCHN50S000155 17-May-1998 (last modified) kehiaElicitor-responsive element (ElRE); Found in tobacco (N. t.)basic class I chitinase gene (CHN50);ELREelicitor chitinase tobacco (Nicotiana tabacum);Fukuda Y{Interaction of tobacco nuclear protein with anelicitor-responsive element in the promoter of a basic class Ichitinase gene. Plant Mol Biol 34:81-87 (1997)PubMed: 9177314; GGTCANNNAGTCERELEE4S000037#02-August-2006 (last modified) kehi�"ERE (ethylene responsive element)" of tomato (L.e.) E4 andcarnation GST1 genes; GST1 is related to senescence; Found in the5'-LTR region of TLC1.1 retrotransposon family in Lycopersiconchilense (Tapia et al.); ERE motifs mediate ethylene-inducedactivation of the U3 promoter region;EthyleneE4GST1
senescenceEREfruitZtomato (Lycopersicon esculentum); carnation (Dianthuscaryophyllus); Lycopersicon chilense;�Itzhaki H, Maxson JM, Woodson WRMontgomery J, Goldman S, Deikman J, Margossian L, Fischer RLTapia G, Verdugo I, Yanez M, Ahumada I, Theoduloz C, Cordero C,Poblete F, Gonzalez E, Ruiz-Lara S.Rawat R, Xu ZF, Yao KM, Chye ML.��An ethylene-responsive enhancer element is involved in thesenescence-related expression of the carnationglutathione-S-transferase (GSTI) gene.Identification of an ethylene-responsive region in the promoterof a fruit ripening gene.Involvement of Ethylene in Stress-Induced Expression of theTLC1.1 Retrotransposon from Lycopersicon chilense Dun.Identification of cis-elements for ethylene and circadianregulation of the Solanum melongena gene encoding cysteineproteinase.�Proc Natl Acad Sci USA 91:8925-8929 (1994)Proc Natl Acad Sci USA 90:5939-5943 (1993)Plant Physiol. 138:2075-2086 (2005)Plant Mol Biol. 57: 629-643 (2005).@PubMed: 8090746;PubMed: 8327464;PubMed: 16040666PubMed: 15988560 AWTTCAAAGARE2S000165 17-May-1998 (last modified) kehi{Putative gibberellin responsive element; Consensus sequence of GAinducible alpha-amylase genes from rice, barley and wheat; gibberellinGAREseedHrice (Oryza sativa); barley (Hordeum vulgare); wheat (Triticumaestivum);?Huang N, Sutliff TD, Litts JC, Rodriguez RLRogers JC, Rogers SW�Classification and characterization of the rice alpha-amylasemultigene family.Definition and functional implications of gibberellin andabscisic acid cis-acting hormone response complexes=Plant Mol Biol 14:655-668 (1990)Plant Cell 4:1443-1451 (1992)1PubMed: 2102847; GenBank: X16509;PubMed: 1477557;&Consensus sequence of GA-induced genesRTAACARANTCYGGGAREATS000439 27-Jan-2004 (last modified) kehi�GARE (GA-responsive element); Occurrence of GARE in GA-inducible,GA-responsible, and GA-nonresponsive genes found in Arabidopsisseed germination was 20, 18, and 12%, respectively; see S000181;GAREGAArabidopsis thaliana;@Ogawa M, Hanada A, Yamauchi Y, Kuwahara A, Kamiya Y, YamaguchiS.IGibberellin biosynthesis and response during Arabidopsis seedgermination. Plant Cell 15: 1591-1604 (2003)PubMed: 12837949; TAACAAR
GBOXLERBCSS000041 7-Sep-2000 (last modified) seki�"G box"; Conserved sequence upstream of light-regulated genes;Sequence found in the promoter region of rbcS of tomato (L.e.)and Arabidopsis; Binding with GBF; M=A/C; See S000345;G boxrbcStomatoG-boxleafshoot7tomato (Lycopersicon esculentum); Arabidopsis thaliana;�Giuliano G, Pichersky E, Malik VS, Timko MP, Scolnik PA, CashmoreARDonald RGK, Cashmore ARVasil V, Marcotte Jr. WR, Rosenkrans L, Cocciolone SM, Vasil IK,Quatrano RS, McCarty DR�fAn evolutionarily conserved protein binding sequence upstream ofa plant light-regulated gene.Mutation of either G box or I box sequences profoundly affectsexpression from the Arabidopsis rbcS-1A promoter.Overlap of viviparous1 (VP1) and abscisic acid response elementsin the EM promoter: G-Box elements are sufficient but notnecessary for VP1 transactivationaProc Natl Acad Sci USA 85:7089-7093 (1988)EMBO J 9:1717-1726 (1990)Plant Cell 7: 1511-1518 (1995)/PubMed: 2902624;PubMed: 2347304;PubMed: 8589631 MCACGTGGC
GLMHVCHORDS000451%29-November-2004 (last modified) kehi�a"GLM (GCN4-like motif)" found in the promoter of barley (H.v.)B1- and c-hordein gene; Involved in the nitrogen response ofc-hordein promoter; R=A/G; S=C/G; See also S000277 (GCN4OSGLUB1);SPA, a seed-specific basic leucine zipper protein from wheat, canactivate transcription from the GCN4-like motif (GLM) of -326LMWG-1D1 promoter (Albani et al., 1997);GLMGCN4hordeinGLM4Hordeum vulgare (barley); Triticum aestivum (wheat);�Muller M, Knudsen S.Albani D, Hammond-Kosack MC, Smith C, Conlan S, Colot V,Holdsworth M, Bevan MW.Onate L, Vicente-Carbajosa J, Lara P, Diaz I, Carbonero P.��The nitrogen response of a barley C-hordein promoter iscontrolled by positive and negative regulation of the GCN4 andendosperm box.The wheat transcriptional activator SPA: a seed-specific bZIPprotein that recognizes the GCN4-like motif in the bifactorialendosperm box of prolamin genes.Barley BLZ2, a seed-specific bZIP protein that interacts withBLZ1 in vivo and activates transcription from the GCN4-like motifof B-hordein promoters in barley endosperm.\Plant J. 4: 343-355 (1993).Plant Cell. 9: 171-184 (1997).J Biol Chem. 274: 9175-9182 (1999)..PubMed: 8220485PubMed: 9061949PubMed: 10092589 RTGASTCAT GT1CONSENSUSS000198 11-May-2006 (last modified) kehi��Consensus GT-1 binding site in many light-regulated genes, e.g.,RBCS from many species, PHYA from oat and rice, spinach RCA andPETA, and bean CHS15; R=A/G; W=A/T; For a compilation of relatedGT elements and factors, see Villain et al. (1996); GT-1 canstabilize the TFIIA-TBP-DNA (TATA box) complex; The activationmechanism of GT-1 may be achieved through direct interactionbetween TFIIA and GT-1; Binding of GT-1-like factors to the PR-1apromoter influences the level of SA-inducible gene expression;
GT-1lightTATATFIIATBPHRSARTMVleafshoot�pea (Pisum sativum); oat (Avena sativa); rice (Oryza sativa);tobacco (Nicotiana tabacum); Arabidopsis thaliana; spinach(Spinacia oleracea); bean;�Terzaghi WB, Cashmore ARVillain P, Mache R, Zhou DXLe Gourrierec J, Li YF, Zhou DXBuchel AS, Brederode FT, Bol JF, Linthorst HJMZhou DX��Light-regulated transcriptionThe mechanism of GT element-mediated cell type-specifictranscriptional controlTranscriptional activation by Arabidopsis GT-1 may be throughinteraction with TFIIA-TBP-TATA complexMutation of GT-1 binding sites in the Pr-1A promoter influencesthe level of inducible gene expression in vivoRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)J Biol Chem 271:32593-32598 (1996)Plant J 18:663-668 (1999)Plant Mol Biol 40:387-396 (1999)Trends in Plant Science 4:210-214 (1999)APubMed: 8955086;PubMed: 10417717PubMed: 10437823;PubMed: 10366876 ReviewReviewGRWAAWGT1MOTIFPSRBCSS000051 15-Oct-1999 (last modified) kehi�"GT-1 motif"; "Consensus sequence of rbcS BOX II, III, II',III'"; "GT-1 box"; 5' upstream region (-151) of pea (P.s.) rbcSgene; binding with trans factor GT-1; See S000125 GT1CORE; K=G/T;W=A/T; R=A/G; For a compilation of related GT elements andfactors, see Villain et al. (1996);RBCSBOX 2Box IIGT-1PEAleafshootpea (Pisum sativum)�Green PJ, Yong M-H, Cuozzo M, Kano-Murakami Y, Silverstein P,Chua N-HGilmartin PM, Sarokin L, Memelink J, Chua N-HVillain P, Mache R, Zhou DXZhou DX�eBinding site requirements for pea nuclear protein factor GT-1correlate with sequences required for light-dependenttranscriptional activation of the rbcS-3A gene.Molecular light switches for plant genes.The mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorsEMBO J 7:4035-4044 (1988)Plant Cell 2:369-378 (1990)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)0PubMed: 3243271;PubMed: 2152164;PubMed: 8955086;Review KWGTGRWAAWRWHBOXCONSENSUSPVCHSS000200 27-Aug-2002 (last modified) uchi��"H-box"; Consensus sequence of H-boxes found in bean (Phaseolusvulgaris) chs15 gene promoter; Essential for both lightregulation and elicitor induction; Similar sequence was found intobacco Tnt1 retrotransposon promoter (LTR); Tnt1 is induced bywounding and by abiotic stress; "KAP-2" binds to the H-box andstimulates transcription from a promoter harboring the H-box;"KAP-2" shares sequence similarity to the large subunit ofmammalian Ku autoantigen; See S000150, S000402 and S000401;H-boxH boxCHSchslight regulationlightelicitorstress
transposonwoundingleafshootKu autoantigenKAP-2#bean (Phaseolus vulgaris); tobacco;�Loake GJ, Faktor O, Lamb CJ, Dixon RATerzaghi WB, Cashmore ARMhiri C, Morel JB, Vernhettes S, Casacuberta JM, Lucas H,Grandbastien MALindsay WP, McAlister FM, Zhu Q, He XZ, Droge-Laser W, Hedrick S,Doerner P, Lamb C, Dixon RA��Combination of H-box [CCTACC(N)7CT] and G-box (CACGTG) ciselements is necessary for feed-forward stimulation of a chalconesynthase promoter by the phenypropanoid-pathway intermediatep-coumaric acidLight-regulated transcriptionThe promoter of the tobacco Tnt1 retrotransposon is induced bywounding and by abiotic stressKAP-2, a protein that binds to the H-box in a bean chalconesynthase promoter, is a novel plant transcription factor withsequence identity to the large subunit of human Ku autoantigen�Proc Natl Acad Sci USA 89:9230-9234(1992)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)Plant Mol Biol 33:257-266 (1997)Plant Mol Biol 49: 503-514 (2002)1PubMed: 1409628;PubMed: 9037144;PubMed: 12090626;ReviewCCTACCNNNNNNNCT HBOXPVCHS15S000361 16-Feb-2001 (last modified) seki�Binding site of two bean protein factors, KAP-1 and KAP-2; KAP-1is a 97 kDa polypeptide; KAP-2 comprises two polypeptides of 76kDa and 56 kDa; Elicitation of bean cell with glutathione causesa rapid increase in specific activities of KAP-1 and KAP2;H-boxKAP-1KAP-2elicitor glutathionebean (Phaseolus vulgaris)Yu LM, Lamb CJ, Dixon RA�Purification and biochemical characterization of proteins whichbind to the H-box cis-element implicated in transcriptionalactivation of plant defense genesPlant J 3: 805-816 (1993)PubMed: 8401613; CCTACCNNNNNNNCTNNNNA
HDZIP2ATATHB2S000373 31-Jul-2001 (last modified) uchi�
Binding site of the Arabidopsis (A.T.) homeobox gene (ATHB-2)found in its own promoter; Located between -72 and -80; Similarto the HD-ZIP-2 binding consensus sequence; ATHB-2 is regulatedby light signals which function as a negative autoregulator ofits own gene; M=C/A;ATHB-2HAT4HD-ZIPshade avoidance responsesArabidopsis thaliana0Ohgishi M, Oka A, Morelli G, Ruberti I, Aoyama T?Negative autoregulation of the Arabidopsis homeobox gene ATHB-2Plant J 25: 389-398 (2001)PubMed: 11260495; TAATMATTA
HDZIPIIIATS000475%05-November-2005 (last modified) kehi�Ath b-9 HD-Zip (HD-Zip-9), a member of a small family of HD-Zipproteins (HD-ZIP III), in Arabidopsis recognize this sequence;See also S000371; S=G/C;HomeoboxHD-ZIPArabidopsis thalianaTSessa G, Steindler C, Morelli G, Ruberti I.Ohashi-Ito K, Kubo M, Demura T, Fukuda H.�The Arabidopsis Athb-8, -9 and -14 genes are members of a smallgene family coding for highly related HD-ZIP proteins.Class III Homeodomain Leucine-Zipper Proteins Regulate Xylem CellDifferentiation.JPlant Mol Biol. 38: 609-622.(1998)Plant Cell Physiol. 46: 1646-1656 (2005) PubMed: 9747806PubMed: 16081527 GTAATSATTACHSES000054 16-Feb-2001 (last modified) seki��"HSE (heat shock response element)"; consensus sequence found inthe promoter regions of heat shock protein genes; HSF bindingsite; HsfA3, a new member of the Hsf (heat stress transcriptionfactor) family; was isolated by yeast two-hybrid screening, usingHsfA1 as a bait; HsfA3 is a single copy gene with all conservedsequence elements characteristic of a heat stress transcriptionfactor;
heat shockHSPHSE<animal; plant; Drosophila; tomato (Lycopersicon peruvianum);EPelham HBharti K, Schmidt E, Lyck R, Heerklotz D, Bublak D, Scharf KD�Activation of heat-shock genes in eukaryotes.Isolation and characterization of HsfA3, a new heat stresstranscription factor of Lycopersicon peruvianum5Trends Genet 1:31-35 (1985)Plant J (2000) 22: 355-365PubMed: 10849352;ReviewCTNGAANNTTCNAGHSELIKENTACIDICPR1S000056 17-May-1997 (last modified) kehi`"HSE-like motif" in -56 region of acidic PR1 gene of tobacco(N.t.); not found in basic PR1 gene;tobacco
PR-proteinhsetobacco (Nicotiana tabacum)%Pfitzner UM, Pfitzner AJP, Goodman HMyDNA sequence analysis of a PR-1a gene from tobacco: Molecularrelationship of heat shock and pathogen responses in plants. Mol Gen Genet 211:290-295 (1988) CNNGAANNNTTCNNG
IBOXCORENTS000424 29-Sep-2003 (last modified) kehi�"I-box core motif" in the CAMs (conserved DNA modular arrays)associated with light-responsive promoter regions; See S000124(GATAAG), S000199 (GATAA), S000213;I-boxCAMlight#Nicotiana plumbaginifolia (tobacco)KMartinez-Hernandez A, Lopez-Ochoa L, Arguello-Astorga G,Herrera-Estrella L.�Functional properties and regulatory complexity of a minimal RBCSlight-responsive unit activated by phytochrome, cryptochrome, andplastid signals.#Plant Physiol. 128:1223-1233 (2002)PubMed: 11950971; GATAAGR
IDRSZMFER1S000445#04-August-2006 (last modified) kehi�."IDRS" (Iron-Dependent Regulatory Sequence) found in maize andArabidopsis ferritin genes (Fer1); IDRS is responsible fortranscriptional repression of ZmFer1 gene under low iron supplyconditions; S=C/G; K=G/T; IDRS is not involved in theFe-regulated expression of the AtAPX1 gene (Fourcroy et al.,2004);ironferritinAPX1AtFer1Fer'Zea mays (maize); Arabidopsis thaliana;�Petit JM, van Wuytswinkel O, Briat JF, Lobreaux S.Fourcroy P, Vansuyt G, Kushnir S, Inze D, Briat JF.Tarantino D, Petit JM, Lobreaux S, Briat JF, Soave C, Murgia I.Arnaud N, Murgia I, Boucherez J, Briat JF, Cellier F, Gaymard F.�Characterization of an iron-dependent regulatory sequenceinvolved in the transcriptional control of AtFer1 and ZmFer1plant ferritin genes by iron.Iron-regulated expression of a cytosolic ascorbate peroxidaseencoded by the APX1 gene in Arabidopsis seedlings.Differential involvement of the IDRS cis-element in thedevelopmental and environmental regulation of the AtFer1 ferritingene from Arabidopsis.An iron-induced nitric oxide burst precedes ubiquitin-dependentprotein degradation for arabidospsis atfer1 ferritin geneexpression.�J Biol Chem. 276:5584-5590. (2001)Plant Physiol. 134: 605-613 (2004). .Planta. 217: 709-716 (2003)J Biol Chem. 2006 Jun 16; [Epub ahead of print]@PubMed: 11092880PubMed: 14739345PubMed: 12728319PubMed: 16782706 CACGAGSCCKCCAC
INRNTPSADBS000395 21-May-2002 (last modified) uchi�"Inr (initiator)" elements found in the tobacco psaDb genepromoter without TATA boxes; Light-responsive transcription ofpsaDb depends on Inr, but not TATA box; initiater light-responsive transcriptionTATA-less promoterpsaDb Inr elementtobacco (Nicotiana tabacum) Nakamura M, Tsunoda T, Obokata JzPhotosynthesis nuclear genes generally lack TATA-boxes: a tobaccophotosystem I gene responds to light through an initiaterPlant J 29: 1-10 (2002)PubMed: 12060222 ; YTCANTYY INTRONUPPERS000085 17-May-1998 (last modified) kehiu"5' exon-intron splice junctions" of plant introns; Plant intronupper sequence; Consensus sequence for plant introns;intronsplice junctionmaize (Zea mays) Brown JWSSA catalog of splice junction and putative branch point sequencesfrom plant introns.%Nucleic Acids Res 14:9549-9559 (1986)PubMed: 3808952;Review MAGGTAAGT L1BOXATPDF1S000386%05-November-2005 (last modified) kehi�|"L1 box" found in promoter of Arabidopsis thaliana (A.t.)PROTODERMAL FACTOR1 (PDF1) gene; Located between -134 and -127;Involved in L1 layer-specific expression; L1-specific homeodomainprotein ATML can bind to the "L1 box"; Y=C/T; A cotton fibergene, RD22-like 1 (RDL1), contains a homeodomain binding L1 boxand a MYB binding motif (Wang et al., 2004); HDZip IV; See alsoS000371; PDF1L1 box L1 layer-specific expression Shoot apicalmeristemSAMorgan primordia cotton fiberHDZip homeodomainleucine zipper-Arabidopsis thaliana; Gossypium spp (cotton);�)Abe M, Takahashi T, Komeda YWang S, Wang JW, Yu N, Li CH, Luo B, Gou JY, Wang LJ, Chen XY.Henriksson E, Olsson AS, Johannesson H, Johansson H, Hanson J,Engstrom P, Soderman E.Abe M, Katsumata H, Komeda Y, Takahashi T.Ohashi Y, Oka A, Rodrigues-Pousada R, Possenti M, Ruberti I,Morelli G, Aoyama T.��Identification of a cis-regulatory element for L1 layer-specificgene expression, which is targeted by an L1-specific homeodomainproteinControl of plant trichome development by a cotton fiber MYBgene.Homeodomain leucine zipper class I genes in Arabidopsis.Expression patterns and phylogenetic reRegulation of shoot epidermal cell differentiation by a pair ofhomeodomain proteins in Arabidopsis.Modulation of phospholipid signaling by GLABRA2 in root-hairpattern formation.�Plant J 26: 487-494 (2001)Plant Cell 16: 2323-2334 (2004)Plant Physiol. 139: 509-518. (2005)Development. 130: 635-643.(2003)Science. 300: 1427-1430 (2003).QPubMed: 11439135;PubMed: 15316114PubMed: 16055682PubMed: 12505995PubMed: 12775839 TAAATGYALEGUMINBOXLEGA5S000060 17-May-1998 (last modified) kehi:"legumin box" in legA 5' legumin gene promoter in legumin;leguminpeatobaccopromoterseed=pea (Pisum sativum); tobacco (Nicotiana tabacum); Vicia faba;QBaumlein H, Wobus U, Pustell J, Kafatos FCShirsat A, Wilford N, Croy R, Boulter D�The legumin gene family: structure of a B type gene of Vicia fabaand a possible legumin gene specific regulatory element.Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco.ENucleic Acids Res 14:2707-2720 (1986)Mol Gen Genet 215:326-331 (1989)1PubMed: 3960730; GenBank: X03677;PubMed: 2710102; TCCATAGCCATGCAWRCTGMAGAATGTCMARABOX1S000063 13-Feb-2001 (last modified) kehiR"A-box" found in SAR(scaffold attachment region; or matrixattachment region, MAR);MARSARmatrixA-boxscaffoldDrosophila; fly;-Gasser SM, Amati BB, Cardenas ME, Hofmann JFXJStudies on scaffold attachment sites and their relation to genomefunction."Intnatl Rev Cyto 119:57-96 (1989)PubMed: 2695485;Review
AATAAAYAAAMARARSS000064 16-Jan-1998 (last modified) kehi("ARS element"; Motif found in SAR (MAR);MARSARARSyeast-Gasser SM, Amati BB, Cardenas ME, Hofmann JFXJStudies on scaffold attachment sites and their relation to genomefunction."Intnatl Rev Cyto 119:57-96 (1989)PubMed: 2695485;Review WTTTATRTTTWMARCEN3S000065 16-Jan-1998 (last modified) kehi@"CEN III element"; Motif found in SAR (MAR); centromere element;MARSARARSCEN
centromereyeast-Gasser SM, Amati BB, Cardenas ME, Hofmann JFXJStudies on scaffold attachment sites and their relation to genomefunction.!Intnatl Rev Cyto 119:57-96 (1989)PubMed: 2695485;ReviewTGTTTWTGNTTTCCGAAANNNNWWWMARTBOXS000067 13-Feb-2001 (last modified) kehiZ"T-Box"; Motif found in SAR (scaffold attachment region; ormatrix attachment region, MAR);MARSART-boxscaffoldmatrixDrosophila; fly;-Gasser SM, Amati BB, Cardenas ME, Hofmann JFXJStudies on scaffold attachment sites and their relation to genomefunction.!Intnatl Rev Cyto 119:57-96 (1989)PubMed: 2695485;Review
TTWTWTTWTT MEJARELELOXS000151 17-May-1998 (last modified) kehi�MeJa-responsive element (MeJaRE) in tomato (L. e.) lipoxygenase(LOX) gene; Related to tomato lipoxygenase gene expression duringdevelopment and for MeJa (methyl jasmonate)-responsiveness; lipoxygenaseloxmethyl jasmonateshootleaf!tomato (Lycopersicon esculentum);Beaudoin N, Rothstein SJ^Developmental regulation of two tomato lipoxygenase promoters intransgenic tobacco and tomato. Plant Mol Biol 33:835-846 (1997))PubMed: 9106507; GenBank: U63117, U63118; GATACANNAATNTGATGMYB1ATS000408 03-Jun-2003 (last modified) kehi}MYB recognition site found in the promoters of thedehydration-responsive gene rd22 and many other genes inArabidopsis; W=A/T;MYBrd22BP1ABAleafseedstressArabidopsis thaliana@Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-ShinozakiK.lArabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function astranscriptional activators in abscisic acid signaling.Plant Cell 15: 63-78 (2003)PubMed: 12509522; WAACCAMYB2CONSENSUSATS000409 03-Jun-2003 (last modified) kehi�MYB recognition site found in the promoters of thedehydration-responsive gene rd22 and many other genes inArabidopsis; Y=C/T; K=G/T; See S000177 (MYB2), S000175(MYBATRD22);MYBrd22BP1ABAleafseedstressArabidopsis thaliana@Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-ShinozakiK.lArabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function astranscriptional activators in abscisic acid signaling.Plant Cell 15: 63-78 (2003)PubMed: 12509522; YAACKGMYBCORES000176 16-May-2001 (last modified) uchi�WBinding site for all animal MYB and at least two plant MYBproteins ATMYB1 and ATMYB2, both isolated from Arabidopsis;ATMYB2 is involved in regulation of genes that are responsive towater stress in Arabidopsis; A petunia MYB protein (MYB.Ph3) isinvolved in regulation of flavonoid biosynthesis (Solano et al.EMBO J 14:1773 (1995)); See S000355;MYBmyb dehydrationwaterstressflavonoid biosynthesisleafshoot8Arabidopsis thaliana; animal; petunia (Petunia hybrida);~Luscher B, Eiseman RNUrao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki KSolano R, Nieto C, Avila J, Canas L, Diaz I, Paz-Ares J�New light on Myc and Myb. Part II. Myb.An Arabidopsis myb homolog is induced by dehydration stress andits gene product binds to the conserved MYB recognition sequenceDual DNA binding specificity of a petal epidermis-specific MYBtranscription factor (MYB.Ph3) from Petunia hybridaTGenes Dev. 4:2235-2241 (1990)Plant Cell 5:1529-1539 (1993)EMBO J 14:1773-1784 (1995)APubMed: 2279697;PubMed: 8312738; GenBank: D14712;PubMed: 7737128;ReviewCNGTTRMYBPLANTS000167 16-May-2001 (last modified) uchi�@Plant MYB binding site; Consensus sequence related to box P inpromoters of phenylpropanoid biosynthetic genes such as PAL, CHS,CHI, DFR, CL, Bz1; Myb305; M=A/C; W=A/T; See S000355; TheAmMYB308 and AmMYB330 transcription factors from Antirrhinummajus regulate phenylpropanoid and lignin biosynthesis intransgenic tobacco;MybMYBMyb305AmMYB308AmMYB330flowerPALCHSDFRCandiBz1phenylpropanoidligninleafshoot�snapdragon (Antirrhinum majus); bean (Phaseolus vulgaris);petunia (Petunia hybrida); Arabidopsis thaliana; maize (Zeamays); parsley (Petroselinum crispum);�Sablowski RWM, Moyano E, Culianez-Macia FA, Schuch W, Martin C,Bevan MTamagnone L, Merida A, Parr A, Mackay S, Culianez-Macia FA,Roberts K, Martin C�A flower-specific Myb protein activates transcription ofphenylpropanoid biosynthetic genes.The AmMYB308 and AmMYB330 transcription factors from antirrhinumregulate phenylpropanoid and lignin biosynthesis in transgenictobacco5EMBO J 13:128-137 (1994)Plant Cell 10: 135-154 (1998) PubMed: 8306956;PubMed: 9490739; MACCWAMCMYBPZMS000179 17-May-1998 (last modified) kehi�Core of consensus maize P (myb homolog) binding site; W=A/T; 6 bpcore; Maize P gene specifies red pigmentation of kernel pericarp,cob, and other floral organs; P binds to A1 gene, but not Bz1gene; Maize C1 (myb homolog) activates both A1 and Bz1 genes(Grotewold et al. 1994); W=A/T;PP gene: P-geneMYBmybseedmaize (Zea mays);-Grotewold E, Drummond BJ, Bowen B, Peterson T�The myb-homologous P gene controls phlobaphene pigmentation inmaize floral organs by directly activating a flavonoidbiosynthetic gene subsetCell 76:543-553 (1994)PubMed: 8313474; CCWACCMYCCONSENSUSATS000407$04-January-2007 (last modified) kehi�MYC recognition site found in the promoters of thedehydration-responsive gene rd22 and many other genes inArabidopsis; Binding site of ATMYC2 (previously known asrd22BP1); see S000144 (E-box; CANNTG), S000174 (MYCATRD22);N=A/T/G/C; MYC recognition sequence in CBF3 promoter; Bindingsite of ICE1 (inducer of CBF expression 1) that regulates thetranscription of CBF/DREB1 genes in the cold in Arabidopsis; ICE1(Chinnusamy et al., 2004);) This sequence is also known as RRE (Rresponse element)(Hartmann et al., 2005); MYCrd22BP1ABAleafseedstressCBF3cold CBF/DREB1ICE1RREArabidopsis thaliana��Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-ShinozakiK.Chinnusamy V, Ohta M, Kanrar S, Lee BH, Hong X, Agarwal M, ZhuJK.Chinnusamy V, Schumaker K, Zhu JK.Oh SJ, Song SI, Kim YS, Jang HJ, Kim SY, Kim M, Kim YK, Nahm BH,Kim JK.Lee BH, Henderson DA, Zhu JK.Hartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B.Agarwal M, Hao Y, Kapoor A, Dong CH, Fujii H, Zheng X, Zhu JK.� Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function astranscriptional activators in abscisic acid signaling.ICE1: a regulator of cold-induced transcriptome and freezingtolerance in Arabidopsis.Molecular genetic perspectives on cross-talk and specificity inabiotic stress signalling in plants.Arabidopsis CBF3/DREB1A and ABF3 in transgenic rice increasedtolerance to abiotic stress without stunting growth.The Arabidopsis Cold-Responsive Transcriptome and Its Regulationby ICE1.Differential combinatorial interactions of cis-acting elementsrecognized by R2R3-MYB, BZIP, and BHLH factors controllight-responsive and tissue-specific activation ofphenylpropanoid biosynthesis genes.A R2R3 type MYB transcription factor is involved in the coldregulation of CBF genes and in acquired freezing tolerance.�Plant Cell 15: 63-78 (2003)Genes Dev. 17: 1043-1054 (2003)J Exp Bot. 55: 225-236 (2004).Plant Physiology 138: 341-351 (2005)Plant Cell. 17: 3155-3175 (2005)Plant Mol Biol. 57: 155-171(2005).J Biol Chem. 281:37636-37645 (2006)rPubMed: 12509522;PubMed: 12672693;PubMed: 14673035PubMed: 15834008PubMed: 16214899PubMed: 15821875PubMed: 17015446Review.CANNTGOCETYPEIIINTHISTONES000269 15-Oct-1999 (last modified) kehi�"Type III element"; Oct-containing composite element Type IIIfound in tobacco (N.t.) histone gene promoter; Oct (octomer)motif is paired with CCAAT-box to form Type III element; Requiredfor S-phase specific and meristematic tissue-specificexpression;histoneOctOCE CCAAT-boxType IIIS-phasemeristemtobacco (Nicotiana tabacum)9Taoka K, Kaya H, Nakayama T, Araki T, Meshi T, Iwabuchi MzIdentification of three Kinds of mutually related compositeelements conferring S phase-specific transcriptional activationPlant J 18:611-623 (1999)PubMed: 10417712; GATCCGCGNNNNNNNNNNNNNNACCAATCSOCETYPEINTHISTONES000267 15-Oct-1999 (last modified) kehi�"Type I element"; Oct-containing composite element Type I foundin tobacco (N.t.) histone gene promoter; Oct (octomer) motif ispaired with Hex motif to form Type I element; Required forS-phase specific and meristematic tissue-specific expression;histoneOctOCE Hex-motifType ImeristemS-phasetobacco (Nicotiana tabacum)9Taoka K, Kaya H, Nakayama T, Araki T, Meshi T, Iwabuchi MzIdentification of three Kinds of mutually related compositeelements conferring S phase-specific transcriptional activationPlant J 18:611-623 (1999)PubMed: 10417712; CCACGTCANCGATCCGCG OCSELEMENTATS000158 16-Feb-2001 (last modified) seki��"OCS element" in octopine synthase gene (OCS) of Ti-plasmid ofAgrobacterium (A.t.); Binding with nuclear protein isolated fromtobacco; See OCS motif (S000074); "ocs-like element"; Also foundin Arabidopsis glutathione S-transferase gene (GST6); OBF (ocselement binding factor)-binding site; See S000346; Tandem OCSTFbinding-sites are essential for the activity of the Ocs-element;The Ocs-element occures rarely in plant gene promoters; SeeS000357;octopine synthaseocsGST6glutathione S-transferase9Agrobacterium tumefaciens; tobacco; Arabidopsis thaliana;�Bouchez D, Tokuhisa JG, Llewellyn DJ, Dennis ES, Ellis JGFoley RC, Grossman C, Ellis JG, Llewellyn DJ, Dennis ES, PeacockWJ, Singh KBChen W, Chao G, Singh KBEllis JG, Tokuhisa JG, Llewellyn DJ, Bouchez D, Singh K, DennisES, Peacock WJ��The ocs-element is a component of the promoters of several T-DNAand plant viral genes.Isolation of a maize bZIP protein subfamily: candidates for theocs-element transcription factor.The promoter of a H2O2-inducible, Arabidopsis glutathioneS-transferase gene contains closely linked OBF- and OBP1-bindingsitesDoes the ocs-element occur as a functional component of thepromoters of plant genes?dEMBO J 8:4197-4204 (1989)Plant J 3: 669-679 (1993)Plant J 10:955-966 (1996)Plant J (1993) 4: 433-443@PubMed: 2591372;PubMed: 8374617;PubMed: 9011080;PubMed: 8220489; TGACGYAAGSRMTKACGYMM OPAQUE2ZMB32S000077 17-May-1998 (last modified) kehi�"opaque-2 binding site" of maize (Z.m.) b-32 (type Iribosome-inactivating protein gene; O2; O2S; O2S and GARE form agibberellin response complex (GARC)(Rogers and Rogers, 1992); opaque-2o2b-32O2O2Scoupling elementGARCGAREseedmaize (Zea mays)�#Muller M, Muth JR, Gallusci P, Knudsen S, Maddaloni M, Motto M,Schmitz D, Sorensen MB, Salamini F, von Wettstein D, Thompson RDCroissant-Sych Y, Okita TWLohmer S, Maddaloni M, Motto M, Di Fonzo N, Hartings H, SalaminiF, Thompson RDRogers JC, Rogers SWLanahan MB, Ho THD, Rogers SW, Rogers JC��Regulation of storage protein synthesis in cereal seeds:developmental and nutritional aspects.Identification of positive and negative regulatory cis-elementsof the rice glutelin Gt3 promoter.The maize regulatory locus Opaque-2 encodes a DNA-binding proteinwhich activates the transcription of the b-32 gene.Definition and functional implications of gibberellin andabscisic acid cis-acting hormone response complexes.A gibberellin response complex in cereal alpha-amylase genepromoters.�J Plant Physiol 145:606-613 (1995)Plant Science 116:27-35 (1996)EMBO J 10:617-624 (1991)Plant Cell 4:1443-1451 (1992)Plant Cell 4:203-211 (1992)0PubMed: 2001677;PubMed: 1477557;PubMed: 1386000;
GATGAYRTGGP1BSS000459"27-March-2004 (last modified) kehi�PHR1-binding sequence found in the upstream regions of phosphatestarvation responsive genes from several plant species; phr1(phosphate starvation response 1) gene codes for PHR1 proteinrelated to PSR1 gene in C. reinhardtii; phosphate
starvationMYBeArabidopsis thaliana; Lycopersicon esculentum (tomato); Medicagotruncatula; Hordeum vulgare (barley);�Rubio V, Linhares F, Solano R, Martin AC, Iglesias J, Leyva A,Paz-Ares J.Schunmann PH, Richardson AE, Smith FW, Delhaize E.Schunmann PH, Richardson AE, Vickers CE, Delhaize E.��A conserved MYB transcription factor involved in phosphatestarvation signaling both in vascular plants and in unicellularalgae.Characterization of promoter expression patterns derived from thePht1 phosphate transporter genes of barley (Hordeum vulgare L.).Promoter analysis of the barley Pht1;1 phosphate transporter geneidentifies regions controlling root expression and responsivenessto phosphate deprivation.bGenes Dev. 15: 2122-2133.(2001)J Exp Bot. 55: 855-865. (2004)Plant Physiol. 136: 4205-4214. (2004)0PubMed: 11511543PubMed: 15020637PubMed: 15542491 GNATATNC PALBOXLPCS000138$06-January-2006 (last modified) kehi��Box L; Consensus; One of three putative cis-acting elements(boxes P, A, and L) of phenylalanine ammonia-lyase (PAL; EC4.3.1.5) genes in parsley (P.c.); "None of these elements (boxesP, A, and L) alone, or the promoter region containing all of themtogether, conferred elicitor or light responsiveness. Theseelements appear to be necessary but not sufficient for elicitor-or light-mediated PAL gene activation." (Logemann et al., 1995);See also S000136 (Box P), S000137 (Box A);Box LPAL parsley (Petroselinum crispum)#Logemann E, Parniske M, Hahlbrock KuModes of expression and common structural features of thecomplete phenylalanine ammonia-lyase gene family in parsley.*Proc Natl Acad Sci USA 92:5905-5909 (1995)1PubMed: 7597051; GenBank: L37355, L37356, L37357; YCYYACCWACC PALBOXPPCS000136$06-January-2006 (last modified) kehi��Box P; Consensus; One of three putative cis-acting elements(boxes P, A, and L) of phenylalanine ammonia-lyase (PAL; EC4.3.1.5) genes in parsley (P.c.); "None of these elements (boxesP, A, and L) alone, or the promoter region containing all of themtogether, conferred elicitor or light responsiveness. Theseelements appear to be necessary but not sufficient for elicitor-or light-mediated PAL gene activation." (Logemann et al., 1995);See also S000137 (Box A), S000138 (Box L);Box PPAL parsley (Petroselinum crispum)#Logemann E, Parniske M, Hahlbrock KuModes of expression and common structural features of thecomplete phenylalanine ammonia-lyase gene family in parsley.*Proc Natl Acad Sci USA 92:5905-5909 (1995)1PubMed: 7597051; GenBank: L37355, L37356, L37357; YTYYMMCMAMCMMCPR2GCNTS000089 10-May-1998 (last modified) kehi�"GC element" conserved in the 5' upstream regions of group 2 PRprotein genes (beta-1,3-glucanase (GLN2), chitinase (CHN17,CHN50)) of tobacco (N.t.);tobaccogroup 2
pr-protein
GC element chitinasebeta-1,3-glucanase tobacco (Nicotiana tabacum);Ohme-Takagi M, Shinshi H>Structure and expression of a tobacco beta-1,3-glucanase gene. Plant Mol Biol 15:941-946 (1990)!PubMed: 2103484; GenBank: X53600; TAARAGCCGCCPRECONSCRHSP70AS000506$04-January-2007 (last modified) kehi�Consensus sequence of PRE (plastid response element) in thepromoters of HSP70A in Chlamydomonas; Involved in induction ofHSP70A gene by both MgProto and light; S=G/C; Y=C/T; R=A/G;H=T/C/A; D=A/T/G;HSP
chlorophylMgProtoChlamydomonas reinhardtii,von Gromoff ED, Schroda M, Oster U, Beck CF.nIdentification of a plastid response element that acts as anenhancer within the Chlamydomonas HSP70A promoter.&Nucleic Acids Res. 34:4767-4779 (2006)PubMed: 16971458
consensus;SCGAYNRNNNNNNNNNNNNNNNHD RHERPATEXPA7S000512$04-January-2007 (last modified) kehi�"Right part of RHEs (Root Hair-specific cis-Elements)" conservedamong the Arabidopsis thaliana A7 (AtEXPA7) orthologous (andparalogous) genes from diverse angiosperm species with differenthair distribution patterns; K=G/T; W=T/A;roothairArabidopsis thaliana@Kim DW, Lee SH, Choi SB, Won SK, Heo YK, Cho M, Park YI, Cho HT.~Functional Conservation of a Root Hair Cell-Specific cis-Elementin Angiosperms with Different Root Hair Distribution Patterns. Plant Cell. 18:2958-2970 (2006)PubMed: 17098810 KCACGWRYREPEATLEGUMINBOXS000100 17-May-1998 (last modified) kehii"RY repeat (CATGCAY)" or legumin box found in seed-storageprotein genes in legume such as soybean (G.m.); RY repeat legumin boxseedstorage protein legume; soybean (Glycine max);Fujiwara T, Beachy RNxTissue-specific and temporal regulation of a beta-conglyciningene: roles of the RY repeat and other cis-acting elements. Plant Mol Biol 24:261-272 (1994)PubMed: 8111031; CATGCAY SE2PVGRP1S000101 17-May-1998 (last modified) kehiF"SE2 (stem element 2)" of bean (P.v.) GRP1.8 gene; part of SE2element;stemSE2GRPGRP1bean (Phaseolus vulgaris)Elmayan T, Tepfer M.�Evaluation in tobacco of the organ specificity and strength ofthe rolD promoter, domain A of the 35S promoter and the 35S2promoter. Transgenic Res 4:388-396 (1995)PubMed: 7581519; TTNNNGTAGCTAGTGTATTTGTATSEBFCONSSTPR10AS000391 20-Feb-2002 (last modified) uchi�Binding site of the potato silencing element binding factor(SEBF) gene found in promoter of pathogenesis-related gene(PR-10a); Located between -45 and -39; Similar to the auxinresponse element; W=A/T;PR-10aSEBF pathogenesis silencingSolanum tuberosum (potato)Boyle B, Brisson NTRepression of the defense gene PR-10a by the single-stranded DNAbinding protein SEBF Plant Cell 13: 2525-2537 (2001)PubMed: 11701886; YTGTCWC SEF1MOTIFS000006 17-May-1998 (last modified) kehi�"SEF1 (soybean embryo factor 1)" binding motif; sequence found in5'-upstream region (-640; -765) of soybean beta-conglicinin (7Sglobulin) gene; W=A/T;SOYBEANSTORAGE PROTEIN7SGLOBULINBETA-CONGLICININseedsoybean (Glycine max)lAllen RD, Bernier F, Lessard PA, Beachy RNLessard PA, Allen RD, Bernier F, Crispino JD, Fujiwara T, BeachyRN�Nuclear factors interact with a soybean beta-conglycininenhancer.Multiple nuclear factors interact with upstream sequences ofdifferentially regulated beta-conglycinin genes.;Plant Cell 1:623-631 (1989)Plant Mol Biol 16:397-413 (1991) PubMed: 2535514;PubMed: 1893110; ATATTTAWW
SEF4MOTIFGM7SS000103 17-May-1998 (last modified) kehi�"SEF4 binding site"; Soybean (G.m.) consensus sequence found in5'upstream region (-199) of beta-conglycinin (7S globulin) gene(Gmg17.1); "Binding with SEF4 (soybean embryo factor 4)"; R=A/G;soybeanseedstorage protein7Sglobulinbeta-conglycininSEFsoybean (Glycine max);lAllen RD, Bernier F, Lessard PA, Beachy RNLessard PA, Allen RD, Bernier F, Crispino JD, Fujiwara T, BeachyRN�Nuclear factors interact with a soybean beta-conglycininenhancer.Multiple nuclear factors interact with upstream sequences ofdifferentially regulated beta-conglycinin genes.;Plant Cell 1:623-631 (1989)Plant Mol Biol 16:397-413 (1991) PubMed: 2535514;PubMed: 1893110; RTTTTTR SITEIIATCYTCS000474#01-August-2006 (last modified) kehi��"Site II element" found in the promoter regions of cytochromegenes (Cytc-1, Cytc-2) in Arabidopsis; Located between -147 and-156 from the translational starts sites (Welchen et al., 2005);Y=C/T; See also S000308; Overrepresented in the promoters ofnuclear genes encoding components of the oxidativephosphorylation (OxPhos) machinery from both Arabidopsis and rice(Welchen and Gonzalez, 2006);)
cytochrome
TCP-domainmeristemoxidative phosphorylation*Arabidopsis thaliana; Oryza sativa (rice);.Welchen E, Gonzalez DH.Welchen E, Gonzalez DH.��Differential expression of the Arabidopsis cytochrome c genesCytc-1 and Cytc-2. Evidence for the involvement of TCP-domainprotein-binding elements in anther- and meristem-specificexpression of the Cytc-1 gene.Overrepresentation of Elements Recognized by TCP-DomainTranscription Factors in the Upstream Regions of Nuclear GenesEncoding Components of the Mitochondrial OxidativePhosphorylation Machinery.APlant Physiol.139: 88-100 (2005)Plant Physiol. 141:540-545 (2006) PubMed: 16113211PubMed: 16760496 in silicoTGGGCY
SV40COREENHANS000123 17-May-1998 (last modified) kehiB"SV40 core enhancer"; Similar sequences found in rbcS genes;W=A/T;enhancerSV40core8virus; plant; pea (Pisum sativum); Arabidopsis thaliana;KWeiher H, Konig M, Gruss PGreen PJ, Kay SA, Chua N-HDonald RGK, Cashmore AR� Multiple point mutations affecting the simian virus 40 enhancer.Sequence-specific interactions of a pea nuclear factor withlight-responsive elements upstream of the rbcs3A gene.Mutation of either G box or I box sequences profoundly affectsexpression from the Arabidopsis rbcs-1A promoter.LScience 219:626-631 (1983)EMBO J 6:2543-2549 (1987)EMBO J 9:1717-1726 (1990)0PubMed: 6297005;PubMed: 3678200;PubMed: 2347304; GTGGWWHGTATCCAYMOTIFOSRAMY3DS000256#01-August-2006 (last modified) kehi�"TATCCAY motif" found in rice (O.s.) RAmy3D alpha-amylase genepromoter; Y=T/C; a GATA motif as its antisense sequence; TATCCAYmotif and G motif (see S000130) are responsible for sugarrepression (Toyofuku et al. 1998);GATAamylasesugar
repressionrice (Oryza sativa)]Toyofuku K, Umemura T, Yamaguchi JRubio-Somoza I, Martinez M, Abraham Z, Diaz I, Carbonero P.�Promoter elements required for sugar-repression of the RAmy3Dgene for alpha-amylase in riceTernary complex formation between HvMYBS3 and other factorsinvolved in transcriptional control in barley seeds.8FEBS Lett 428:275-280 (1998)Plant J. 47: 269-281 (2006) PubMed: 9654148;PubMed: 16762033 TATCCAYTOPOISOMS000112 13-Feb-2001 (last modified) kehi�Topoisomerase cleavage site consensus sequence; Motif found inSAR (scaffold attachment region; or matrix attachment region,MAR); W=T/A,MARSAR topoisomerasscaffoldmatrix(fruit fly; Drosophila melanogaster; fly;>Sander M, Hsieh TGasser SM, Amati BB, Cardenas ME, Hofmann JFX�Drosophila topoisomerase II double-strand DNA cleavage: analysisof DNA sequence homology at the cleavage site.Studies on scaffold attachment sites and their relation to genomefunction.ENucleic Acid Res 13:1057-1072 (1985)Intnatl Rev Cyto 119:57-96 (1989)9PubMed: 2987816; GenBank: M30907, M30908;PubMed: 2695485;ReviewGTNWAYATTNATNNGTRANSINITDICOTSS000201 3-May-1998 (last modified) kehiCContext sequence of translational initiation codon in dicots;M=A/C; Translation
Initiationdicots;$Joshi CP, Zhou H, Huang X, Chiang VL;Context sequences of translation initiation codon in plants!Plant Mol Biol 35:993-1001 (1997)PubMed: 9426620; AMNAUGGCTRANSINITMONOCOTSS000202 3-May-1998 (last modified) kehiLContext sequence of translational initiation codon in monocots;R=A/G; M=A/C; Translation
Initiation monocots;$Joshi CP, Zhou H, Huang X, Chiang VL;Context sequences of translation initiation codon in plants!Plant Mol Biol 35:993-1001 (1997)PubMed: 9426620; RMNAUGGCUP1ATMSDS000471#13-August-2005 (last modified) kehi�"Up1" motif found in 162 of the 1184 up-regulated genes aftermain stem decapitation in Arabidopsis; W=A/T; See also S000470,S000472;Axillary bud outgrowthArabidopsis thaliana3Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E.wIdentification of cis-elements that regulate gene expressionduring initiation of axillary bud outgrowth in Arabidopsis.$Plant Physiology 138: 757-766 (2005)PubMed: 15908603 GGCCCAWWW UPRMOTIFIIATS000426 29-Sep-2003 (last modified) kehi�"Motif II" in the conserved UPR (unfolded protein response)cis-acting element in Arabidopsis genes coding for SAR1B, HSP-90,SBR-like, Ca-ATPase 4, CNX1, PDI, etc.; See S000425, S000428,S000429;UPRunfolded protein responseArabidopsis thalianaGMartinez IM, Chrispeels MJ.Oh DH, Kwon CS, Sano H, Chung WI, Koizumi N.�Genomic analysis of the unfolded protein response in Arabidopsisshows its connection to important cellular processes.Conservation between animals and plants of the cis-acting elementinvolved in the unfolded protein response.KPlant Cell. 15:561-576 (2003)Biochem Biophys Res Commun. 301:225-230 (2003)"PubMed: 12566592;PubMed: 12535667; CCNNNNNNNNNNNNCCACGVOZATVPPS000456%29-November-2004 (last modified) kehi�"VOZ-binding sequence" found in the promoter of A. thalianaV-PPase (vacuolar H+-pyrophosphatase) gene; Involved in itsexpression during pollen development; one-zinc finger;(Mitsuda etal., 2004);VOZV-PPasepollenArabidopsis thaliana+Mitsuda N, Hisabori T, Takeyasu K, Sato MH.�VOZ; isolation and characterization of novel vascular planttranscription factors with a one-zinc finger from Arabidopsisthaliana.'Plant Cell Physiol. 45: 845-854 (2004).PubMed: 15295067 GCGTNNNNNNNACGC WBBOXPCWRKY1S000310!22-June-2006 (last modified) kehi�v"WB box"; WRKY proteins bind specifically to the DNA sequencemotif (T)(T)TGAC(C/T), which is known as the W box; Found inamylase gene in sweet potato, alpha-Amy2 genes in wheat, barley,and wild oat, PR1 gene in parsley, and a transcription factorgene in Arabidopsis; The motif was initially registered inPLACEdb as TTGACT, and was corrected to TTGACY on 22 June, 2006;Y=C/T;W boxWRKY�Ipomoea batatas (sweet potato); Triticum aestivum (wheat);Hordeum vulgare (barley); Avena fatua (wild oat); Petroseliumcrispum (parsley); Arabidopsis thaliana;�Ishiguro S, Nakamura K.Rushton PJ, Macdonald H, Huttly AK, Lazarus CM, Hooley R.Rushton PJ, Torres JT, Parniske M, Wernert P, Hahlbrock K,Somssich IE.de Pater S, Greco V, Pham K, Memelink J, Kijne J.Eulgem T, Rushton PJ, Robatzek S, Somssich IE�-Characterization of a cDNA encoding a novel DNA-binding protein,SPF1, that recognizes SP8 sequences in the 5' upstream regions ofgenes coding for sporamin and beta-amylase from sweet potato.Members of a new family of DNA-binding proteins bind to aconserved cis-element in the promoters of alpha-Amy2 genes.Interaction of elicitor-induced DNA-binding proteins withelicitor response elements in the promoters of parsley PR1genes.Characterization of a zinc-dependent transcriptional activatorfrom Arabidopsis.The WRKY superfamily of plant transcription factors�Mol Gen Genet. 244:563-571.(1994)Plant Mol Biol. 29:691-702 (1995)EMBO J. 15:5690-5700 (1996)Nucleic Acids Res. 24:4624-4631 (1996)Trends Plant Sci 5: 199-206 (2000)MPubMed: 7969025PubMed: 8541496PubMed: 8896462PubMed: 8972846PubMed: 10785665;ReviewTTTGACY WBOXNTCHN48S000508$04-January-2007 (last modified) kehi� "W box" identified in the region between -125 and -69 of atobacco class I basic chitinase gene CHN48; NtWRKY1, NtWRKY2 andNtWRKY4 bound to W box; NtWRKYs possibly involved inelicitor-respsonsive transcription of defense genes in tobacco;Y=C/T; see also S000442 (TGACT) and S000447 (TGAC);W-boxW boxWRKYelicitorNicotiana tabacum (tobacco)*Yamamoto S, Nakano T, Suzuki K, Shinshi H.�Elicitor-induced activation of transcription via W box-relatedcis-acting elements from a basic chitinase gene by WRKYtranscription factors in tobacco.)Biochim Biophys Acta. 1679:279-287(2004).PubMed: 15358520 CTGACY
WBOXNTERF3S000457%29-November-2004 (last modified) kehi�"W box" found in the promoter region of a transcriptionalrepressor ERF3 gene in tobacco; May be involved in activation ofERF3 gene by wounding;(Nishiuchi et al., 2004) Y=C/T; SeeS000142, S000390, S000442, S000447;W boxERF3woundingNicotiana tabacum (tobacco)!Nishiuchi T, Shinshi H, Suzuki K.�Rapid and transient activation of transcription of the ERF3 geneby wounding in tobacco leaves: Possible involvement of NtWRKYsand autorepression.$J Biol Chem. 279: 55355-55361 (2004)PubMed: 15509567 TGACY WRECSAA01S000496 10-May-2006 (last modified) kehi�"Wound-responsive element (WRE)" found in the promoter region ofcucumber (C.s.) ascorbate oxidase gene, CsAAO1; Binding site ofproteins in tobacco nuclear extracts; W=A/T; S=C/G;woundAAOwoundingCucumis sativas (cucumber)!Palm CJ, Costa MA, An G, Ryan CA.lWound-inducible nuclear protein binds DNA fragments that regulatea proteinase inhibitor II gene from potato.,Proc Natl Acad Sci U S A. 87: 603-607 (1990)PubMed: 2405385
AAWGTATCSA�� -10PEHVPSBDS000392 20-Feb-2002 (last modified) uchi�� "-10 promoter element" found in the barley (H.v.) chloroplastpsbD gene promoter; Involved in the expression of the plastidgene psbD which encodes a photosystem II reaction centerchlorophyll-binding protein that is activated by blue, white orUV-A light;psbDchloroplast gene expressioncircadian rhythmslight
regulationbarley (Hordeum vulgare)8Thum KE, Kim M, Morishige DT, Eibl C, Koop HU, Mullet JE_Analysis of barley chloroplast psbD light-responsive promoterelements in transplastomic tobacco"Plant Mol Biol 47: 353-366 (2001)PubMed: 11587507; TATTCT -141NTG13S000335 16-Feb-2001 (last modified) seki��"-141 sequence"; Binding site of tobacco (N.t.) TGA1a-relatedprotein,PG13, found in the G13 gene promoter; PG13 (Proteinencoded by G13) shows high homology to TGA1a; ASF-1, PG13, andTGA1a bind to the same target sequence in the 5' upstream regionof G13 suggesting that autoregulation of transcription mayinvolved in the control of G13 expression; TGA1a ispreferentially expressed in root tip meristems; TGA1a maycontribute to the expression of GST isoenzymes, especially inroot tip meristems;TGA1aG13ASF1ASF-1bZipxenobiotic stressrootmeristemtobacco (Nicotiana tabacum)PFromm H, Katagiri F, Chua NHKlinedinst S, Pascuzzi P, Redman J, Desai M, Arias J� The tobacco transcription activator TGA1a binds to a sequence inthe 5' upstream region of a gene encoding a TGA1a-relatedproteinA xenobiotic-stress-activated transcription factor and itscognate target genes are preferentially expressed in root tipmeristemsBMol Gen Genet 229: 181-188 (1991)Plant Mol Biol 42: 679-688 (2000)2PubMed: 1921969; GenBank: M62855;PubMed: 10809441; GCTTTTGATGACTTCAAACAC-284MOTIFZMSBE1S000285 10-Feb-2000 (last modified) seki�Located between -284 and -255 region of maize (Z.m.) Sbe1 genepromoter; Critical positive cis element; Important for thehigh-level, sugar-responsive expression of the Sbe1 gene in maizeendosperm cells; Recognized by nuclear protein; See S000284; Starch-branching enzyme (Sbe1)starchkernelsugar endospermseedmaize (Zea mays)Kim K-N, Guiltinan MJvIdentification of cis-acting elements important for expression ofthe starch-branching enzyme I gene in Maize endosperm"Plant Physiol 121: 225-236 (1999)PubMed: 10482678 CGTGCAAGCCCAAAGGCCAATCGGCCCAGA-300CORES000001 10-May-2006 (last modified) kehi�>"TGTAAAG core motif" in "-300 elements" of alpha-zein genes ofmaize; "-300 element core"; "prolamin box" by Vicente-Carbajosaet al. (Proc Natl Acad Sci USA 94:7685 (1997)); P-box; Binds withP-box binding factor (PBF); Binds with BPBF (Barley PBF); PBF isa DNA-binding protein of the DOF class of transcription factors; zein
core motifmaize -300 elementpromoter prolamin-boxP-boxseed endospermamaize (Zea mays); wheat (Triticum aestivum); barley (Hordeumvulgare); tobacco (Nicotiana tabacum)�Forde BG, Heyworth A, Pywell J, Kreis MColot V, Robert LS, Kavanagh TA, Bevan MW, Thompson RDThomas MS, Flavell RBThompson GA, Boston RS, Lyznik LA, Hodges TK, Larkins BAVicente-Carbajosa J, Moose SP, Parsons RL, Schmidt RMena M, Vicente-Carbajosa J, Schmidt RJ, Carbonero PSingh KB��Nucleotide sequence of a B1 hordein gene and the identificationof possible upstream regulatory elements in endosperm storageprotein genes from barley, wheat and maize.Localization of sequences in wheat endosperm protein genes whichconfer tissue-specific expression in tobacco.Identification of an enhancer element for the endosperm-specificexpression of high molecular weight glutenin.Analysis of promoter activity from an alpha-zein gene 5' flankingsequence in transient expression assays.A maize zinc-finger protein binds the prolamin box in zein genepromoters and interacts with the basic leucine zippertranscriptional activator Opaque2.An endosperm-specific DOF protein from barley, highly conservedin wheat, binds to and activates transcription from theprolamin-box of a native B-hordein promoter in barley endospermTranscriptional regulation in plants: the importance ofcombinatorial control.�Nucleic Acids Res 13:7327-7339 (1985)EMBO J 6:3559-3564 (1987)Plant Cell 2:1171-1180 (1990)Plant Mol Biol 15:755-764 (1990)Proc Natl Acad Sci USA 94:7685-7690 (1997)Plant J 16:53-62 (1998)Plant Physiol 118: 1111-1120 (1998)�PubMed: 4059057; GenBank: X03103;PubMed: 15467781PubMed: 2152160;PubMed: 2102884;PubMed: 9207153; GenBank: U82230;PubMed: 9807827; GenBank: AJ012284, AJ000991PubMed: 9847085reviewTGTAAAG -300ELEMENTS000122 11-May-2006 (last modified) kehi�Present upstream of the promoter from the B-hordein gene ofbarley and the alpha-gliadin, gamma-gliadin, and low molecularweight glutenin genes of wheat; See S000001 -300CORE; See S000002-300MOTIF; -300 elementhordeingliadingluteninseedwheat (Triticum aestivum)�Kreis M, Williamson MS, Forde J, Schmitz D, Clark J, Buxton B,Pywell J, Marris C, Henderson J, Harris N, Shewry PR, Forde BG,Miflin BJColot V, Robert LS, Kavanagh TA, Bevan MW, Thompson RDThomas MS, Flavell RB�Differential gene expression in the developing barley endosperm.Localization of sequences in wheat endosperm protein genes whichconfer tissue-specific expression in tobacco.Identification of an enhancer element for the endosperm-specificexpression of high molecular weight glutenin.aPhilos Trans R Soc Lond B314:355-365 (1986)EMBO J 6:3559-3564 (1987)Plant Cell 2:1171-1180 (1990) PubMed: 15467781PubMed: 2152160; TGHAAARK-300MOTIFZMZEINS000002 17-May-1998 (last modified) kehi�Motif in -300 elements of alpha-zein genes of maize (Z.m.);homologous to the sequence to which transacting factors of AP-1,fos, jun or yeast hisS bind;zein
core motifmaize -300 elementseed endospermmaize (Zea mays)Thomas MS, Flavell RBmIdentification of an enhancer element for the endosperm-specificexpression of high molecular weight glutenin. Plant Cell 2:1171-1180 (1990)PubMed: 2152160; RTGAGTCAT-314MOTIFZMSBE1S000284 10-Feb-2000 (last modified) seki�Located between -314 and -295 region of maize (Z.m.) Sbe1 genepromoter; Critical positive cis element; Important for thehigh-level, sugar-responsive expression of the Sbe1 gene in maizeendosperm cells; Recognized by nuclear protein; See S000285; Starch-branching enzyme (Sbe1)kernelsugar endospermseedmaize (Zea mays)Kim K-N, Guiltinan MJvIdentification of cis-acting elements important for expression ofthe starch-branching enzyme I gene in maize endosperm"Plant Physiol 121: 225-236 (1999)PubMed: 10482678 ACATAAAATAAAAAAAGGCA
14BPATERD1S000412 03-Jun-2003 (last modified) kehi~"14 bp region" (from -599 to -566) necessary for expression oferd1 (early responsive to dehydration) in dehydratedArabidopsis; water-stresserdArabidopsis thalianaOSimpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K,Yamaguchi-Shinozaki K.�Two different novel cis-acting elements of erd1, a clpAhomologous Arabidopsis gene function in induction by dehydrationstress and dark-induced senescence.Plant J. 33: 259-270 (2003)PubMed: 12535340; CACTAAATTGTCAC 20NTNTNOSS000312 7-Sep-2000 (last modified) seki�"20nt (20 nucleotide sequence)" found in the promoter on tobacco(N.t.) nopalin synthase (nos) gene promoter; Containing twohexamer motifs (TGAGCT) and a spacer region; The spacer regionbetween two hexamer motifs is essential; Important for the geneexpression; Essential for response to wounding, auxin, MJ, andSA; Very similar to ASF-1 binding site (See S000073); SeeS000053(ACGTCA);nopalin synthasenosauxinwoundingmethyl jasmonatetobacco (Nicotiana tabacum) Kim Y, Buckley K, Costa MA, An G^A 20 nucleotide upstream element is essential for the nopalinesynthase (nos) promoter activity Plant Mol Biol 24:105-117 (1994)PubMed: 8111010; TGAGCTAAGCACATACGTCA23BPUASNSCYCB1S000283 10-Feb-2000 (last modified) seki�,"23 bp UAS (Upstream activating sequence)" found in the promoterof Nicotiana sylvestris (N.s.) CycB1 gene; Located between -386and -409; Contains a 5 bp element identical to the MYB bindingcore (ACGT); Required for M-phase-specific expression; Bindsprotein complexes in a cell cycle-regulated manner;B-type cyclinsMYB
Cell cycleM-phase tobacco (Nicotiana sylvestris)8Trehin C, Glab N, Perennes C, Planchais S, Bergounioux CoM phase-specific activation of the Nicotiana sylvestris Cyclin B1promoter involves multiple regulatory elementsPlant J 17: 263-273 (1999) TTTATTTACCAAACGGTAACATC23BPZM27KDAZEINS000341 7-Sep-2000 (last modified) seki�z23 bp sequence found in the maize (Z.m.) gamma-class 27kDa zeingene promoter; Contains -300 element (also called the endospermbox or prolamin box); Binding site of nuclear protein; Confers ahigh level of transcriptional activity in anorientation-dependent manner; -300 element is involved in thecommon regulatory mechanisms mediating the coordinated expressionof the zein genes;gamma-class 27kDa zein -300 element prolamin box endospermboxseedmaize (Zea mays)!Ueda T, Wang Z, Pham N, Messing JqIdentification of a transcriptional activator-binding element inthe 27-kilodalton zein promoter, the -300 element"Mol Cell Biol 14: 4350-4359 (1994)PubMed: 8007944; GACGTGTAAAGTAAATTTACAAC27BPDRCONSENSUSPS25SS000286 10-Feb-2000 (last modified) seki�The consensus sequence of 27 bp imperfect repeats found in theuntrascribed spacer close to the 3'end of the pea (P.s.) 25Sgene; Involved in the rDNA replication fork barrier; Nuclearprotein(s) specifically bound to this repeat; W=T/A; M=A/C;rDNA25S
tandem repeat fork barrierpea (Pisum sativum)8Lopez-Estrano C, Schivartzman JB, Krimer DB, Hernandez PfCharacterization of the pea rDNA replication fork barrier:putative cis-acting and trans-acting factors!Plant Mol Biol 40: 99-110 (1999)PubMed: 10394949 TCCGCCWCTTGTATTCGTTGCGTTGMA2SSEEDPROTBANAPAS000143 10-May-1998 (last modified) kehiiConserved in many storage-protein gene promoters; May beimportant for high activity of the napA promoter;storage proteinABREnapA2SseedBrassica napus;3Stalberg K, Ellerstom M, Ezcurra I, Ablov S, Rask L�Disruption of an overlapping E-box/ABRE motif abolished hightranscription of the napA storage-protein promoter in transgenicBrassica napus seeds.Planta 199:515-519 (1996)PubMed: 8818291; CAAACAC3AF1BOXPSRBCS3S000004 17-May-1998 (last modified) kehi�"3AF1 binding site"; tetramer in the light-responsive promoter ofpea (P.s.) rbcS-3A gene; "Box VI"; One of "AT-rich sequences"which have been found in numerous light-regulated promoters(Terzaghi & Cashmore, 1995); 3AF1 site includes a GATA motif;3AF1 boxpromoterAT-rich sequencesGATArbcsrbcs-3leafshootpea (Pisum sativum){Lam E, Kano-Murakami Y, Gilmartin P, Niner B, Chua N-HGilmartin PM, Sarokin L, Memelink J, Chua N-HTerzaghi WB, Cashmore AR�A metal-dependent DNA-binding protein interacts with aconstitutive element of a light-responsive promoter.Molecular light switches for plant genes.Light-regulated transcriptionmPlant Cell 2:857-866 (1990)Plant Cell 2:369-378 (1990)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)1PubMed: 2152132; GenBank: X62746;PubMed: 2152164;ReviewAAATAGATAAATAAAAACATT5256BOXLELAT5256S000279 27-Feb-2000 (last modified) kehi��"52/56 box"; A sequence motif shared between the tomato (L.e.)LAT(Late Anther Tomato)52 and LAT56 promoters; Encompassing "PBcore motif" (TGTGGTT), and is closely related to the box IIsequence motif in the pea rbcS-3A gene promoter; Involved inmodulating the activity of the LAT gene promoters in pollen;Dispensable for the developmental regulation of the LAT52 gene inpollen; 52/56 box may be a target for the binding of a member ofthe GT-1 transcription factor family;52/56latlat52lat56GT-1pollenanther tomato (Lycopersicon esculentum)rTwell D, Yamaguchi J, Wing RA, Ushiba J, McCormick SEyal Y, Curie C, McCormick SVillain P, Mache R, Zhou DXZhou DX��Promoter analysis of genes that are coordinately expressed duringpollen development reveals pollen-specific enhancer sequences andshared regulatory elementsPollen specificity elements reside in 30 bp of the proximalpromoters of two pollen-expressed genesThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�Genes Dev 5:496-507 (1991)Plant Cell 7:373-384 (1995)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)RPubMed: 1840556; GenBank: X56487;PubMed: 7734969;PubMed: 8955086;PubMed: 10366876Review TGTGGTTATATA5659BOXLELAT5659S000280 29-Sep-2003 (last modified) kehi�"56/59 box"; A sequence motif shared between the tomato (L.e.)LAT(Late Anther Tomato)56 and LAT59 promoters; Found in -103 to-94 in LAT56 and in -114 to -105 in LAT59; Involved in modulatingthe activity of the LAT gene promoters in pollen; W=A/T;56/59latlat56lat59GT-1pollenanther tomato (Lycopersicon esculentum)rTwell D, Yamaguchi J, Wing RA, Ushiba J, McCormick SEyal Y, Curie C, McCormick SVillain P, Mache R, Zhou DXZhou DX��Promoter analysis of genes that are coordinately expressed duringpollen development reveals pollen-specific enhancer sequences andshared regulatory elementsPollen specificity elements reside in 30 bp of the proximalpromoters of two pollen-expressed genesThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�Genes Dev 5:496-507 (1991)Plant Cell 7:373-384 (1995)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)RPubMed: 1840556; GenBank: X56488;PubMed: 7734969;PubMed: 8955086;PubMed: 10366876Review
GAAWTTGTGAAACACOREOSGLUB1S000353 16-Feb-2001 (last modified) seki�OCore of AACA motifs found in rice (O.s.) glutelin genes, involvedin controlling the endosperm-specific expression; AACA is alsoclosely associated with the GCN4 motif in all rice glutelin genesand together have been shown to confer endosperm-specificenhancement to the truncated -90 CaMV 35S promoter; See alsoS000045, S000181, S000276;glutelinAACAGCN4seed endospermrice (Oryza sativa)/Wu C, Washida H, Onodera Y, Harada K, Takaiwa F�Quantitative nature of the Prolamin-box, ACGT and AACA motifs ina rice glutelin gene promoter: minimal cis-element requirementsfor endosperm-specific gene expressionPlant J 23: 415-421 (2000)PubMed: 10929134; AACAAAC AACAOSGLUB1S000276 15-Oct-1999 (last modified) kehi�"AACA motif" found in GluB-1 gene in rice (O.s.); Required forendosperm-specific expression; Highly conserved in the5'-flanking region of glutelin genes; See S000277;GluB-1glutelin endospermseedstorage protein
AACA motifrice (Oryza sativa)GWashida H, Wu CY, Suzuki A, Yamanouchi U, Akihama T, Harada K,Takaiwa F{Identification of cis-regulatory elements required for endospermexpression of the rice storage protein glutelin gene GluB-1 Plant Mol Biol 40:1-12 (1999)PubMed: 10394940; CAACAAACTATATCAAGACGTAGATACL12S000344 7-Sep-2000 (last modified) sekiwSequence found in Arabidopsis (A.t.) acyl carrier protein (ACP),Acl1.2, gene promoter; Contains bZIP core motif (ACGT);Acl1.2bZIPacyl carrier proteinArabidopsis thaliana'Baerson SR, Vander Heiden MG, Lamppa GK|Identification of domains in an Arabidopsis acyl carrier proteingene promoter required for maximal organ-specific expression#Plant Mol Biol 26: 1947-1959 (1994)PubMed: 7858229; AAGACGTAGABADESI1S000007 10-Feb-2000 (last modified) seki�Responsive to ABA and desiccation; "Motif I" of rice rab16A-D(initially called rab-21); Expressed in seeds late duringembryogenesis; Induced by ABA and osmotic stress in vegetativetissues; Contains ACGT motif; transacting factor: TAF-1;rab16ABAABRETAF-1ACGTMotif iseedembryorice (Oryza sativa)nMundy J, Yamaguchi-Shinozaki K, Chua N-HOeda K, Salinas J, Chua N-HThomas TLBusk PK, Pages MSkriver K, Mundy J�~Nuclear proteins bind conserved elements in the abscisicacid-responsive promoter of a rice rab gene.A tobacco bZip transcription activator (TAF-1) binds to aG-box-like motif conserved in plant genes.Gene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcriptionGene expression in response to abscisic acid and osmotic stress�Proc Natl Acad Sci USA 87:1406-1410 (1990)EMBO J 10:1793-1802 (1991)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998)Plant Cell 2: 503-512 (1990)`PubMed: 2137613;PubMed: 2050116; GenBank: X60363;PubMed: 8281041;PubMed: 9617810;PubMed: 2152172?Gel retardation; DNase I cleavage inhibition;ReviewReviewreview
RTACGTGGCRABADESI2S000008 29-Sep-1999 (last modified) kehi�Synthetic element (hex-3) related to response to ABA and todesiccation; seed expression; Gene: synthetic; hex-3, mutant ofhex-1 sequence from wheat histone H3 promoter; transactingfactor: bZIP ?;ABASEEDbZIPhex-1hex-3histone.rice (Oryza sativa); wheat (Triticum aestivum)(Lam E, Chua N-HThomas TLBusk PK, Pages M�
Tetramer of a 21-base pair synthetic element confers seedexpression and transcriptional enhancement in response to waterstress and abscisic acid.Gene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcription_J Biol Chem 266:17131-17135 (1991)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998)/PubMed: 1832669;PubMed: 8281041;PubMed: 9617810 ReviewReview GGACGCGTGGCABAREG2S000009 29-Sep-1999 (last modified) kehiXMotif related to ABA regulation; Gene: sunflower helianthinin;transacting factor: bZIP ?ABAbZIPseed sunflower (Helianthus annuus)TNunberg A, Li Z, Bogue M, Vivekananda J, Reddy A, Thomas TLThomas TLBusk PK, Pages MxGene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcriptionwunpublished results (cited in a review by Thomas TL, 1993)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998) PubMed: 8281041;PubMed: 9617810 ReviewReview ATGTACGAAGCABASEED1S000011 29-Sep-1999 (last modified) kehibABA regulation; seed expression; Gene: carrot Dc3; Transactingfactor: bZIP ?; Contains ACGT motif;Dc3ABAABREbZIPseedACGTcarrot (Daucus carota)+Chung H, Thomas TLThomas TLBusk PK, Pages MxGene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcriptionwunpublished results (cited in a review by Thomas TL, 1993)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998) PubMed: 8281041;PubMed: 9617810 ReviewReview TGTTACGTGCCABFOSS000190 11-Oct-1999 (last modified) kehi�1ABF (as-1-like box binding factor) binding site; as-1-like (ASL)box is found at -98 to -79 of RTBV (rice tungro bacilliformvirus) promoter; ASL box is required for phloem-specific geneexpression of Rice Tungro Bacilliform Virus (RTBV); See alsoRNFG1OS (S000188), and RNFG2OS (S000189); See as-1 (S000023);ASLas-1phloemRTBVABFstemphloem9RTBV; rice tungro bacilliform virus; rice (Oryza sativa);Yin Y, Chen L, Beachy R\Promoter elements required for phloem-specific gene expressionfrom the RTBV promoter in ricePlant J 12:1179-1188 (1997)PubMed: 9418055; GCATCTTTACTTTAGCATC ABRE2HVA1S000134 29-Sep-1999 (last modified) kehi�ABA responsive element, ABRE2, found in barley (H.v.) HVA1 geneencoding a class 3 late embryogenesis-abundant protein; stressresponse;ABREABAHVA1ABRE2seedembryobarley (Hordeum vulgare);)Straub PF, Shen Q, Ho THDBusk PK, Pages M�Structure and promoter analysis of an ABA- and stress-regulatedbarley gene, HVA1.Regulation of abscisic acid-induced transcription@Plant Mol Biol 26:617-630 (1994)Plant Mol Biol 37:425-435 (1998)1PubMed: 7948917; GenBank: X78205;PubMed: 9617810;Review CCTACGTGGCGG
ABRE2HVA22S000117 29-Sep-1999 (last modified) kehi�"ABRE2" of barley HVA22 gene; G-box; component of ABA responsecomplex in HVA22 gene; see S0118 (ABRE3 of HVA22 gene); see CE1(coupling element 1 = TGCCACCGG); See S000014;ABREG-boxcoupling elementCE1HVA22barley (Hordeum vulgare); Shen Q, Ho THBusk PK, Pages M�Functional dissection of an abscisic acid(ABA)-inducible genereveals two independent ABA-responsive complexes each containinga G-box and a novel cis-acting element.Regulation of abscisic acid-induced transcription;Plant Cell 7:295-307 (1995)Plant Mol Biol 37:425-435 (1998) PubMed: 7734964;PubMed: 9617810;Review
CGCACGTGTC ABRE3HVA1S000135 29-Sep-1999 (last modified) kehi�ABA responsive element, ABRE3, found in barley (H.v.) HVA1 geneencoding a class 3 late embryogenesis-abundant protein; stressresponse;ABREABAHVA1ABRE3seedembryobarley (Hordeum vulgare);)Straub PF, Shen Q, Ho THDBusk PK, Pages M�Structure and promoter analysis of an ABA- and stress-regulatedbarley gene, HVA1.Regulation of abscisic acid-induced transcription@Plant Mol Biol 26:617-630 (1994)Plant Mol Biol 37:425-435 (1998)1PubMed: 7948917; GenBank: X78205;PubMed: 9617810;Review
GCAACGTGTC
ABRE3HVA22S000118 17-May-2001 (last modified) uchi�R"ABRE3" of barley HVA22 gene; Newly designated "A3" by Shen etal., Plant Cell 8:1107 (1996); G-box; component of ABA responsecomplex in HVA22 gene; see S0117 (ABRE2 of HVA22 gene); see CE1(coupling element 1 = TGCCACCGG); See S000014; ABA responsecomplex 1(ABRC1)=A3(previously designated ABRE3)+CE1 (Shen etal., Plant Cell 8:1107(1996));ABREG-boxcoupling elementCE1HVA22barley (Hordeum vulgare);=Shen Q, Ho THDShen Q, Zhang P, Ho THDBusk PK, Pages MSingh KB��Functional dissection of an abscisic acid(ABA)-inducible genereveals two independent ABA-responsive complexes each containinga G-box and a novel cis-acting element.Modular nature of abscisic acid (ABA) response complexes:composite promoter units that are necessary and sufficient forABA induction of gene expression in barley.Regulation of abscisic acid-induced transcriptionTranscriptional Regulation in Plants: The Importance ofCombinatorial ComtroltPlant Cell 7:295-307 (1995)Plant Cell 8:1107-1119 (1996)Plant Mol Biol 37:425-435 (1998)Plant Physiol 118: 1111-11200PubMed: 7734964;PubMed: 8768371;PubMed: 9617810; Reviewreview
GCCACGTACA ABRE3OSRAB16S000120 29-Sep-1999 (last modified) kehiCABA-responsive element of rice (O.s.) rab16 and alpha-amylasegenes;ABArab16
alpha-amylaseABREseedrice (Oryza sativa);7Skriver K, Olsen FL, Rogers JC, Mundy JBusk PK, Pages M�Cis-acting DNA elements responsive to gibberellin and itsantagonist abscisic acid.Regulation of abscisic acid-induced transcriptionJProc Natl Acad Sci USA 88:7266-7270 (1991)Plant Mol Biol 37:425-435 (1998) PubMed: 1831269;PubMed: 9617810;Review GTACGTGGCGC
ABREA2HVA1S000140 17-May-2001 (last modified) uchi�A2 of ABRC3; ABRC3 (ABA response complex 3) of HVA1 consists ofCE3 and A2; ABA responsive element; stress response; Found inbarley HVA1 gene encoding a class 3 late embryogenesis-abundant(Lea) protein; ABRC1 OF HVA22 consists of CE1 and A3;CE1=S000014; A3=ABRE3=S000118; See S000118;A2ABRC3ABREABAHVA1Leaseedbarley (Hordeum vulgare)'Shen Q, Zhang P, Ho THDBusk PK, Pages M�Modular nature of abscisic acid (ABA) response complexes:composite promoter units that are necessary and sufficient forABA induction of gene expression in barley.Regulation of abscisic acid-induced transcription=Plant Cell 8:1107-1119 (1996)Plant Mol Biol 37:425-435 (1998) PubMed: 8768371;PubMed: 9617810;Review
CCTACGTGGCABREATCONSENSUSS000406$06-January-2006 (last modified) kehi�ABA-responsive elements (ABREs) found in the promoter of ABAand/or stress-regulated genes; ABFs, a family of ABRE bindingfactors; ABF3 and ABF4 function in ABA signaling; Y=C/T;ABAABF bZIP factorsArabidopsis thaliana�Choi H, Hong J, Ha J, Kang J, Kim SYKang JY, Choi HI, Im MY, Kim SYOh SJ, Song SI, Kim YS, Jang HJ, Kim SY, Kim M, Kim YK, Nahm BH,Kim JK.Choi HI, Park HJ, Park JH, Kim S, Im MY, Seo HH, Kim YW, Hwang I,Kim SY.��ABFs, a family of ABA-responsive element binding factorsArabidopsis basic leucine zipper proteins that mediatestress-responsive abscisic acid signalingArabidopsis CBF3/DREB1A and ABF3 in transgenic rice increasedtolerance to abiotic stress without stunting growth.Arabidopsis Calcium-Dependent Protein Kinase AtCPK32 Interactswith ABF4, a Transcriptional Regulator of AbscisicAcid-Responsive Gene Expression, and Modulates Its Activity.�J Biol Chem. 275: 1723-1730 (2000)Plant Cell. 14: 343-357 (2002)Plant Physiology 138: 341-351 (2005)Plant Physiol. 139: 1750-1761(2005)BPubMed: 10636868;PubMed: 11884679;PubMed: 15834008PubMed: 16299177 YACGTGGC
ABREATRD22S000013 29-Sep-1999 (last modified) kehid"ABRE (ABA responsive element)" in Arabidopsis (A.t.)dehydration-responsive gene rd22; R=A/G; Y=C/T;ABAresponsive elementABRErd22RD22 dehydrationshootArabidopsis thalianaCIwasaki T, Yamaguchi-Shinozaki K,Shinozaki KBray EABusk PK, Pages M�Identification of a cis-regulatory region of a gene inArabidopsis thaliana whose induction by dehydration is mediatedby abscisic acid and requires protein synthesis.Plant responses to water deficitRegulation of abscisic acid-induced transcriptionfMol Gen Genet 247:391-398 (1995)Trends in Plant Science 2:48-54 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 7770045;PubMed: 9617810;Review
RYACGTGGYR ABREAZMRAB28S000218 11-May-2006 (last modified) kehi�ABA-responsive element (ABRE A) found at -148 to -139 in maizerab28 (Busk & Pages, 1997); Maize rab28 is ABA-inducible inembryos and vegetative tissues;ABAABRErab28seedshootmaize (Zea mays) Busk PK, Pages MBusk PK, Pages M�Protein binding to the abscisic acid-responsive element isindependent of VIVIPAROUS1 in vivoRegulation of abscisic acid-induced transcription=Plant Cell 9:2261-2270 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 11407411PubMed: 9617810;Review
GCCACGTGGG
ABREBNNAPAS000145 16-Feb-2001 (last modified) seki��ABRE of napA storage-protein gene of Brassica napus (B.n.); ABAresponsive element; dist B ABRE mediated transactivation by ABI3adn ABI3-dependent response to ABA; a tetramer of the compositeRY/G complex mediated only ABA-independent transactivation byABI3; B2 domain of ABI3 is necessary for ABA-independent andABA-dependent activation through the dist B ABRE; B3 domain ofABI3 interacts with the RY/G complex;napAstorage proteinABREnapinseedBrassica napus;xStalberg K, Ellerstom M, Ezcurra I, Ablov S, Rask LBusk PK, Pages MEzcurra I, Wycliffe P, Nehlin L, Ellerstrom M, Rask L��Disruption of an overlapping E-box/ABRE motif abolished hightranscription of the napA storage-protein promoter in transgenicBrassica napus seeds.Regulation of abscisic acid-induced transcriptionTransactivation of the Brassica napus napin promoter by ABI3requires interaction of the conserved B2 and B3 domains of ABI3with different cis-elements: B2 mediates activation through anABRE, whereas B3 interacts with an RY/G-boxPPlanta 199:515-519 (1996)Plant Mol Biol 37:425-435 (1998)Plant J 24:57-66 (2000)1PubMed: 8818291;PubMed: 9617810;PubMed: 11029704;Review CGCCACGTGTCC ABREBZMRAB28S000219 11-May-2006 (last modified) kehi�ABA-responsive element (ABRE B) found at -105 to -96 in maize(Z.m.) rab28 (Busk & Pages, 1997); Maize rab28 is ABA-induciblein embryos and vegetative tissues;ABAABRErab28embryoseedshootmaize (Zea mays) Busk PK, Pages MBusk PK, Pages M�Protein binding to the abscisic acid-responsive element isindependent of VIVIPAROUS1 in vivoRegulation of abscisic acid-induced transcription=Plant Cell 9:2261-2270 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 11407411PubMed: 9617810;Review
TCCACGTCTC ABRECE1HVA22S000014 03-Jun-2003 (last modified) kehi�CE1(coupling element 1) of barley HVA22 gene; possible bindingsite for nuclear bZIP protein; ABA responsive complex consists ofa G-box, namely ABRE3 (GCCACGTACA), and CE1;ABACE1bZIPG boxG-boxABREshootbarley (Hordeum vulgare)7Shen Q, Ho THBray EABusk PK, Pages MCasaretto J, Ho TH.�wFunctional dissection of an abscisic acid(ABA)-inducible genereveals two independent ABA-responsive complexes each containinga G-box and a novel cis-acting element.Plant responses to water deficitRegulation of abscisic acid-induced transcriptionThe transcription factors HvABI5 and HvVP1 are required for theabscisic acid induction of gene expression in barley aleuronecells.~Plant Cell 7:295-307 (1995)Trends in Plant Science 2:48-54 (1997)Plant Mol Biol 37:425-435 (1998)Plant Cell 15: 271-284 (2003)1PubMed: 7734964;PubMed: 9617810;PubMed: 12509536;Review TGCCACCGG ABRECE3HVA1S000141 03-jun-2003 (last modified) kehi�DCE3 (coupling element 3) of ABRC3 in barley HVA1 gene; ABRC3 (ABAresponse complex 3) of HVA1 consists of CE3 and A2; ABAresponsive element; stress response; Found in barley HVA1 geneencoding a class 3 late embryogenesis-abundant (Lea) protein;ABRC1 OF HVA22 consists of CE1 and A3; CE1=S000014;A3=ABRE3=S000118; See S000118;CE3coupling elementABRC3ABREABAHVA1Leaseedbarley (Hordeum vulgare);AShen Q, Zhang P, Ho THDBray EABusk PK, Pages MCasaretto J, Ho TH.�uModular nature of abscisic acid (ABA) response complexes:composite promoter units that are necessary and sufficient forABA induction of gene expression in barley.Plant responses to water deficitRegulation of abscisic acid-induced transcriptionThe transcription factors HvABI5 and HvVP1 are required for theabscisic acid induction of gene expression in barley aleuronecells.�Plant Cell 8:1107-1119 (1996)Trends in Plant Science 2:48-54 (1997)Plant Mol Biol 37:425-435 (1998)Plant Cell 15: 271-284 (2003)1PubMed: 8768371;PubMed: 9617810;PubMed: 12509536;Review ACGCGTGTCCTCABRECE3ZMRAB28S000221 11-May-2006 (last modified) kehi�CE3 (coupling element 3) in maize (Z.m.) rab28 gene promoter; ABAresponsive element; stress response; Similar (10 of 12) to CE3 inA1 gene of barley; See S000141 (ABRECE3HVA1); Found at -126 to-115;CE3coupling elementRAB28rabABREABAseedmaize (Zea mays) Busk PK, Pages MBusk PK, Pages M�Protein binding to the abscisic acid-responsive element isindependent of VIVIPAROUS1 in vivoRegulation of abscisic acid-induced transcription=Plant Cell 9:2261-2270 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 11407411PubMed: 9617810;Review ACGCGCCTCCTCABREDISTBBNNAPAS000262 16-Feb-2001 (last modified) seki��"dist B (distal portion of B-box)" found in napA gene of Brassicanapus (B.n.); Shows similarity to ABRE; Found between -148 and-124; Required for seed specific expression and ABAresponsiveness; See S000263, S000264; dist B ABRE mediatedtransactivation by ABI3 adn ABI3-dependent response to ABA; atetramer of the composite RY/G complex mediated onlyABA-independent transactivation by ABI3; B2 domain of ABI3 isnecessary for ABA-independent and ABA-dependent activationthrough the dist B ABRE;ABREABAdistBB-boxseednapAnapinBrassica napus|Ezcurra I, Ellerstrom M, Wycliffe P, Stalberg K, Rask LBusk PK, Pages MEzcurra I, Wycliffe P, Nehlin L, Ellerstrom M, Rask L��Interaction between composite elements in the napA promoter: boththe B-box ABA-responsive complex and the RY/G complex arenecessary for seed-specific expressionRegulation of abscisic acid-induced transcriptionTransactivation of the Brassica napus napin promoter by ABI3requires interaction of the conserved B2 and B3 domains of ABI3with different cis-elements: B2 mediates activation through anABRE, whereas B3 interacts with an RY/G-boxYPlant Mol Biol 40:699-709 (1999)Plant Mol Biol 37:425-435 (1998)Plant J 24:57-66 (2000)2PubMed: 10480393;PubMed: 9617810;PubMed: 11029704;
GCCACTTGTC ABRELATERD1S000414#01-August-2006 (last modified) kehi�ABRE-like sequence (from -199 to -195) required foretiolation-induced expression of erd1 (early responsive todehydration) in Arabidopsis;ABRE
etiolationerdArabidopsis thaliana�Simpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K,Yamaguchi-Shinozaki K.Nakashima K, Fujita Y, Katsura K, Maruyama K, Narusaka Y, Seki M,Shinozaki K, Yamaguchi-Shinozaki K.�+Two different novel cis-acting elements of erd1, a clpAhomologous Arabidopsis gene function in induction by dehydrationstress and dark-induced senescence.Transcriptional regulation of ABI3- and ABA-responsive genesincluding RD29B and RD29A in seeds, germinating embryos, andseedlings of Arabidopsis.;Plant J. 33: 259-270 (2003)Plant Mol Biol. 60:51-68 (2006).!PubMed: 12535340;PubMed: 16463099 ACGTGABREMOTIFAOSOSEMS000299 16-Feb-2001 (last modified) seki�"motif A" ABRE-like sequence found in rice (O.s.) Osem genepromoter; Essential for activation by VP1; Important forregulation by ABA; See S000102, S000300; TRAB1, bZIPtranscription factor, interacts with VP1 and mediates abscisicacid-induced transcritption;ABREEmOsemABAVP1seedrice (Oryza sativa);Hattori T, Terada t, Hamasuna SHobo T, Kowyama Y, Hattori T�Regulation of the Osem gene by abscisic acid and thetranscriptional activator VP1: analysis of cis-acting promoterelements required for regulation by abscisic acid and VP1A bZIP factor, TRAB1, interacts with VP1 and mediates abscisicacid-induced transcriptionFPlant J 7: 913-925 (1995)Proc Natl Acad Sci USA 96: 15348-15353 (1999)1PubMed: 7599651; GenBank: U22102PubMed: 10611387; TACGTGTCABREMOTIFIIIOSRAB16BS000291 10-Feb-2000 (last modified) seki�"Motif III" found in the promoter of rice (O.s.) rab16B gene;Motif I (S000290) and motif III are both required for ABAresponsiveness; However, each can substitute for the other;ABAABRE motif IIIrab16Brice (Oryza sativa)%Ono A, Izawa T, Chua N-H, Shimamoto KRThe rab16B promoter of rice contains two distinct abscisicacid-responsive elements!Plant Physiol 112: 483-491 (1996)PubMed: 8883374
GCCGCGTGGCABREMOTIFIOSRAB16BS000290 10-Feb-2000 (last modified) seki�"Motif I" found in the promoter of rice (O.s.) rab16B gene; MotifI and motif III (S000291) are both required for ABAresponsiveness; However, each can substitute for the other; SeeS000019, S000120;ABAABREmotif Irab16Brice (Oryza sativa)%Ono A, Izawa T, Chua N-H, Shimamoto KRThe rab16B promoter of rice contains two distinct abscisicacid-responsive elements!Plant Physiol 112: 483-491 (1996)PubMed: 8883374
AGTACGTGGC ABREOSRAB21S000012 10-Feb-2000 (last modified) seki�"ABA responsive element (ABRE)" of wheat Em and rice (O.s.) rab21genes; Proposed consensus sequence for the repeated motif (Em1aand Em1b) of wheat Em gene; S=C/G;ABAABREEmrabEm1aEm1bseed.rice (Oryza sativa); wheat (Triticum aestivum)IMarcotte WR Jr, Russell SH, Quatrano RSBusk PK, Pages MSkriver K, Mundy J�Abscisic acid-responsive sequences from the Em gene of wheat.Regulation of abscisic acid-induced transcriptionGene expression in response to abscisic acid and osmotic stressWPlant Cell 1:969-976 (1989)Plant Mol Biol 37:425-435 (1998)Plant Cell 2: 503-512 (1990)/PubMed: 2562556;PubMed: 9617810;PubMed: 2152172 reviewreviewACGTSSSC
ABRERATCALS000507$04-January-2007 (last modified) kehi�"ABRE-related sequence" or "Repeated sequence motifs" identifiedin the upstream regions of 162 Ca(2+)-responsive upregulatedgenes; see also ABRE; M=C/A; Y=T/C; B=T/C/G;ABREcalciumArabidopsis thalianaCKaplan B, Davydov O, Knight H, Galon Y, Knight MR, Fluhr R, FrommH.�Rapid Transcriptome Changes Induced by Cytosolic Ca2+ TransientsReveal ABRE-Related Sequences as Ca2+-Responsive cis Elements inArabidopsis. Plant Cell. 18:2733-2748 (2006)PubMed: 16980540 MACGYGBABRETAEMS000015 29-Sep-1999 (last modified) kehi�"ABRE (ABA responsive element)" found in wheat (T.a.) Em gene;transacting factor: EMBP-1; EMBP-1 binds to CACGTGGC; See S000119EMBP1;ABAABREEMBP-1seedwheat (Triticum aestivum)BGuiltinan MJ, Marcotte WR Jr, Quatrano RSThomas TLBusk PK, Pages M�A plant leucine zipper protein that recognizes an abscisic acidresponse elementGene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcriptionWScience 250:267-270 (1990)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998)HPubMed: 2145628; GenBank: M62893, M63999;PubMed: 8281041;PubMed: 9617810 ReviewReview GGACACGTGGC ABREZMRAB28S000133!23-June-2006 (last modified) kehi��ABRE; ABA and water-stress responses; Found in maize (Z.m.)rab28; maize rab28 is ABA-inducible in embryos and vegetativetissues; Found in the Arabidopsis (A.t.) alcohol dehydrogenase(Adh) gene promoter; "ABRE2"; Found in the maize (Z.m.) Cat1 genepromoter; Responsible for the induction by ABA; Binding site ofCBF2; Arabidopsis CBF1 overexpression induces COR genes andenhances freezing tolerance; The CBF genes do not appear to beautoregulated through the CRT/DRE sequence;ABRErab28G-boxAdhCat1ABACBF1DRERGA1CORfreezing toleranceseedshootCBF2Imaize (Zea mays); Arabidopsis thaliana; rice (Oryza sativa);Populus spp.;��Suzuki M, Ketterling MG, McCarty DR.Busk PK, Pages MAlonso-Blanco C, Gomez-Mena C, Llorente F, Koornneef M, SalinasJ, Martinez-Zapater JMGuan LM, Zhao J, Scandalios JGBenedict C, Skinner JS, Meng R, Chang Y, Bhalerao R, Huner NPA,Finn CE, Chen THH, Hurry VJaglo-Ottosen KR, Gilmour SJ, Zarka DG, Schabenberger O,Thomashow MFGilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM,Thomashow MF�aQuantitative statistical analysis of cis-regulatory sequences inABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis.Regulation of abscisic acid-induced transcriptionGenetic and Molecular Analyses of Natural Variation Indicate CBF2as a Candidate Gene for Underlying a Freezing ToleranceQuantitative Trait Locus in ArabidopsisCis-elements and trans-factors that regulate expression of themaize Cat1 antioxidant gene in response to ABA and osmoticstress: H2O2 is the likely intermediary signaling molecule forthe responseThe CBF1-dependent low temperature signalling pathway, regulonand increase in freeze tolerance are conserved in Populus spp.Arabidopsis CBF1 overexpression induces COR genes and enhancesfreezing toleranceLow temperature regulation of the Arabidopsis CBF family of AP2transcriptional activators as an early step in cold-induced CORgene expression�Plant Physiol.139: 437-447 (2005)Plant Mol Biol 37:425-435 (1998)Plant Physiology 139: 1304-1312 (2005)Plant J 22: 87-95 (2000)Plant, Cell and Environment 29:1259-1272 (2006)Science 1998 3: 104-106 (1998)Plant J 16: 433-442 (1998)aPubMed: 16113229PubMed: 9617810;PubMed: 16244146PubMed: 10792824;PubMed: 9525853;PubMed: 9881163;in silicoReviewCCACGTGGACEATCHSS000355#02-August-2006 (last modified) kehi��"ACEAtCHS (ACGT containing element)" found in the LRU(light-responsive unit) in Arabidopsis (A.t.) chalcone synthase(CHS) gene promoter; Required for UV-B and UV-1/blue lightresponsiveness; See S000356; Transcriptional repression by AtMYB4controls production of UV-protecting sun screens in Arabidopsis;AtMYB4 mutant shows enhanced levels of sinapate ester in leavesand tolerance of UV-B irradiation; AtMYB4 expression isdownregulated by exposure to UV-B light; CHSACEMYBlightUV-AUV-BMYB4leafshootArabidopsis thaliana�Hartmann U, Valentine WJ, Christie JM, Hays J, Jenkins GI,Weisshaar BJin H, Cominelli E, Bailey P, Parr A, Mehrtens F, Jones J,Tonelli C, Weisshaar B, Martin CHartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B.��Identification of UV/blue light-response elements in theArabidopsis thaliana chalcone synthase promoter using ahomologous protoplast transient expression systemTranscriptional repression by AtMYB4 controls production ofUV-protecting sunscreens in ArabidopsisDifferential combinatorial interactions of cis-acting elementsrecognized by R2R3-MYB, BZIP, and BHLH factors controllight-responsive and tissue-specific activation ofphenylpropanoid biosynthesis genes._Plant Mol Biol (1998) 36: 741-754EMBO J 19: 6150-6161 (2000)Plant Mol Biol. 57: 155-171 (2005).1PubMed: 9526507;PubMed: 11080161;PubMed: 15821875
GACACGTAGAACGTABOXS000130 7-Sep-2000 (last modified) seki�p"A-box" according to the nomenclature of ACGT elements by Fosteret al. (FASEB J 8:192-200 (1994)); One of ACGT elements; Found inocs gene; RITA-1 binding site (Izawa et al. 1994); "G motif" byToyofuku et al. (1998); G motif and TATCCAY motif (a GATA motifas its antisense sequence; see S000256) are responsible forsugar repression (Toyofuku et al. 1998); See S000346;A-box ACGT elementG motifsugar
repressionseedplant; rice (Oryza sativa);qFoster R, Izawa T, Chua N-HIzawa T, Foster R, Nakajima M, Shimamoto K, Chua N-HToyofuku K, Umemura T, Yamaguchi J�Plant bZIP Proteins gather at ACGT elements.The rice bZIP transcriptional activator RITA-1 is highlyexpressed during seed development.Promoter elements required for sugar-repression of the RAmy3Dgene for alpha-amylase in riceRFASEB J 8:192-200 (1994)Plant Cell 6:1277-1287 (1994)FEBS Lett 428:275-280 (1998)@PubMed: 8119490;PubMed: 7919992; GenBank: L34551;PubMed: 9654148ReviewTACGTAACGTABREMOTIFA2OSEMS000394$06-January-2006 (last modified) kehi�Experimentally determined sequence requirement of ACGT-core ofmotif A in ABRE of the rice gene, OSEM; See S000281; DRE and ABREare interdependent in the ABA-responsive expression of the rd29Ain Arabidopsis; K=G/T;ABAABREmotif ADRE*rice (Oryza sativa); Arabidopsis thaliana;�Hattori T, Totsuka M, Hobo T, Kagaya Y, Yamamoto-Toyoda ANarusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, AbeH, Narusaka M, Shinozaki K, Yamaguchi-Shinozaki K.�Experimentally Determined Sequence Requirement of ACGT-ContainingAbscisic Acid Response ElementInteraction between two cis-acting elements, ABRE and DRE, inABA-dependent expression of Arabidopsis rd29A gene in response todehydration and high-salinity stresses.@Plant Cell Physiol 43: 136-140 (2002)Plant J. 34: 137-148 (2003)"PubMed: 11828032;PubMed: 12694590; ACGTGKCACGTABREMOTIFAOSOSEMS000281 16-Feb-2001 (last modified) seki�="ABRE motif A" found in the promoter of the rice (O.s.) Osemgene; ACGT-containing ABRE; Required for ABA-responsiveness andVP1 activation; Binding site of TRAB1; Motif A and CE3 (S000282)are functionally equivalent; TRAB1, bZIP transcription factor,interacts with VP1 and mediates abscisic acid-inducedtranscritption;
Motif AABRECE3ABAVP1TRAB1OsemEmbZIPseedrice (Oryza sativa)AHobo T, Asada M, Kowyama Y, Hattori THobo T, Kowyama Y, Hattori T�ACGT-containing abscisic acid response element (ABRE) andcoupling element 3 (CE3) are functionally equivalentA bZIP factor, TRAB1, interacts with VP1 and mediates abscisicacid-induced transcriptionHPlant J 19: 679-689 (1999)Proc Natl Acad Sci USA 96: 15348-15353 (1999)"PubMed: 10571853;PubMed: 10611387; TACGTGTC
ACGTATERD1S000415 03-Jun-2003 (last modified) kehi�ACGT sequence (from -155 to -152) required for etiolation-inducedexpression of erd1 (early responsive to dehydration) inArabidopsis;ACGT
etiolationerdArabidopsis thalianaOSimpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K,Yamaguchi-Shinozaki K.�Two different novel cis-acting elements of erd1, a clpAhomologous Arabidopsis gene function in induction by dehydrationstress and dark-induced senescence.Plant J. 33: 259-270 (2003)PubMed: 12535340; ACGTACGTCBOXS000131 16-Jan-1998 (last modified) kehi�"C-box" according to the nomenclature of ACGT elements by Fosteret al. (FASEB J 8:192-200 (1994)); One of ACGT elements; Factorsgroups 1, 2 and 3 have affinity for C-box (Izawa et al. J MolBiol. 230:1131-1144 (1993)); RITA-1 binding site (Izawa et al.1994);C-box ACGT elementseedplant;jFoster R, Izawa T, Chua N-HIzawa T, Foster R, Nakajima M, Shimamoto K, Chua N-HIzawa T, Foster R, Chua N-H�Plant bZIP Proteins gather at ACGT elements.The rice bZIP transcriptional activator RITA-1 is highlyexpressed during seed development.Plant bZIP protein DNA binding specificity.TFASEB J 8:192-200 (1994)Plant Cell 6:1277-1287 (1994)J Mol Biol 230:1131-1144 (1993)BPubMed: 8119490;PubMed: 7919992; GenBank: L345501;PubMed: 8487298;ReviewGACGTC ACGTOSGLUB1S000278 16-Feb-2001 (last modified) seki�<"ACGT motif" found in GluB-1 gene in rice (O.s.); Required forendosperm-specific expression; Conserved in the 5'-flankingregion of glutelin genes; See S000276, S000277; SeeS000019;Combination of GCN4, AACA and ACGT motifs was foundsufficient to confer a detectable level of endosperm expression;See S000353, S000354;GluB-1glutelin endospermseedstorage protein
ACGT motifrice (Oryza sativa)vWashida H, Wu CY, Suzuki A, Yamanouchi U, Akihama T, Harada K,Takaiwa FWu C, Washida H, Onodera Y, Harada K, Takaiwa F� Identification of cis-regulatory elements required for endospermexpression of the rice storage protein glutelin gene GluB-1Quantitative nature of the Prolamin-box, ACGT and AACA motifs ina rice glutelin gene promoter: minimal cis-element requirementsfor endosperm-specific gene expression7Plant Mol Biol 40:1-12 (1999)Plant J 23: 415-421 (2000)"PubMed: 10394940;PubMed: 10929134; GTACGTG ACGTROOT1S000016 31-Jul-2001 (last modified) uchi�S"ACGT motif" related to root expression; Gene: synthetic; perfectpalindromic sequence (PA) containing G-box-related sequence;transacting factor: TAF-1 ?; Binding of SGBF-1 (a Soybean G-boxbinding bZIP transcription factor) to ABRE is enhanced by SCOF-1(a zinc finger protein ); Transcription of SCOF-1 is induced bylow temperature and ABA;
rootACGTG boxG-box
ABRE motifbZIP binding enhancementcold toleranceCORSGBF-1SCOF-12tobacco (Nicotiana tabacum); soybean (Glycine max)~Salinas J, Oeda K, Chua N-HThomas TLKim JC, Lee SH, Cheong YH, Yoo CM, Lee SI, Chun HJ, Yun DJ, HongJC, Lee SY, Lim CO, Cho MJ�Two G-box-related sequences confer different expression patternsin transgenic tobaccoGene expression during plant embryogenesis and germination: Anoverview.A novel cold-inducible zinc finger protein from soybean, SCOF-1,enhances cold tolerance in transgenic plantsTPlant Cell 4:1485-1493 (1992)Plant Cell 5:1401-1410 (1993)Plant J 25: 247-259 (2001)1PubMed: 1467649;PubMed: 8281041;PubMed: 11208017;Review
GCCACGTGGC ACGTSEED2S000018 17-May-1998 (last modified) kehi\"ACGT motif" related to seed expression; Gene: French beanphaseolin; transacting factor: 02; phaseolinseedACGT&French bean; bean (Phaseolus vulgaris)Bustos MThomas TLGGene expression during plant embryogenesis and germination: Anoverview.Zpersonal communication (cited in a review by Thomas TL, 1993)Plant Cell 5:1401-1410 (1993)PubMed: 8281041;Review ACACACGTCAA ACGTSEED3S000019 10-Feb-2000 (last modified) seki�"ACGT motif" related to seed expression; Gene: synthetic;wild-type motif (Iwt) containing G-box-related sequence;transacting factor: bZIP ?; A tobacco bZip transcriptionactivator (TAF-1) binding site;seedACGTG-boxG boxtobacco?Salinas J, Oeda K, Chua N-HThomas TLOeda K, Salinas J, Chua N-H�� Two G-box-related sequences confer different expression patternsin transgenic tobacco.Gene expression during plant embryogenesis and germination: Anoverview.A tobacco bZip transcription activator (TAF-1) binds to aG-box-like motif conserved in plant genesUPlant Cell 4:1485-1493 (1992)Plant Cell 5:1401-1410 (1993)EMBO J 10: 1792-1802 (1991)/PubMed: 1467649;PubMed: 8281041;PubMed: 2050116Review
GTACGTGGCGACGTTBOXS000132 18-Mar-1998 (last modified) kehi�"T-box" according to the nomenclature of ACGT elements by Fosteret al. (FASEB J 8:192-200 (1994)); One of ACGT elements; See alsoACGTABOX (S000130), ACGTCBOX (S000131), and CACGTGMOTIF(S000042);T-boxT box
ACGT element:plant;Foster R, Izawa T, Chua N-H,Plant bZIP Proteins gather at ACGT elements.FASEB J 8:192-200 (1994)PubMed: 8119490;ReviewAACGTT ACIIIPVPAL2S000194&15-September-2006 (last modified) kehi��ACIII element found at -246 to -238 of bean (P.v.) PAL2 promoter;ACIII element is required for vascular-specific gene expression;See also ACIPVPAL2 (S000192) and ACIIPVPAL2 (S000193); ThreeAC-elements, which are possible Myb protein binding sites,together with a G-box, interact to direct the complex patterns oftissu-specific expression of pAL2 gene; Implicated in thexylem-localized regulation of genes encoding lignin biosyntheticenzymes in loblolly pine (Patzlaff et al., 2003);
vascularPALPAL2ACIIIphloemxylemstemligninMYBR2R3-MYB7bean (Phaseolus vulgaris); Pinus taeda (loblolly pine);�Hatton D, Sablowski R, Yung MH, Smith C, Schuch W, Bevan MPatzlaff A, Newman LJ, Dubos C, Whetten RW, Smith C, McInnis S,Bevan MW, Sederoff RR, Campbell MMGomez-Maldonado J, Avila C, Torre F, Canas R, Canovas FM,Campbell MM�Tow classes of cis sequences contribute to tissue-specificexpression of a PAL2 promoter in transgenic tobaccoCharacterisation of Pt MYB1, an R2R3-MYB from pine xylem.Functional interactions between a glutamine synthetase promoterand MYB proteins.UPlant J 7:859-876 (1995)Plant Mol Biol. 53:597-608 (2003).Plant J. 39:513-526 (2004).0PubMed: 7599647;PubMed: 15010621PubMed: 15272871 GTTAGGTTC
ACIIPVPAL2S000193&15-September-2006 (last modified) kehi��ACII element found at -131 to -120 of bean (P.v.) PAL2 promoter;ACII element is required for vascular-specific gene expression;See also ACIPVPAL2 (S000192) and ACIIIPVPAL2 (S000194); ThreeAC-elements, which are possible Myb protein binding sites,together with a G-box, interact to direct the complex patterns oftissu-specific expression of pAL2 gene; Implicated in thexylem-localized regulation of genes encoding lignin biosyntheticenzymes in loblolly pine (Patzlaff et al., 2003); vascularPALACIIphloemxylemstemligninMYBR2R3-MYB7bean (Phaseolus vulgaris); Pinus taeda (loblolly pine);�Hatton D, Sablowski R, Yung MH, Smith C, Schuch W, Bevan MPatzlaff A, Newman LJ, Dubos C, Whetten RW, Smith C, McInnis S,Bevan MW, Sederoff RR, Campbell MMGomez-Maldonado J, Avila C, Torre F, Canas R, Canovas FM,Campbell MM�Tow classes of cis sequences contribute to tissue-specificexpression of a PAL2 promoter in transgenic tobaccoCharacterisation of Pt MYB1, an R2R3-MYB from pine xylem.Functional interactions between a glutamine synthetase promoterand MYB proteins.UPlant J 7:859-876 (1995)Plant Mol Biol. 53:597-608 (2003).Plant J. 39:513-526 (2004).0PubMed: 7599647;PubMed: 15010621PubMed: 15272871 CCACCAACCCCC ACIPVPAL2S000192&15-September-2006 (last modified) kehi��ACI element found at -83 to -74 of bean (P.v.) PAL2 promoter;AC-rich element; ACI element is required for vascular-specificgene expression; See also ACIIPVPAL2 (S000193) and ACIIIPVPAL2(S000194); Three AC-elements, which are possible Myb proteinbinding sites, together with a G-box, interact to direct thecomplex patterns of tissue-specific expression of pAL2 gene;Implicated in the xylem-localized regulation of genes encodinglignin biosynthetic enzymes in loblolly pine (Patzlaff et al.,2003); vascularPALACIphloemxylemstemligninMYBR2R3-MYB6Phaseolus vulgaris(bean); Pinus taeda (loblolly pine);�Hatton D, Sablowski R, Yung MH, Smith C, Schuch W, Bevan MPatzlaff A, Newman LJ, Dubos C, Whetten RW, Smith C, McInnis S,Bevan MW, Sederoff RR, Campbell MMGomez-Maldonado J, Avila C, Torre F, Canas R, Canovas FM,Campbell MM�Tow classes of cis sequences contribute to tissue-specificexpression of a PAL2 promoter in transgenic tobaccoCharacterisation of Pt MYB1, an R2R3-MYB from pine xylem.Functional interactions between a glutamine synthetase promoterand MYB proteins.UPlant J 7:859-876 (1995)Plant Mol Biol. 53:597-608 (2003).Plant J. 39:513-526 (2004).0PubMed: 7599647;PubMed: 15010621PubMed: 15272871
CCCACCTACCAGAMOUSATCONSENSUSS000342 16-May-2001 (last modified) uchi��Binding consensus sequence of Arabidopsis (A.t.) AGAMOUS MADSdomain; MCM1 binding-sites in a-mating-type-specific promoters ofSaccharomyces cerevisiae show similarities with the binding-sitesequence of the AGAMOUS MADS domain; See S000316; MADS domain andI region of AGAMOUS are sufficient and necessary for DNA binding;Both the K domain and C region are indispensable for AG functionin flower development; See S000338;AGAMOUS MADS domainflowerArabidopsis thalianaGShiraishi H, Okada K, Shimura YMizukami Y, Huang H, Tudor M, Hu Y, Ma H�Nucleotide sequences recognized by the AGAMOUS MADS domain ofArabidopsis thaliana in vitroFunctional domains of the floral regulator AGAMOUS:characterization of the DNA binding domain and analysis ofdominant negative mutations4Plant J 4: 385-398 (1993)Plant Cell 8:831-845 (1996) PubMed: 8106084;PubMed: 8672883; TTDCCWWWWWWGGHAA
AGATCONSENSUSS000316 16-May-2001 (last modified) uchi��Binding consensus sequence for the product of the Arabidopsis(A.t.) floral homeotic gene AGAMOUS (AG); AG protein contains aregion similar to the DNA binding domain of SRF and MCM1; Theconsensus sequence contains a CArG box; AG protein is a putativetranscription factor for floral genes; H=A/T/C; W=A/T; SeeS000342; MADS domain and I region of AGAMOUS are sufficient andnecessary for DNA binding; Both the K domain and C region areindispensable for AG function in flower development; SeeS000338;floral homeotic geneAGAMOUSAGMCM1SRFGArG boxAPETALA2flower"Arabidopsis (Arabidopsis thaliana)iHuang H, Mizukami Y, Hu Y, Ma HMizukami Y, Huang H, Tudor M, Hu Y, Ma HDrews GN, Bowman JL, Meyerowitz EM�QIsolation and characterization of the binding sequences for theproduct of the Arabidopsis floral homeotic gene AGAMOUSFunctional domains of the floral regulator AGAMOUS:characterization of the DNA binding domain and analysis ofdominant negative mutationsNegative regulation of the Arabidopsis homeotic gene AGAMOUS bythe APETALA2 productZNucleic Acids Res. 21: 4769-4776 (1993)Plant Cell 8:831-845 (1996)Cell 65 :991-1002 (1991)0PubMed: 7901838;PubMed: 8672883;PubMed: 1675158; TTWCCWWWWNNGGWW AGCBOXNPGLBS000232#02-August-2006 (last modified) kehi��"AGC box" repeated twice in a 61 bp enhancer element in tobacco(N.p.) class I beta-1,3-glucanase (GLB) gene; See S000036,S000089; "GCC-box"; Binding sequence of Arabidopsis AtERFs;AtERF1,2 and 5 functioned as activators of GCC box-dependenttranscription; AtERF3 and 4 acted as repressors; AtERF proteinsare stress signal-response factors; EREBP2 binding site;Conserved in most PR-protein genes; Rice MAPK (BWMK1)phosphorylates OS EREBP1, which enhance DNA-binding activity ofthe factor to the GCC box; AGC boxGLBEREERFsEthyleneGCC-box Neutral PR-5osmotin-like proteinEREBP2MAPKBWMK1PR box{tobacco (Nicotiana plumbaginifolia); Arabidopsis (Arabidopsisthaliana); tobacco (Nicotiana sylvestris); Oryza sativa; rice;��Hart CM, Nagy F, Meins Jr FFujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi MSato F, Kitajima S, Koyama T, Yamada YOhme-Takagi M, Suzuki K, Shinshi HRushton PJ, Reinstadler A, Lipka V, Lippok B, Somssich IECheong YH, Moon BC, Kim JK, Kim CY, Kim MC, Kim IH, Park CY, KimJC, Park BO, Koo SC, Yoon HW, Chung WS, Lim CO, Lee SY, Cho MJZhang H, Huang Z, Xie B, Chen Q, Tian X, Zhang X, Zhang H, Lu X,Huang D, Huang R.��A 61 bp enhancer element of the tobacco beta-1,3-glucanase B geneinteracts with one or more regulated nuclear proteinsArabidopsis ethylene-responsive element binding factors act astranscriptional activators or repressors of GCC box-mediated geneexpressionEthylene-induced gene expression of osmotin-like protein, aneutral isoform of tobacco PR-5, is mediated by the AGCCGCCcis-sequenceRegulation of Ethylene-Induced Transcription of Defense GenesSynthetic plant promoters containing defined regulatory elementsprovide novel insights into pathogen- and wound-inducedsignalingBWMK1, a rice mitogen-activated protein kinase, locates in thenucleus and mediates pathogenesis-related gene expression byactivation of a transcription factor.The ethylene-, jasmonate-, abscisic acid- and NaCl-responsivetomato transcription factor JERF1 modulates expression of GCCbox-containing genes and salt tolerance in tobacco.�Plant Mol Biol 21:121-131 (1993)Plant Cell 12:393-404 (2000)Plant Cell Physiol 37: 249-255 (1996)Plant Cell Physiol 41: 1187-1192 (2000)Plant Cell 14: 749-762 (2002)Palnt Physiol. 132: 1961-1972 (2003)Planta. 220: 262-270 (2004)tPubMed: 8425042;PubMed: 10715325;PubMed: 8673338;PubMed: 11092902;PubMed: 11971132;PubMed: 12913152;PubMed: 15300440 AGCCGCCAGL1ATCONSENSUSS000338 16-May-2001 (last modified) uchi��Binding consensus sequence of Arabidopsis (A.t.) AGL1(AGAMOUS-like 1); AGL1 contains MADS domain; See S000339; AGL20is a MADS domain gene from Arabidopsis that is activated in shootapical meristem during the transition to flowering; AGL20 is alsoregulated by the Gibberellin pathway; Complex regulatory networks involving several MADS-genes underlie development ofvegetative structures;
MADSAGL1AGAMOUSAGL20floral induction photoperiod endosperm
gurd cellsroottrichomeleafshootflowerArabidopsis thaliana�Huang H, Tudor M, Su T, Zhang Y, Hu Y, Ma HBorner R, Kampmann G, Chandler J, Gleissner R, Wisman E, Apel K,Melzer SAlvarez-Buylla ER, Liljegren SJ, Pelaz S, Gold SE, Burgeff C,Ditta GS, Vergara-Silva F, Yanofsky MF�DNA binding properties of two Arabidopsis MADS domain proteins:binding consensus and dimer formationA MADS domain gene involved in the transition to flowering inArabidopsisMADS-box gene evolution beyond flowers: expression in pollen,endosperm, guard cells, roots and trichomesNPlant Cell 8: 81-94 (1996)Plant J 24: 591-599 (2000)Plant J 24: 457-466 (2000)1PubMed: 8597661;PubMed: 11123798;PubMed: 11115127 NTTDCCWWWWNNGGWAANAGL2ATCONSENSUSS000339 16-May-2001 (last modified) uchi�Binding consensus sequence of Arabidopsis (A.t.) AGL2(AGAMOUS-like 2); AGL2 contains MADS domain; AGL2 binds DNA as adimer; See S000338;MADSAGL1AGAMOUSflowerArabidopsis thaliana+Huang H, Tudor M, Su T, Zhang Y, Hu Y, Ma HdDNA binding properties of two Arabidopsis MADS domain proteins:binding consensus and dimer formationPlant Cell 8: 81-94 (1996)PubMed: 8597661; NNWNCCAWWWWTRGWWANAGL3ATCONSENSUSS000343 7-Sep-2000 (last modified) seki�Binding consensus sequence of Arabidopsis(A.t.) AGL3; AGL3 isMADS-box domain protein; AGL3 is expressed in all above-groundvegetative organs; AGL3 may be involved the transcriptionalregulation of genes;MADS-boxAGL3CArGstemleafflowershootArabidopsis thaliana&Huang H, Tudor M, Weiss CA, Hu Y, Ma HiThe Arabidopsis MADS-box gene AGL3 is widely expressed andencodes a sequence-specific DNA-binding protein Plant Mol Biol 28:549-567 (1995)1PubMed: 7632923; GenBank: U81368; U81369; U81370; TTWCYAWWWWTRGWAA
AGMOTIFNTMYB2S000444 28-Jan-2004 (last modified) kehi�+AG-motif found at -114 of the promoter of NtMyb2 gene; NtMyb2 isa regulator of the tobacco retrotransposon Tto1 and thedefence-related gene phenylalanine ammonia lyase (PAL), which areinduced by various stress such as wounding or elicitor treatment;AGP1 (GATA-type zinc finger protein) binding site;MYBTto1PALAGP1GATANicotiana tabacum (tobacco)!Sugimoto K, Takeda S, Hirochika H�Transcriptional activation mediated by binding of a plantGATA-type zinc finger proteinAGP1 to the AG-motif (AGATCCAA) ofthe wound-inducible Myb gene NtMyb2.Plant J, 36: 550-564 (2003)PubMed: 14617085; AGATCCAAAGTACSAOS000258 14-Oct-1999 (last modified) kehi�"AGTA repeat" in pumpkin (C.s.) ascorbate oxidase gene (AO)promoter; Found in silencer region; AOBP (AGTA repeat bindingprotein) binding site; AOBP protein has DOF domain; Required forrepression of expression of AO gene; AGTA repeatDOFAOBPascorbate oxidasesilencer regionpumpkin (Cucurbita sp.)1Kisu Y, Ono T, Shimofurutani N, Suzuki M, Esaka M|Characterization and expression of a new class of zinc fingerprotein that binds to silencer region of ascorbate oxidase gene&Plant Cell Physiol 39:1054-1064 (1998)"PubMed: 9871365; GenBank: D45066; AAAAAGTAAAAAGTAAAAAAGTAAAAAG
ALF1NTPARCS000238 11-Oct-1999 (last modified) kehi�"ALF-1 (as-1-like sequence binding factor)" binding site found intobacco (N.t.) parC gene; Found in auxin-responsive regions;as-1-like sequences in parA, parB and parC bind with ASF-1,ALF-2, and ALF-1, respectively; See S000190 (ABFOS);as-1ALF-1parauxin tobacco (Nicotiana tabacum); Sakai T, Takahashi Y, Nagata T{The identification of DNA binding factor specific for as-1-likesequences in auxin-responsive regions of parA, parB and parC%Plant Cell Physiol 39:731-739 (1998)PubMed: 9729895; TTACGCAAGCAATGACA
ALF2NTPARBS000239 11-Oct-1999 (last modified) kehi�"ALF-2 (as-1-like sequence binding factor 2)" binding site foundin tobacco (N.t.) parB gene; Found in auxin-responsive regions;as-1-like sequences in parA, parB and parC bind with ASF-1,ALF-2, and ALF-1, respectively; See S000190 (ABFOS);as-1ALF-2parauxin tobacco (Nicotiana tabacum); Sakai T, Takahashi Y, Nagata T{The identification of DNA binding factor specific for as-1-likesequences in auxin-responsive regions of parA, parB and parC%Plant Cell Physiol 39:731-739 (1998)PubMed: 9729895; TGAGGAGACTTGTGAGGTAMMORESIIUDCRNIA1S000374 31-Jul-2001 (last modified) uchi�Motifs (IIU and IID) found in the Chlamydomonas (C.R.) Nia1 genepromoter; Involved in ammonium-response; Located between -231 and-219 and also between -76 and -65; Involved in Nia1 transcriptionactivation; W=T/A;nitrate reductaseammonium responseChlamydomonas reinhardtiiLoppes R, Radoux M�Identification of short promoter regions involved in thetranscriptional expression of the nitrate reductase gene inChlamydomonas reinhardtii!Plant Mol Biol 45: 215-227 (2001)PubMed: 11289512; GGWAGGGTAMMORESIVDCRNIA1S000375 31-Jul-2001 (last modified) uchi�Motif (IVD) found in the Chlamydomonas (C.R.) Nia1 gene promoter;Located between -51 and -42; Involved in Nia1 transcriptionrepression;nitrate reductaseammonium responseChlamydomonas reinhardtiiLoppes R, Radoux M�Identification of short promoter regions involved in thetranscriptional expression of the nitrate reductase gene inChlamydomonas reinhardtii!Plant Mol Biol 45: 215-227 (2001)PubMed: 11289512; CGAACTTAMMORESVDCRNIA1S000376 31-Jul-2001 (last modified) uchi�Motif (VD) found in the Chlamydomonas (C.R.) Nia1 gene promoter;Located between -33 and -8; Involved in Nia1 transcriptionactivation;nitrate reductaseammonium responseChlamydomonas reinhardtiiLoppes R, Radoux M�Identification of short promoter regions involved in thetranscriptional expression of the nitrate reductase gene inChlamydomonas reinhardtii!Plant Mol Biol 45: 215-227 (2001)PubMed: 11289512; GGCCCCGGGAMYBOX1S000020 17-May-1998 (last modified) kehij"amylase box"; Conserved sequence found in 5'-upstream region ofalpha-amylase gene of rice, wheat, barley;amylaseseedGbarley (Hordeum vulgare); rice (Oryza sativa); wheat (Triticumaestivum)+Huang N, Sutliff TD, Litts JC, Rodriguez RLOClassification and characterization of the rice alpha-amylasemultigene family. Plant Mol Biol 14:655-668 (1990)!PubMed: 2102847; GenBank: X16509; TAACARAAMYBOX2S000021 17-May-1998 (last modified) kehi�"amylase box"; "amylase element"; Conserved sequence found in5'upstream region of alpha-amylase gene of rice, wheat, barley;"amylase box" (Huang et al. 1990); "amylase element" (Hwang etal., 1998);amylaseseedGbarley (Hordeum vulgare); rice (Oryza sativa); wheat (Triticumaestivum)_Huang N, Sutliff TD, Litts JC, Rodriguez RLHwang YS, Karrer EE, Thomas BR, Chen L, Rodriguez RL�Classification and characterization of the rice alpha-amylasemultigene family.Three cis-elements required for rice alpha-amylase Amy3Dexpression during sugar starvation@Plant Mol Biol 14:655-668 (1990)Plant Mol Biol 36:331-341 (1998)1PubMed: 2102847; GenBank: X16509;PubMed: 9484474; TATCCATANAERO1CONSENSUSS000477%05-November-2005 (last modified) kehi�One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway (anaerobic set1)(Mohanty et al., 2005); Arbitrary named ANAERO1CONSENSUS by thePLACEdb curator; See also S000478, S000479, S000480, S000481; anaerobic�Zea mays (maize); Arabidopsis thaliana; Pisum sativum (pea);Hordeum vulgare (barley); Oryza sativa (rice); Petunia hybrida(petunia); Lycopersicon esculentum (tomato);+Mohanty B, Krishnan SP, Swarup S, Bajic VB.sDetection and preliminary analysis of motifs in promoters ofanaerobically induced genes of different plant species.!Ann Bot (Lond).96: 669-681 (2005)PubMed: 16027132 in silicoAAACAAAANAERO2CONSENSUSS000478%05-November-2005 (last modified) kehi�One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway (anaerobic set1)(Mohanty et al., 2005); Arbitrary named ANAERO2CONSENSUS by thePLACEdb curator; See also S000477, S000479, S000480, S000481; anaerobic�Zea mays (maize); Arabidopsis thaliana; Pisum sativum (pea);Hordeum vulgare (barley); Oryza sativa (rice); Petunia hybrida(petunia); Lycopersicon esculentum (tomato);+Mohanty B, Krishnan SP, Swarup S, Bajic VB.sDetection and preliminary analysis of motifs in promoters ofanaerobically induced genes of different plant species.!Ann Bot (Lond).96: 669-681 (2005)PubMed: 16027132 in silicoAGCAGCANAERO3CONSENSUSS000479%05-November-2005 (last modified) kehi�One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway (anaerobic set1)(Mohanty et al., 2005); Arbitrary named ANAERO3CONSENSUS by thePLACEdb curator; See also S000477, S000478, S000480, S000481; anaerobic�Zea mays (maize); Arabidopsis thaliana; Pisum sativum (pea);Hordeum vulgare (barley); Oryza sativa (rice); Petunia hybrida(petunia); Lycopersicon esculentum (tomato);+Mohanty B, Krishnan SP, Swarup S, Bajic VB.sDetection and preliminary analysis of motifs in promoters ofanaerobically induced genes of different plant species.!Ann Bot (Lond).96: 669-681 (2005)PubMed: 16027132 in silicoTCATCACANAERO4CONSENSUSS000480%05-November-2005 (last modified) kehi�� One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway (anaerobic set1)(Mohanty et al., 2005); Arbitrary named ANAERO4CONSENSUS by thePLACEdb curator; See also S000477, S000478, S000479, S000481;H=A/T/C; anaerobic�Zea mays (maize); Arabidopsis thaliana; Pisum sativum (pea);Hordeum vulgare (barley); Oryza sativa (rice); Petunia hybrida(petunia); Lycopersicon esculentum (tomato);+Mohanty B, Krishnan SP, Swarup S, Bajic VB.sDetection and preliminary analysis of motifs in promoters ofanaerobically induced genes of different plant species.!Ann Bot (Lond).96: 669-681 (2005)PubMed: 16027132 in silico GTTTHGCAAANAERO5CONSENSUSS000481%05-November-2005 (last modified) kehi�One of 16 motifs found in silico in promoters of 13 anaerobicgenes involved in the fermentative pathway (anaerobic set1)(Mohanty et al., 2005); Arbitrary named ANAERO5CONSENSUS by thePLACEdb curator; See also S000477, S000478, S000479, S000480; anaerobic�Zea mays (maize); Arabidopsis thaliana; Pisum sativum (pea);Hordeum vulgare (barley); Oryza sativa (rice); Petunia hybrida(petunia); Lycopersicon esculentum (tomato);+Mohanty B, Krishnan SP, Swarup S, Bajic VB.sDetection and preliminary analysis of motifs in promoters ofanaerobically induced genes of different plant species.!Ann Bot (Lond).96: 669-681 (2005)PubMed: 16027132 in silico TTCCCTGTTANAEROBICCISZMGAPC4S000350 16-Feb-2001 (last modified) seki�20 bp anaerobic cis-regulatory sequence found in the maize (Z.m.)GapC4 (Glyceraldehyde-3-phosphate dehydrogenase 4) gene promoter;Located between -286 and -266; Required for anaerobic geneexpression in transgenic tobacco; See S000351; anaerobicGapC4(Glyceraldehyde-3-phosphate dehydrogenasemaize (Zea mays)Geffers R, Cerff R, Hehl RuAnaerobiosis-specific interaction of tobacco nuclear factors withcis-regulatory sequences in the maize GapC4 promoter Plant Mol Biol 43: 11-21 (2000)PubMed: 10949370; CGAAACCAGCAACGGTCCAGARE1S000022 16-Jan-1998 (last modified) kehi�"ARE (antioxidant response element)"; antioxidant responseelement of rat glutathione S-transferase Ya subunit, and ratNAD(P)H:quinone reductase genes; antioxidant response elementAREoxidative stressactiveoxygenrat"Rushmore TH, Morton MR, Pickett CB�The antioxidant responsive element. Activation by oxidativestress and identification of the DNA consensus sequence requiredfor functional activity."J Biol Chem 266:11632-11639 (1991)PubMed: 1646813; RGTGACNNNGCARECOREZMGAPC4S000393 21-May-2002 (last modified) uchi�Putative binding site for a Myb found in the promoter of maizeglycolytic glyceraldehyde-3-phospate dehydrogenase 4 (GapC4)gene; Essential for anaerobic induction; anaerobicGapC4 Myb proteinmaize (Zea mays)"Geffers R, Sell S, Cerff R, Hehl RvThe TATA box and a Myb binding site are essential for anaerobicexpression of a maize GapC4 minimal promoter in tobacco)Biochim Biophys Acta 1521: 120-125 (2001)PubMed: 11690643;
AGCAACGGTCARELIKEGHPGDFR2S000437%28-November-2004 (last modified) kehi�Sequence highly similar to ARE (anthocyanin regulatory element)found in maize anthocyanin promoter (Tuerck and Fromm 1994;Lesnick and Chandler 1998); Binding site of R2R3-type MYB factor,GMYB 10 of G. hybrida; anthocyaninaAREDRFC1R2R3MYBa2-Gerbera hybrida (Astraceae); Zea mays (maize)�Elomaa P, Uimari A, Mehto M, Albert VA, Latinen RAE, Teeri TH.Hernandez JM, Heine GF, Irani NG, Feller A, Kim MG, Matulnik T,Chandler VL, Grotewold E.Lesnick ML, Chandler VL.��Activation of anthocyanin biosynthesis in Gerbera hybrida(Asteraceae) suggests conserved protein-protein andprotein-promoter interactions between the anciently divergedmonocots and eudicots.Different mechanisms participate in the R-dependent activity ofthe R2R3 MYB transcription factor C1.Activation of the maize anthocyanin gene a2 is mediated by anelement conserved in many anthocyanin promoters.lPlant Physiol. 133: 1831-1842 (2003)J Biol Chem. 279: 48205-48213 (2004).Plant Physiol. 117: 437-445 (1998).0PubMed: 14605235;PubMed: 15347654PubMed: 9625696 AGTTGAATGGGGGTGCAARFATS000270#01-August-2006 (last modified) kehi��ARF (auxin response factor) binding site found in the promotersof primary/early auxin response genes of Arabidopsis thaliana(A.t.); AuxRE; See S000337; Binding site of Arabidopsis ARF1(Auxin response factor1); Sequence found in NDE element inSoybean (G.m.) SAUR (Small Auxin-Up RNA) 15A gene promoter; SeeS000359, S000360; Found in D1 or D4 element in Soybean (G.m.) GH3promoter; This element was enriched in the 5'-flanking region ofgenes up-regulated by both IAA and BL (Goda et al., 2004);
auxinAuxREARFARF1Aux/IAASAURNDEGH3D1D4@Arabidopsis thaliana; Soybean (Glycine max); Oryza sativa (rice)�xUlmasov T, Hagen G, Guilfoyle TJNag R, Maity MK, Dasgupta M.Inukai Y, Sakamoto T, Ueguchi-Tanaka M, Shibata Y, Gomi K,Umemura I, Hasegawa Y, Ashikari M, Kitano H, Matsuoka M.Harper RM, Stowe-Evans EL, Luesse DR, Muto H, Tatematsu K,Watahiki MK, Yamamoto K, Liscum ENemhauser JL, Mockler TC, Chory J.Goda H, Sawa S, Asami T, Fujioka S, Shimada Y, Yoshida S.Hagen G, Guilfoyle T��Dimerization and DNA binding of auxin response factorsDual DNA binding property of ABA insensitive 3 like factorstargeted to promoters responsive to ABA and auxin.Crown rootless1, Which Is Essential for Crown Root Formation inRice, Is a Target of an AUXIN RESPONSE FACTOR in AuxinSignaling.The NPH4 locus encodes the auxin response factor ARF7, aconditional regulator of differential growth in aerialArabidopsis tissueInterdependency of brassinosteroid and auxin signaling inArabidopsis.Comprehensive comparison of auxin-regulated andbrassinosteroid-regulated genes in Arabidopsis.Auxin-responsive gene expression: genes, promoters and regulatoryfactors�Plant J 19:309-319 (1999)Plant Mol Biol. 59: 821-838 (2005).Plant Cell 17: 1387-1396 (2005)Plant Cell 12: 757-770 (2000)PLoS Biol. 2(9):E258. (2004)Plant Physiol. 134: 1555-1573 (2004).Plant Mol Biol. 49 :373-385 (2002)sPubMed: 10476078;PubMed: 16270233PubMed: 15829602PubMed: 10810148;PubMed: 15328536PubMed: 15047898PubMed: 12036261;ReviewTGTCTCARR1ATS000454"27-March-2004 (last modified) kehi�"ARR1-binding element" found in Arabidopsis; ARR1 is a responseregulator; N=G/A/C/T; AGATT is found in the promoter of ricenon-symbiotic haemoglobin-2 (NSHB) gene (Ross et al., 2004);ARR1Response regulatorArabidopsis thaliana^Sakai H, Aoyama T, Oka A.Ross EJ, Stone JM, Elowsky CG, Arredondo-Peter R, Klucas RV,Sarath G.�Arabidopsis ARR1 and ARR2 response regulators operate astranscriptional activators.Activation of the Oryza sativa non-symbiotic haemoglobin-2promoter by the cytokinin-regulated transcription factor, ARR1.<Plant J. 24: 703-711 (2000).J Exp Bot. 55: 1721-1731 (2004). PubMed: 11135105PubMed: 15258171 NGATTAS1CAMVS000023 16-Jan-1998 (last modified) kehi�"as-1 (activation sequence 1)" in CaMV 35S promoter; from -85 to-58 (subdomain AI); Binding with ASF-1 (activation sequencefactor 1) from pea and tobacco; Expression in root and leaf;CaMV 35S promoterASF-1leafrootas-1 Cauliflower mosaic virus; CaMV;DLam E, Benfey PN, Gilmartin PM, Fang R-X, Chua N-HBenfey PN, Chua NH�Site-specific mutations alter in vitro factor binding and changepromoter expression pattern in transgenic plants.The cauliflower mosaic virus 35S promoter: combinatorialregulation of transcription in plantsFProc Natl Acad Sci USA 86:7890-7894 (1989)Science 250:959-966 (1990)PubMed: 2813365; CCACTGACGTAAGGGATGACGCACAATCC
AS1LIKECSHPRAS000260 14-Oct-1999 (last modified) kehi�as-1-like motif found in cucumber (C.s.) hydroxypyruvatereductase (hprA) gene; Required for cytokinin responsiveness;Also see S000261 (CYTOSITECSHPRA); cytokininas-1as-1 TGACG motifcucumber (Cucumis sativus)CJin G, Davey MC, Ertl JR, Chen R, Yu Z, Daniel SG, Becker WM,Chen CInteraction of DNA-binding proteins with the 5'-flanking regionof a cytokinin-responsive cucumber hydroxypyruvate reductasegene Plant Mol Biol 38:713-724 (1998)PubMed: 9862489; AAATGACGAAAATGC ASF1ATNOSS000073 7-Sep-2000 (last modified) seki�Tobacco ASF-1 binding site in nopaline synthase (NOS) promoter ofTi-plasmid of Agrobacterium tumefaciens (A.t.); From -131 to-111; See S000312; Containing two hexamer motifs; Essential forthe nos promoter activity;nopaline synthaseASF-1auxinmethyl jasmonate salicylicacidAgrobacterium tumefaciens:Lam E, Katagiri F, Chua NHKim Y, Buckley K, Costa MA, An G�Plant nuclear factor ASF-1 binds to an essential region of thenopaline synthase promoter.A 20 nucleotide upstream element is essential for the nopalinesynthase (nos) promoter activityAJ Biol Chem 265:9909-9913 (1990)Plant Mol Biol 24: 105-117 (1994) PubMed: 2351681;PubMed: 8111010; TGAGCTAAGCACATACGTCAG
ASF1MOTIFCAMVS000024 11-May-2006 (last modified) kehi��"ASF-1 binding site" in CaMV 35S promoter; ASF-1 binds to twoTGACG motifs; See S000023 (AS1); Found in HBP-1 binding site ofwheat histone H3 gene; TGACG motifs are found in many promotersand are involved in transcriptional activation of several genesby auxin and/or salicylic acid; May be relevant to lightregulation; Binding site of tobacco TGA1a; TGA1a and b showhomology to CREB; TGA6 is a new member of the TGA family; Abioticand biotic stress differentially stimulate "as-1 element"activity;TGACGrootleafCaMV35Spromoterauxinsalicylic acidlightas-1 TGA1a, TGA1bCREBASF1TGA6shoot
xenobioticstressSARSADisease resistanceXCaMV; Cauliflower mosaic virus; plant; tobacco (Nicotianatabacum); Arabidopsis thaliana;�� Despres C, Chubak C, Rochon A, Clark R, Bethune T, Desveaux D,Fobert PR.Terzaghi WB, Cashmore ARBenfey PN, Chua NHKatagiri F, Lam E, Chua NHXiang C, Miao Z, Lam EKlinedinst S, Pascuzzi P, Redman J, Desai M, Arias JRedman J, Whitcraft J, Johnson C, Arias J��The Arabidopsis NPR1 disease resistance protein is a novelcofactor that confers redox regulation of DNA binding activity tothe basic domain/leucine zipper transcription factor TGA1.Light-regulated transcriptionThe cauliflower mosaic virus 35S promoter: combinatorialregulation of transcription in plantsTwo tobacco DNA-binding proteins with homology to the nuclearfactor CREBDNA-binding properties, genomic organization and expressionpattern of TGA6,a new member of the TGA family of bZIPtranscription factors in Arabidopsis thalianaA xenobiotic-stress-activated transcription factor and itscognate target genes are preferentially expressed in root tipmeristemsAbiotic and biotic stress differentially stimulate as-1 elementactivity in Arabidopsis�Plant Cell 15: 2181-2191 (2003)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)Science 250:959-966 (1990)Nature 31: 727-730 (1989)Plant Mol Biol 34: 403-415 (1997)Plant Mol Biol 42: 679-688 (2000)Plant Cell Rep. 21: 180-185 (2002)APubMed: 12953119;PubMed: 2528073;PubMed: 9225852PubMed: 10809441; TGACG
ASF1NTPARAS000240 11-Oct-1999 (last modified) kehi�"ASF-1 (as-1 binding nuclear factor)" binding site found intobacco (N.t.) parA gene; Found in auxin-responsive regions;as-1-like sequences in parA, parB and parC bind with ASF-1,ALF-2, and ALF-1, respectively; See S000190 (ABFOS), S000238(ALF1NTPARC), S000239 (ALF2NTPARB);as-1ASF-1parauxin tobacco (Nicotiana tabacum); Sakai T, Takahashi Y, Nagata T{The identification of DNA binding factor specific for as-1-likesequences in auxin-responsive regions of parA, parB and parC%Plant Cell Physiol 39:731-739 (1998)PubMed: 9729895; TTACGCAAGCAATGACATAT1BOXS000025!17-May-1998 (last modified) kehi;��"AT-1 box (AT-rich element)" found in the promoter region of thegenes for tobacco ( N.p.) chlorophyll a/b binding protein (cab)and small subunit of ribulose-1,5-bisphosphate carboxylase(rbcS); Deletion of a region containing the AT-1 site in thetomato RBCS3A gene strongly inhibited reporter gene expression,whereas AT-1 site in N. plumbaginifolia CAB gene (cab-E) is in anegative element (Terzaghi & Cashmore, 1995);AT-1cabrbcSphotoregulated geneslight-regulated geneslightleafshootZpea (Pisum sativum); tobacco (Nicotiana plumbaginifolia); tomato(Lycopersicon esculentum);�Datta N, Cashmore ARGilmartin PM, Sarokin L, Memelink J, Chua N-HCastresana C, Garcia-Luque I, Alonso E, Malik VS, Cashmore ARUeda T, Pichersky E, Malik VS, Cashmore ARTerzaghi WB, Cashmore AR��Binding of a pea nuclear protein to promoters of certainphotoregulated genes is modulated by phosphorylation.Molecular light switches for plant genes.Both positive and negative regulatory elements mediate expressionof a photoregulated CAB gene from Nicotiana plumbaginifolia.The level of expression of the tomato rbcs-3A gene is modulatedby a far-upstream promoter element in a developmentary regulatedmanner.Light-regulated transcription�Plant Cell 1:1069-1077 (1989)Plant Cell 2:369-378 (1990)EMBO J 7:1929-1936 (1988)Plant Cell 1:217-227 (1989)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)bPubMed: 2562560;PubMed: 2152164;PubMed: 2901343; GenBank: X12512;PubMed: 2535544; GenBank: S44160;Review AATATTTTTATTATHB1ATCONSENSUSS000317 7-Sep-2000 (last modified) seki�Recognition sequence of Arabidopsis Athb-1 protein; Athb-1protein has a HD-Zip motif (homeodomain (HD) with a closelylinked leucine zipper motif (Zip)); HD-Zip domain binds to DNA asa dimer; See S000318; W=A/T;Athb-1 homeodomainZip HD-Zip motifArabidopsis thaliana Sessa G, Morelli G, Ruberti IeThe Athb-1 and -2 HD-Zip domains homodimerize forming complexesof different DNA binding specificitiesEMBO J 12:3507-3517 (1993)PubMed: 8253077; CAATWATTGATHB2ATCONSENSUSS000318 7-Sep-2000 (last modified) seki�Recognition sequence of Arabidopsis Athb-2 protein; Athb-2protein has a HD-Zip motif (homeodomain (HD) with a closelylinked leucine zipper motif (Zip)); See S000317; S=C/G;Athb-2 homeodomainZip HD-Zip motifArabidopsis thaliana Sessa G, Morelli G, Ruberti IeThe Athb-1 and -2 HD-Zip domains homodimerize forming complexesof different DNA binding specificitiesEMBO J 12:3507-3517 (1993)PubMed: 8253077; CAATSATTG ATHB5ATCORES000371%05-November-2005 (last modified) kehi�Consensus binding sequence for Arabidopsis (A.T.) class I HDzip(Homeodomein-leucine zipper) protein, ATHB5; ATHB5 protein formsdimers in solution; ATHB5 and ATHB6 exhibit identical DNA bindingspecificities; ATHB5 forms heterodimers with other class I HDzipproteins; See also S000475;Homeodomein-leucine zipperHDzipATHB5class IHDZip IArabidopsis thalianavJohannesson H, Wang Y, Engstrom PHenriksson E, Olsson AS, Johannesson H, Johansson H, Hanson J,Engstrom P, Soderman E.�DNA-binding and dimerization preferences of Arabidopsishomeodomain-leucine zipper transcription factors in vitroHomeodomain leucine zipper class I genes in Arabidopsis.Expression patterns and phylogenetic relationships.BPlant Mol Biol 45: 63-73 (2001)Plant Physiol. 139: 509-518. (2005)!PubMed: 11247607;PubMed: 16055682 CAATNATTG ATHB6COREATS000399 27-Aug-2002 (last modified) uchi�Consensus binding sequence for Arabidopsis (A.T.)homeodomain-leucine zipper protein, ATHB6; ATHB6 is a target ofthe protein phosphatase ABI1 and regulates hormone responses; SeeS000371;ATHB6ABAABI1homeodomain-leucine zipperArabidopsis thaliana5Himmelbach A, Hoffmann T, Leube M, Hohener B, Grill EsHomeodomain protein ATHB6 is a target of the protein phosphataseABI1 and regulates hormone responses in ArabidopsisEMBO J. 21:3029-3038 (2002)PubMed: 12065416; CAATTATTA ATRICHPSPETES000248 11-Oct-1999 (last modified) kehi�A/T-rich sequences found in pea (P.s.) plastocyanin gene (petE)promoter; Act as quantitative enhancer; Found at -289 to -255 ofpea PetE gene;A/T-richAT-richAT richenhancerpea (Pisum sativum) Sandhu JS, Webster CI, Gray JCjA/T-rich sequences act as quantitative enhancers of geneexpression in transgenic tobacco and potato plants!Plant Mol Biol 37:885-896 (1998)PubMed: 9678583; AATATACTAGTATTATTTACTAAAAAAAATC AUXREPSIAA4S000026 16-Feb-2001 (last modified) seki� "AuxRE (Auxine responsive element )" of pea (P.s.) PS-IAA4/5gene; Indoleacetic acid-inducible genes; domain A; TGA1a ispreferentially expressed in root tip meristems; TGA1a maycontribute to the expression of GST isoenzymes, especially inroot tip meristems;AuxinAuxRErootmeristempea (Pisum sativum)|Ballas N, Wong LM, Theologis AGuilfoyle T, Hagen G, Ulmasov T, Murfett JKlinedinst S, Pascuzzi P, Redman J, Desai M, Arias J�%Identification of the auxin-responsive element, AuxRE, in theprimary indoleacetic acid-inducible gene, PS-IAA4/5, of pea(Pisum sativum).How does auxin turn on genes?A xenobiotic-stress-activated transcription factor and itscognate target genes are preferentially expressed in root tipmeristems_J Mol Biol 233:580-596 (1993)Plant Physiol 118: 341-347 (1998)Plant Mol Biol 42: 679-688 (2000)BPubMed: 8411166; GenBank: X68216;PubMed: 9765520;PubMed: 10809441;ReviewKGTCCCATAUXRETGA1GMGH3S000234 7-Sep-2000 (last modified) seki�"TGA-box #1" in putative auxin-resonsive element (AUXRE) ofsoybean (G.m.) GH3 promoter; Strong binding site for proteins inplant nuclear extracts;TGAAUXREauxinGH3soybean (Glycine max)vLiu ZB, Ulmasov T, Shi X, Hagen G, Guilfoyle TJLiu ZB, Hagen G, Guilfoyle TJGuilfoyle T, Hagen G, Ulmasov T, Murfett J�Soybean GH3 promoter contains multiple auxin-inducible elementsA G-box-binding protein from soybean binds to the E1auxin-response element in the Soybean GH3 promoter and contains aproline-rich repression domainHow does auxin turn on genes?\Plant Cell 6:645-657 (1994)Plant Physiol 115:397-407 (1997)Plant Physiol 118: 341-347 (1998)0PubMed: 8038604;PubMed: 9342862;PubMed: 9765520;ReviewTGACGTAAAUXRETGA2GMGH3S000235 7-Sep-2000 (last modified) seki�"TGA-box #2" in putative auxin-resonsive element (AUXRE) E1 ofsoybean (G.m.) GH3 promoter; Strong binding site for proteins inplant nuclear extracts; Hex-like element; E1 element=-249 to-203; E2 element=-241 to -224; Called G-box by Liu et al.(1997);TGAAUXREauxinGH3E1G-boxsoybean (Glycine max)vLiu ZB, Ulmasov T, Shi X, Hagen G, Guilfoyle TJLiu ZB, Hagen G, Guilfoyle TJGuilfoyle T, Hagen G, Ulmasov T, Murfett J�Soybean GH3 promoter contains multiple auxin-inducible elementsA G-box-binding protein from soybean binds to the E1auxin-response element in the Soybean GH3 promoter and contains aproline-rich repression domainHow does auxin turn on genes?\Plant Cell 6:645-657 (1994)Plant Physiol 115:397-407 (1997)Plant Physiol 118: 341-347 (1998)0PubMed: 8038604;PubMed: 9342862;PubMed: 9765520;Review TGACGTGGC B2GMAUX28S000325 7-Sep-2000 (last modified) seki�"B2"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; Located between -310 and-301; Contains a TGACGACA sequence which is similar to TGACGT/Csequence found in Ocs, CaMV35S and histone H3 promoter; Containsas-1 motif;auxinAux28as-1soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133;
CTTGTCGTCABBOXSITE1STPATS000398 27-Aug-2002 (last modified) uchi�"10 base pair motif (site 1)" within the B-box found in thepotato patatin gene promoter; Involved in potato tuber-specificand sucrose-inducible gene expression; Storekeeper (STK) binds tothis region and regulates patatin expression in potato;STK (Storekeeper)tuberpatatinB-boxSolanum tuberosum (potato)3Zourelidou M, de Torres-Zabala M, Smith C, Bevan MWwStorekeeper defines a new class of plant-specific DNA-bindingproteins and is a putative regulator of patatin expressionPlant J. 30 :489-497 (2002)PubMed: 12028578;
GCTAAACAATBIHD1OSS000498#02-August-2006 (last modified) kehiEBinding site of OsBIHD1, a rice BELL homeodomain transcriptionfactor;HD homeodomainOryza sativa (rice)#Luo H, Song F, Goodman RM, Zheng Z.wUp-regulation of OsBIHD1, a rice gene encoding BELL homeodomaintranscriptional factor, in disease resistance responses.'Plant Biol (Stuttg). 7: 459-468 (2005).PubMed: 16163610FElectrophoretic mobility shift assays with recombinant OsBIHD1protein;TGTCA BOX1PSGS2S000222#19-August-2004 (last modified) kehi�,Box 1 element in pea (P.s.) glutamine synthetase (GS2) gene; Anelement in a 33-bp AT-rich sequence (box 1) of the 5' end of aGS2 promoter; Located at -837 to -827 of pea GS2; Multimer of box1 element was used to isolate a cDNA encoding an AT-rich DNAbinding protein (ATBP-1) (Tjaden & Coruzzi, 1994);Box 1glutamine synthetaseGS2ATBpATBP-1pea (Pisum sativum)4Tjaden G, Coruzzi GMTjaden G, Edwards JW, Coruzzi GM�� A novel AT-rich DNA binding protein that combines an HMG I-likeDNA binding domain with a putative transcription domaincis elements and trans-acting factors affecting regulation of anonphotosynthetic light-regulated gene for chloroplast glutaminesynthetase=Plant Cell 6:107-118 (1994)Plant Physiol 108:1109-1117 (1995)1PubMed: 7907505;PubMed: 7630938; GenBank: U22971; ATAGAAATCAA BOX1PVCHS15S000208 11-May-2006 (last modified) kehi��Box 1 of bean (P.v.) chs15 promoter; one of SBF-1 binding sitesin chs15 promoter; Located at -318 to -305; Involved inorgan-specific expression in plant development; Functions as atranscriptional silencer in electroporated protoplasts derivedfrom undifferentiated suspension-cultured soybean cells; Resemblethe binding site for the GT-1 factor in light-responsiveelements; For a compilation of related GT elements and factors,see Villain et al. (1996);
Box 1chschs15CHSSBF-1silencerorgan-specificGtGT-1GTbean (Phaseolus vulgaris)�Lawton MA, Dean SM, Dron M, Kooter JM, Kragh KM, Harrison MJ, YuL, Tanguay L, Dixon RA, Lamb CJVillain P, Mache R, Zhou DXZhou DX�Silencer region of a chalcone synthase promoter contains multiplebinding sites for a factor, SBF-1, closely related to GT-1The mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorskPlant Mol Biol 16:235-249 (1991)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)BPubMed: 1893099; GenBank: X59469;PubMed: 8955086;PubMed: 10366876ReviewTAAAAGTTAAAAAC BOX2PSGS2S000204 17-May-1998 (last modified) kehi�Box 2 in glutamine synthetase (GS2) gene in pea (P.s.); Repeatedin tandem with a partial palindrome located between the repeats;Located at ca. -300 of pea GS2;Box 2glutamine synthetaseGS2pea (Pisum sativum); Tjaden G, Edwards JW, Coruzzi GM�cis elements and trans-acting factors affecting regulation of anonphotosynthetic light-regulated gene for chloroplast glutaminesynthetase"Plant Physiol 108:1109-1117 (1995)!PubMed: 7630938; GenBank: U22971; TCTAAGCAAAG BOX2PVCHS15S000209 11-May-2006 (last modified) kehi�Box 2 of bean (P.v.) chs15 promoter; SBF-1 binding site; For acompilation of related GT elements and factors, see Villain etal. (1996);Box 2chschs15CHSSBF-1GT-1GTbean (Phaseolus vulgaris)�Lawton MA, Dean SM, Dron M, Kooter JM, Kragh KM, Harrison MJ, YuL, Tanguay L, Dixon RA, Lamb CVillain P, Mache R, Zhou DXZhou DX�Silencer region of a chalcone synthase promoter contains multiplebinding sites for a factor, SBF-1, closely related to GT-1The mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorskPlant Mol Biol 16:235-249 (1991)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)BPubMed: 1893099; GenBank: X59469;PubMed: 8955086;PubMed: 10366876ReviewCTGTGATTAAATAT BOX3PVCHS15S000210 11-May-2006 (last modified) kehi�Box 3 of bean (P.v.) chs15 promoter; SBF-1 binding site; For acompilation of related GT elements and factors, see Villain etal. (1996);Box 3chschs15CHSSBF-1GT-1GTbean (Phaseolus vulgaris)�Lawton MA, Dean SM, Dron M, Kooter JM, Kragh KM, Harrison MJ, YuL, Tanguay L, Dixon RA, Lamb CJVillain P, Mache R, Zhou DXZhou DX�Silencer region of a chalcone synthase promoter contains multiplebinding sites for a factor, SBF-1, closely related to GT-1The mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorskPlant Mol Biol 16:235-249 (1991)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)BPubMed: 1893099; GenBank: X59469;PubMed: 8955086;PubMed: 10366876ReviewTATTGGTTACTAAA BOXBPSAS1S000225 17-May-1998 (last modified) kehi�Box B in pea (P.s.) asparagine synthetase (AS1) gene; Found at-61; AS1 is negatively regulated by light; Box B binds withnuclear proteins;BOX BASAS1light
repressionnegative regulationpea (Pisum sativum)Ngai N, Tsai FY, Coruzzi GlLight-induced transcriptional repression of the pea AS1 gene:identification of cis-elements and transfactorsPlant J 12:1021-1234 (1997)PubMed: 9418044; AAACGACACCGTTT
BOXC'PSAS1S000227 17-May-1998 (last modified) kehi�Box C' in pea asparagine synthetase (AS1) gene; Found at -88; AS1is negatively regulated by light; Box C' binds with nuclearproteins, which was competed by a putative repressor element RE1(see S000195);BOX C'ASAS1pea (Pisum sativum);Ngai N, Tsai FY, Coruzzi GlLight-induced transcriptional repression of the pea AS1 gene:identification of cis-elements and transfactorsPlant J 12:1021-1234 (1997)PubMed: 9418044; TCCCGGTACACACTTCTT BOXCPSAS1S000226 10-May-1998 (last modified) kehi�Box C in pea (P.s.) asparagine synthetase (AS1) gene; Found at-45; AS1 is negatively regulated by light; Box C binds withnuclear proteins, which was competed by a putative repressorelement RE1 (see S000195);BOX CASAS1pea (Pisum sativum)Ngai N, Tsai FY, Coruzzi GlLight-induced transcriptional repression of the pea AS1 gene:identification of cis-elements and transfactorsPlant J 12:1021-1234 (1997)PubMed: 9418044; CTCCCACBOXICHSS000228 16-May-1998 (last modified) kehi�"Box I consensus sequence in the promoters of mustard and parsleychs genes; Essential for light regulation (Terzaghi & Cashmore,1995); M=A/C;Box IBox 1Unit 1CHSchslight regulation7parsley (Petroselinum crispum); mustard (Sinapis alba);{Block A, Dangl JL, Hahlbrock K, Schulze-Lefert PRocholl M, Talke-Messerer C, Kaiser T, Batschauer ATerzaghi WB, Cashmore AR�0Functional borders, genetic fine structure, and distancerequirements of cis elements mediating light responsiveness ofthe parsley chalcone synthase promoterUnit 1 of the mustard chalcone synthase promoter is sufficient tomediate light responses from different photoreceptors.Light-regulated transcriptionzProc Natl Acad Sci USA 87:5387-5391(1990)Plant Sci 97:189-198(1994)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)PubMed: 2371277ReviewGTCCMTCMAACCTAMC BOXIINTPATPBS000296 10-Feb-2000 (last modified) seki�"Box II" found in the tobacco (N.t.) plastid atpB gene promoter;Conserved in several NCII (nonconsensus type II) promoters ofplastid genes; Important for the activity of this NCII promoter;See S000295;plastidNEPatpBPatpBNCIIBox IBox IItobacco (Nicotiana tabacum)Kapoor S, Sugiura M�Identification of two essential sequence elements in thenonconsensus type II PatpB-290 plastid promoter by using plastidtranscription extracts from cultured tobacco BY-2 cells Plant Cell 11: 1799-1810 (1999)PubMed: 10488244 ATAGAA
BOXIIPCCHSS000229#01-August-2006 (last modified) kehi�Core of "Box II/G box" found in the parsley (P.c.) chs genes;Essential for light regulation (Terzaghi & Cashmore, 1995); SeeS000345;Box IIBox 2CHSchslight regulation parsley (Petroselinum crispum)�Block A, Dangl JL, Hahlbrock K, Schulze-Lefert PTerzaghi WB, Cashmore ARNakashima K, Fujita Y, Katsura K, Maruyama K, Narusaka Y, Seki M,Shinozaki K, Yamaguchi-Shinozaki K.�JFunctional borders, genetic fine structure, and distancerequirements of cis elements mediating light responsiveness ofthe parsley chalcone synthase promoterLight-regulated transcriptionTranscriptional regulation of ABI3- and ABA-responsive genesincluding RD29B and RD29A in seeds, germinating embryos, andseedlings of Arabidopsis.�Proc Natl Acad Sci USA 87:5387-5391(1990)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)Plant Mol Biol. 60: 51-68 (2006) PubMed: 2371277PubMed: 16463099ReviewACGTGGC BOXINTPATPBS000295 10-Feb-2000 (last modified) seki�"Box I" found in the tobacco (N.t.) plastid atpB gene promoter;Conserved in several NCII (nonconsensus type II) promoters ofplastid genes; Important for the activity of this NCII promoter;See S000296;plastidNEPatpBPatpBNCIIBox IBox IItobacco (Nicotiana tabacum)Kapoor S, Sugiura M�Identification of two essential sequence elements in thenonconsensus type II PatpB-290 plastid promoter by using plastidtranscription extracts from cultured tobacco BY-2 cells Plant Cell 11: 1799-1810 (1999)PubMed: 10488244 AATTCCATAGAATAGATAATA
BOXLCOREDCPALS000492$06-January-2006 (last modified) kehi�Consensus of the putative "core" sequences of box-L-likesequences in carrot (D.c.) PAL1 promoter region; DCMYB1 bound tothese sequences in vitro; See also S000136 (Box P), S000137 (BoxA), S000138 (Box L); W=A/T;MYB R2R3 type
PAL: ElicitorUV-BDilutionDaucus carota (carrot)/Maeda K, Kimura S, Demura T, Takeda J, Ozeki Y.�DcMYB1 acts as a transcriptional activator of the carrotphenylalanine ammonia-lyase gene (DcPAL1) in response to elicitortreatment, UV-B irradiation and the dilution effect."Plant Mol Biol. 59: 739-752.(2005)PubMed: 16270227 ACCWWCCBP5OSWXS000436 27-Jan-2004 (last modified) kehi3OsBP-5 (a MYC protein) binding site in Wx promoter;MYCWxWaxyOryza sativa (rice);#Zhu Y, Cai X-L, Wang Z-Y, Hong M-M.wAn interaction between a MYC protein and an EREBP protein isinvolved in transcriptional regulation of the rice Wx gene.&J. Biol. Chem. 278: 47803-47811 (2003)PubMed: 12947109; CAACGTGBS1EGCCRS000352 16-Feb-2001 (last modified) seki�"BS1 (binding site 1)" found in E. gunnii Cinnamoyl-CoA reductase(CCR) gene promoter; nuclear protein binding site; Required forvascular expression;cinnamoyl-CoA reductasevascularBS1stemEucalyptus gunniiELacombe E, Van Doorsselaere J, Boerjan W, Boudet AM,Grima-Pettenati J�Characterization of cis-elements required for vascular expressionof the cinnamoyl CoA reductase gene and for protein-DNA complexformationPlant J 23: 663-676 (2000)PubMed: 10972892; AGCGGG C1GMAUX28S000326 7-Sep-2000 (last modified) seki�"C1"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; Located between -463 and-448; A/T-rich sequence;AuxinAux28soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133; TGAAAACAGTGAGTTA C1MOTIFZMBZ2S000237 23-Sep-1999 (last modified) kehi�"C1-motif"; Similar to Myb-box; Found in the promoter region ofmaize (Z.m.) Bronze2 ( glutathione S-transferase) gene; C1binding; C1-motif and R-motif were shown to be important for fullR and C1 activation of the Bz2 promoter; S=C or G;C1-motifBronze2Myb-boxglutathione S-transferaseC1seedmaize (Zea mays)Bodeau JP, Walbot V6Structure and regulation of the maize Bronze2 promoter Plant Mol Biol 32:599-609 (1996)PubMed: 8980512; TAACTSAGTTA C2GMAUX28S000327 7-Sep-2000 (last modified) seki�"C2"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; Located between -552 and-553; Contains (ATT)4 sequence;AuxinAux28soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133; AATAATAATAATAATAAATACAATBOX1S000028 17-May-1998 (last modified) kehi="CAAT promoter consensus sequence" found in legA gene of pea;CAATlegAseedpea (Pisum sativum)'Shirsat A, Wilford N, Croy R, Boulter D`Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco. Mol Gen Genet 215:326-331 (1989)PubMed: 2710102; CAATCAATBOX2S000029 5-Jun-1997 (last modified) kehiZ"CAAT box" found in the 5' upstream region (-80) of manyeukaryotic genes; GGC(or T)CAATCT;eukaryotic geneCAAT
eukaryote; GGCCAATCT
CACGCAATGMGH3S000368 16-Feb-2001 (last modified) seki�Sequence found in D4 element in Soybean (G.m.) GH3 gene promoter;Showed constitutive activity with TGTCTC element (See S000270);Confers auxin inducibility; Binding site of nuclear protein; Seealso S000369;D1D4GH3AuxinSoybean (Glycine max)(Ulmasov T, Liu ZB, Hagen G, Guilfoyle TJ.Composite structure of auxin response elements Plant Cell 7: 1611-1623 (1995)PubMed: 7580254; CACGCAAT CACGTGMOTIFS000042$06-January-2006 (last modified) kehi��"CACGTG motif"; "G-box"; Binding site of Arabidopsis GBF4; C.roseus G-box binding factor 1 (CrGBF1) and 1 (CrGBF2) can act astranscriptional repressors of the Str promoter via directinteraction with the G-box; See S000345; Essential for expressionof beta-phaseolin gene during embryogenesis in bean, tobacco,Arabidopsis; Tomato Pti4 (ERF) regulates defense-related geneexpression via GCC box and non-GCC box cis-element (Myb1(GTTAGTT) and G-box (CACGTG)); A prominent hit by in silicoanalysis in both induced and repressed phyA-responsive promoters(Hudson and Quail 2003); Review by Terzaghi WB, Cashmore AR."Light-regulated transcription" in Annu Rev Plant Physiol PlantMol Biol 46:445-474 (1995);G boxG-boxrbcschs ACGT elementadhBz-2R-motifSTRGT-1GBFelicitorbZIPnapinstrictosidine synthasecellleafshootPti4ERFPR�tomato (Lycopersicon esculentum); Arabidopsis thaliana;snapdragon (Antirrhinum majus); wheat (Triticum aestivum);parsley: maize (Zea mays); periwinkle (Catharanthus roseus);Brassica napus; bean (Phaseolus vulgaris);�SChandrasekharan MB, Bishop KJ, Hall TC.Busk PK, Pages MHudson ME, Quail PH.Pasquali G, Erven ASW,Ouwerkerk PBF, Menke FLH, Memelink JMenkens AE, Schindler U, Cashmore ARChakravarthy S, Tuori RP, DAscenzo MD, Fobert PR, Despres C,Martin GBSiberil Y, Benhamron S, Memelink J, Giglioli-Guivarc'h N,Thiersault M, Boisson B, Doireau P, Gantet P�Module-specific regulation of the beta-phaseolin promoter duringembryogenesis.Regulation of abscisic acid-induced transcriptionIdentification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.The promoter of the strictosidine synthase gene from periwinkleconfers elicitor-inducible expression in transgenic tobacco andbinds nuclear factors GT-1 and GBFThe G-box: a ubiquitous regulatory DNA element in plants bound bythe GBF family of bzip proteinsThe tomato transcription factor Pti4 regulates defence-relatedgene expression via GCC box and non-GCC box cis elementsCatharanthus roseus G-box binding factors 1 and 2 act asrepressors of strictosidine synthase gene expression in cellcultures�Plant J. 33: 853-866 (2003)Plant Mol Biol 37:425-435 (1998)Plant Physiol. 133: 1605-1616 (2003)Plant Mol Biol 39:1299-1310 (1999)Trends in Biochemistry 20:506-510 (1995)Plant Cell 15: 3033-3050 (2003)Plant Mol Biol 45: 477-488 (2001)tPubMed: 12609027;PubMed: 9617810;PubMed: 14681527PubMed: 10380815;PubMed: 8571452;PubMed: 14630974;PubMed: 11352466;.Reviewin silico; over-represented motif;ReviewCACGTG CACTFTPPCA1S000449#19-August-2004 (last modified) kehi�Tetranucleotide (CACT) is a key component of Mem1 (mesophyllexpression module 1) found in the cis-regulatory element in thedistal region of the phosphoenolpyruvate carboxylase (ppcA1) ofthe C4 dicot F. trinervia; Y=T/C; mesohpyllCACTFlaveria trinerviaMGowik U, Burscheidt J, Akyildiz M, Schlue U, Koczor M, StreubelM, Westhoff P.�cis-Regulatory elements for mesophyll-specific gene expression inthe C4 plant Flaveria trinervia, the promoter of the C4phosphoenolpyruvate carboxylase gene. Plant Cell. 16:1077-1090(2004)PubMed: 15100398 YACT CANBNNAPAS000148 10-May-1998 (last modified) kehi�Core of "(CA)n element" in storage protein genes in Brasica napus(B.n.); embryo- and endosperm-specific transcription of napin(storage protein) gene, napA; seed specificity; activator andrepressor;
(CA)n elementnapAnapinseedstorage proteinBrassica napus;+Ellerstrom M, Stalberg K, Ezcurra I, Rask L�Functional dissection of a napin gene promoter: identification ofpromoter elements required for embryo and endosperm-specifictranscription."Plant Mol Biol 32:1019-1027 (1996)PubMed: 9002600; CNAACAC
CAREOSREP1S000421%28-November-2004 (last modified) kehin"CAREs (CAACTC regulatory elements)" found in the promoter regionof a cystein proteinase (REP-1) gene in rice;aleuroneGARE gibberellinseedOryza sativa (rice)Sutoh K, Yamauchi D.oTwo cis-acting elements necessary and sufficient forgibberellin-upregulated proteinase expression in rice seedsPlant J. 34:635-645 (2003)PubMed: 12787245; CAACTC
CARG1ATAP3S000347 31-May-2006 (last modified) kehi�#"CArG1" found in the Arabidopsis (A.t.) APETALA3 (AP3) genepromoter; Binding site of AP3/PI heterodimer; Binding site ofAP3/PI heterodimer; Binding site for a positively acting factors;MADS domain transcription factors bind with a consensus sequencecalled the CArG box; See S000348, S000349;APETALA3MADSCArG boxPIflowerArabidopsis thalianabTilly JJ, Allen DW, Jack THill TA, Day CD, Zondlo SC, Thackeray AG, Irish VFFolter S, Angenent GC.�The CArG boxes in the promoter of the Arabidopsis floral organidentity gene APETALA3 mediate diverse regulatory effectsDiscrete spatial and temporal cis-acting elements regulatetranscription of the Arabidopsis floral homeotic gene APETALA3trans meets cis in MADS science.dDevelopment 125: 1647-1657 (1998)Development125: 1711-1721 (1998)Trends Plant Sci. 11:224-231 (2006)0PubMed: 9521903;PubMed: 9521909;PubMed: 16616581ReviewGTTTACATAAATGGAAAA
CARG2ATAP3S000348 31-May-2006 (last modified) kehi�"CArG2" found in the Arabidopsis (A.t.) APETALA3 (AP3) genepromoter; Mutations in CArG2 result in a decrease in theexpression in petals, but the expression pattern in stamens isunchanged; See S000348, S000349;APETALA3MADSCArG boxPIflowerArabidopsis thalianabTilly JJ, Allen DW, Jack THill TA, Day CD, Zondlo SC, Thackeray AG, Irish VFFolter S, Angenent GC.�The CArG boxes in the promoter of the Arabidopsis floral organidentity gene APETALA3 mediate diverse regulatory effectsDiscrete spatial and temporal cis-acting elements regulatetranscription of the Arabidopsis floral homeotic gene APETALA3trans meets cis in MADS science.cDevelopment 125: 1647-1657 (1998)Development125: 1711-1721 (1998)Trends Plant Sci. 11:224-231(2006)0PubMed: 9521903;PubMed: 9521909;PubMed: 16616581 CTTACCTTTCATGGATTA
CARG3ATAP3S000349 31-May-2006 (last modified) kehi�~"CArG3" found in the Arabidopsis (A.t.) APETALA3 (AP3) genepromoter; Binding site of AP3/PI heterodimer; Binding site for anegatively acting factors; Binding sequence of Arabidopsis (A.t.)MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA, andAGAMOUS; AP1, AG, and AP3-PI complexes induce similarconformational changes on a CArG-box sequence; See S000347,S000348, S000338;APETALA3MADSCArG boxPI
PISTILLATAAPETALA1flowerArabidopsis thaliana�Tilly JJ, Allen DW, Jack THill TA, Day CD, Zondlo SC, Thackeray AG, Irish VFRiechmann JL, Wang M, Meyerowitz EMFolter S, Angenent GC.�|The CArG boxes in the promoter of the Arabidopsis floral organidentity gene APETALA3 mediate diverse regulatory effectsDiscrete spatial and temporal cis-acting elements regulatetranscription of the Arabidopsis floral homeotic gene APETALA3DNA-binding properties of Arabidopsis MADS domain homeoticproteins APETALA1, APETALA3, PISTILLATA and AGAMOUStrans meets cis in MADS science.�Development 125: 1647-1657 (1998)Development125: 1711-1721 (1998)Nucleic Acids Res 24: 3134-3141 (1996)Trends Plant Sci. 11:224-231(2006)@PubMed: 9521903;PubMed: 9521909;PubMed: 8774892;PubMed: 16616581 CTTTCCATTTTTAGTAACCARGATCONSENSUSS000404 31-May-2006 (last modified) kehi�<"CArG consensus" sequence found in the promoter of Arabidopsis(A.t.) SOC1 which is the MADS-box flowering-time gene; FLC is acomponent of the vernalization (low-temperature) pathway bindsdirectly to this site and blocks transcriptional activation ofSOC1 by CONSTANS (CO); See also S000342 (AGAMOUSATCONSENSUS);W=A/T;SOC1Flowering timeCONSTANSFLCArabidopsis thaliana�Hepworth SR, Valverde F, Ravenscroft D, Mouradov A, Coupland GMichaels SD, Ditta G, Gustafson-Brown C, Pelaz S, Yanofsky M,Amasino RM.Hong RL, Hamaguchi L, Busch MA, Weigel D.Folter S, Angenent GC.�QAntagonistic regulation of flowering-time gene SOC1 by CONSTANSand FLC via separate promoter motifsAGL24 acts as a promoter of flowering in Arabidopsis and ispositively regulated by vernalization.Regulatory elements of the floral homeotic gene AGAMOUSidentified by phylogenetic footprinting and shadowing.trans meets cis in MADS science.wEMBO J. 21: 4327-4337 (2002)Plant J. 33: 867-874 (2003)Plant Cell 15:1296-1309 (2003)Trends Plant Sci. 11:224-231(2006)BPubMed: 12169635;PubMed: 12609028;PubMed: 12782724PubMed: 16616581Review
CCWWWWWWGG
CARGCW8GATS000431 31-May-2006 (last modified) kehisA variant of CArG motif (see S000404), with a longer A/T-richcore; Binding site for AGL15 (AGAMOUS-like 15); W=A/T;CArGAGL15AGAMOUSMADSArabidopsis thaliana'Tang W, Perry SE.Folter S, Angenent GC.}Binding site selection for the plant MADS domain protein AGL15:an in vitro and in vivo study.trans meets cis in MADS science.EJ Biol Chem.278:28154-28159 (2003)Trends Plant Sci. 11:224-231 (2006)!PubMed: 12743119;PubMed: 16616581review
CWWWWWWWWGCARGNCATS000446 31-May-2006 (last modified) kehi�Noncanonical CArG motif (CC-Wx8-GG) found in the promoter regionof DTA1 (AtGA2ox6); A relevant cis element for the response toAGL15 (AGAMOUS-like 15) in vivo; W=A/T; See S000431 (C-Wx8-G),S000404 (CArG consensus; CC-Wx6-GG);MADSAGAMOUSAGLembryoArabidopsis thaliana;=Wang H, Caruso LV, Downie AB, Perry SE.Folter S, Angenent GC.�The embryo MADS domain protein AGAMOUS-Like 15 directly regulatesexpression of a gene encoding an enzyme involved in gibberellinmetabolism.trans meets cis in MADS science.BPlant Cell 16:1206-1219 (2004)Trends Plant Sci. 11:224-231 (2006) PubMed: 15084721PubMed: 16616581review CCWWWWWWWWGG CATATGGMSAURS000370 11-Mar-2001 (last modified) kehi�Sequence found in NDE element in soybean (G.m.) SAUR (SmallAuxin-Up RNA) 15A gene promoter; Involved in auxinresponsiveness; See S000359, S000360;SAURNDEauxinsoybean (Glycine max)Xu N, Hagen G, Guilfoyle T@Multiple auxin response modules in the soybean SAUR 15A promoter Plant Sci 126: 193-201 (1997) CATATGCBFHVS000497!22-June-2006 (last modified) kehi�Binding site of barley (H.v.) CBF1, and also of barley CBF2; CBF= C-repeat (CRT) binding factors; CBFs are also known asdehydration-responsive element (DRE) binding proteins (DREBs);See also S000411 (SQ=GTCGAC); R=A/G; Y=C/T;CBF
AP2 domainCRT/DRElow temperatureHordeum vulgare (barley)TXue GPSvensson JT, Crosatti C, Campoli C, Bassi R, Stanca AM, Close TJ,Cattivelli L.�Characterisation of the DNA-binding profile of barley HvCBF1using an enzymatic method for rapid, quantitative andhigh-throughput analysis of the DNA-binding activity.Transcriptome analysis of cold acclimation in barley albina andxantha mutants.CNucleic Acids Res. 30: e77 (2002)Plant Physiol. 141:257-270. (2006) PubMed: 12140339PubMed: 16603669 RYCGAC CCA1ATLHCB1S000149 10-May-1998 (last modified) kehi�CCA1 binding site; CCA1 protein (myb-related transcriptionfactor) interact with two imperfect repeats of AAMAATCT inLhcb1*3 gene of Arabidopsis thaliana (A.t.); Related toregulation by phytochrome;CCA1LhcbshootleafArabidopsis thaliana;8Wang Z-Y, Kenigsbuch D, Sun L, Harel E, Ong MS, Tobin EMhA myb-related transcription factor is involved in the phytochromeregulation of an Arabidopsis Lhcb gene.Plant cell 9:491-507 (1997)PubMed: 9144958; AAMAATCT CCAATBOX1S000030$04-January-2007 (last modified) kehi�Common sequence found in the 5'-non-coding regions of eukaryoticgenes; "CCAAT box" found in the promoter of heat shock proteingenes; Located immediately upstream from the most distal HSE ofthe promoter; "CCAAT box" act cooperatively with HSEs to increasethe hs promoter activity;HSE (Heat shock element) CCAAT box!eukaryotes; Glycine max (Soybean)�Rieping M, Schoffl FHaralampidis K, Milioni D, Rigas S, Hatzopoulos PWenkel S, Turck F, Singer K, Gissot L, Le Gourrierec J, Samach A,Coupland G.�}Synergistic effect of upstream sequences, CCAAT box elements, andHSE sequences for enhanced expression of chimaeric heat shockgenes in transgenic tobaccoCombinatorial interaction of cis elements specifies theexpression of the Arabidopsis AtHsp90-1 geneCONSTANS and the CCAAT Box Binding Complex Share a FunctionallyImportant Domain and Interact to Regulate Flowering ofArabidopsis.eMol Gen Genet. 231: 226-232 (1992)Plant Physiol. 129: 1138-1149 (2002)Plant Cell. 18:2971-2984 (2006)1PubMed: 1736093;PubMed: 12114568;PubMed: 17138697 CCAATCCTCGTGTCTCGMGH3S000369 16-Feb-2001 (last modified) seki�Sequence found in D1 element in Soybean (G.m.) GH3 gene promoter;Showed constitutive activity with TGTCTC element (See S000270);Confers auxin inducibility; Binding site of nuclear protein; Seealso S000368;D1D4GH3AuxinSoybean (Glycine max)(Ulmasov T, Liu ZB, Hagen G, Guilfoyle TJ.Composite structure of auxin response elements Plant Cell 7: 1611-1623 (1995)PubMed: 7580254; CCTCGTGTCTC
CDA1ATCAB2S000440 28-Jan-2004 (last modified) kehi�CDA-1 (CAB2 DET1-associated factor 1) binding site in DtRE (darkresponse element) f of chlorophyll a/b-binding protein2 (CAB2)gene in Arabidopsis;
dark responseCAB2Arabidopsis thaliana4Maxwell BB, Andersson CR, Poole DS, Kay SA, Chory J.�HY5, circadian clock-assosiated 1, and a cis-lelement, DET1 darkresponse element, mediate DET1 regulation of chlorophylla/b-binding protein2 expression.$Plant Physiol. 133: 1565-1577 (2003)PubMed: 14563928; CAAAACGC CE3OSOSEMS000282 16-Feb-2001 (last modified) seki�3"CE3 (Coupling Element 3)" found in the promoter of the rice(O.s.) Osem gene; Required for ABA-responsiveness and VP1activation; Binding site of TRAB1; Motif A and CE3 (S000281) arefunctionally equivalent; TRAB1, bZIP transcription factor,interacts with VP1 and mediates abscisic acid-inducedtranscritption; CE3Motif AAVRECE3ABAVP1TRAB1OsemEmbZIPseedrice (Oryza sativa)AHobo T, Asada M, Kowyama Y, Hattori THobo T, Kowyama Y, Hattori T�ACGT-containing abscisic acid response element (ABRE) andcoupling element 3 (CE3) are functionally equivalentA bZIP factor, TRAB1, interacts with VP1 and mediates abscisicacid-induced transcriptionHPlant J 19: 679-689 (1999)Proc Natl Acad Sci USA 96: 15348-15353 (1999)"PubMed: 10571853;PubMed: 10611387;
AACGCGTGTC CELLCYCLESCS000031 17-May-1998 (last modified) kehiv"cell cycle box" found in URS2 (-940/-200) of HO gene ofS.cerevisiae; cell-cycle-specific activation of transcription;cell cycle boxURS2HO gene yeast (Saccharomyces cerevisiae):Breeden L, Nasmyth KNasmyth K, Adolf G, Lydall D, Seddon A�Cell cycle control of the yeast HO gene: cis- and trans-actingregulators.The identification of a second cell cycle control on the HOpromoter in yeast: cell cycle regulation of SW15 nuclear entry.,Cell 48:389-397 (1987)Cell 62:631-647 (1990) PubMed: 3542227;PubMed: 2167175; CACGAAAACEREGLUBOX1PSLEGAS000032 17-May-1998 (last modified) kehi�"cereal glutenin box" in pea legumin gene (legA); sequencehomologous to the cereal glutenin gene control element ("-300element");cerealgluteninleguminlegAseedpea (Pisum sativum)'Shirsat A, Wilford N, Croy R, Boulter D`Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco. Mol Gen Genet 215:326-331 (1989)PubMed: 2710102; TGTTAAAGTCEREGLUBOX2PSLEGAS000033 17-May-1998 (last modified) kehi�"cereal glutenin box" in pea legumin gene (legA); sequencehomologous to the cereal glutenin gene control element ("-300element");leguminglutenincereallegAseedpea (Pisum sativum)'Shirsat A, Wilford N, Croy R, Boulter D`Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco. Mol Gen Genet 215:326-331 (1989)PubMed: 2710102; TGAAAACTCEREGLUBOX3PSLEGAS000034 17-May-1998 (last modified) kehiy"cereal glutenin box" in pea (P.s.) legumin gene (legA); sequencehomologous to the cereal glutenin gene control elements;legumincerealgluteninseedpea (Pisum sativum)'Shirsat A, Wilford N, Croy R, Boulter D`Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco. Mol Gen Genet 215:326-331 (1989)PubMed: 2710102; TGTAAAAGT CGACGOSAMY3S000205 17-May-1998 (last modified) kehi�"CGACG element" found in the GC-rich regions of the rice (O.s.)Amy3D and Amy3E amylase genes, but not in Amy3E gene; Mayfunction as a coupling element for the G box element;amylaserice (Oryza sativa);4Hwang YS, Karrer EE, Thomas BR, Chen L, Rodriguez RLZThree cis-elements required for rice alpha-amylase Amy3Dexpression during sugar starvation Plant Mol Biol 36:331-341 (1998)PubMed: 9484474; CGACG CGCGBOXATS000501#04-August-2006 (last modified) kehi�"CGCG box" recognized by AtSR1-6 (Arabidopsis thalianasignal-responsive genes); Multiple CGCG elements are found inpromoters of many genes; Ca++/calmodulin binds to all AtSRs;V=A/C/G; B=G/T/C;
calmodulinArabidopsis thalianaYang T, Poovaiah BW.jA calmodulin-binding/CGCG box DNA-binding protein family involvedin multiple signaling pathways in plants.$J Biol Chem. 277:45049-45058. (2002)PubMed: 12218065 VCGCGB
CGF1ATCAB2S000213 11-May-2006 (last modified) kehi��CGF-1 binding site in the Arabidopsis (A.t.) cab2 gene promoter;CGF-1=CAB GATA Factor 1; Found at -74 to -42; Contains a highlyconserved, repeated GATA motif termed I-box (see S000124,S000199); For GATA motif, see S000039; The binding specificity ofCGF-1 appears to be related to GT-family of DNA-binding proteins;For a compilation of related GT elements and factors, see Villainet al. (1996);CGFcabcab2CGF-1GTleafshootArabidopsis thaliana;QAnderson SL, Teakle GR, Martino-Catt SJ, Kay SAVillain P, Mache R, Zhou DXZhou DX� Circadian clock- and phytochrome-regulated transcription isconferred by a 78 bp cis-acting domain of the Arabidopsis CAB2promoterThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorscPlant J 6:457-470 (1994)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)0PubMed: 7987408;PubMed: 8955086;PubMed: 10366876review!GATAAAGATTACTTCAGATATAACAAACGTTAC CGTGTSPHZMC1S000294 10-Feb-2000 (last modified) seki�Sequence found in the maize (Z.m.) C1 gene promoter; Locatedbetween -147 to -132; Containing Sph element; Required for ABAresponsiveness; See S000154, S000293;C1anthocyanin pathwayABAVP1lightSphmaize (Zea mays)+Kao CY, Cocciolone SM, Vasil IK, McCarty DR�Localization and interaction of the cis-acting elements forabscisic acid, VIVIPAROUS1, and light activation of the C1 geneof maize Plant Cell 8: 1171-1179 (1996)PubMed: 8768375 CGTGTCGTCCATGCATCIACADIANLELHCS000252 11-Oct-1999 (last modified) kehiCRegion necessary for circadian expression of tomato (L.e.) Lhcgene; circadianlightLhcleafshoot tomato (Lycopersicon esculentum)"Piechulla B, Merforth N, Rudolph BOIdentification of tomato Lhc promoter regions necessary forcircadian expression!Plant Mol Biol 38:655-662 (1998)PubMed: 9747810;
CAANNNNATC CMSRE1IBSPOAS000511$04-January-2007 (last modified) kehizCMSRE-1 (Carbohydrate Metabolite Signal Responsive Element 1)found in the promoter of sweet potato (I.b.) sporamin A gene;sucrosesporamin
sugar-inducedSpoA Ipomoea batatas (sweet potato)@Morikami A, Matsunaga R, Tanaka Y, Suzuki S, Mano S, Nakamura K.�Two cis-acting regulatory elements are involved in thesucrose-inducible expression of the sporamin gene promoter fromsweet potato in transgenic tobacco.&Mol Genet Genomics. 272:690-699 (2005)PubMed: 15654621 TGGACGGCONSERVED11NTZMATP1S000301 10-Feb-2000 (last modified) seki�Conserved 11 nt sequence found in the maize (Z.m.) mitochondrialatp1 promoter; Located between -5 and +6; Essential for theexpression; mitochondriaatp1maize (Zea mays)Rapp WD, Stern DBmA conserved 11 nucleotide sequence contains an essential promoterelement of the maize mitochondrial atp1 geneEMBO J 11: 1065-1073 (1992)PubMed: 1372246 ACGTATTAAAACOREOSS000469"24-April-2005 (last modified) kehi�CORE (coordinate regulatory element for antioxidant defense)conserved on the promoter regions of three antioxidant defensegenes in rice: cytosolic superoxide dismutase, cytosolicthioredoxin, and glutaredoxin; K=T/G; W=T/A; Y=T/C; R=A/G;M=C/A;oxidative stress antioxidantOryza sativa (rice)?Tsukamoto S, Morita S, Hirano E, Yokoi H, Masumura T, Tanaka K.lA novel cis-element that is responsive to oxidative stressregulates three antioxidant defense genes in rice."Plant Physiol. 137: 317-327.(2005)PubMed: 15618434 AAKAATWYRTAWATAAAAMTTTTATWTACPBCSPORS000491%30-November-2005 (last modified) kehi�The sequence critical for Cytokinin-enhanced Protein Binding invitro, found in -490 to -340 of the promoter of the cucumber (CS)POR (NADPH-protochlorophyllide reductase) gene; cytokinin chlorophyll chloroplast Cucumis sativus L. (cucumber)<Fusada N, Masuda T, Kuroda H, Shimada H, Ohta H, Takamiya K.�Identification of a Novel Cis-Element ExhibitingCytokinin-Dependent Protein Binding in Vitro in the 5'-region ofNADPH-Protochlorophyllide Oxidoreductase Gene in Cucumber.#Plant Mol Biol. 59: 631-645 (2005).PubMed: 16244912 TATTAG CPRFPCCHSS000313$8-February-2006 (last modified) kehi��"BoxII"; Binding site of CPRF-1, -2, -3 and -4(Common PlantRegulatory Factor) in the parsley (P.c.) light responsivechalcone synthase (CHS) gene promoter; CPRF proteins are bZIPclass transcription factors; CPRF proteins participates in thelight-mediated activation of the CHS gene in parsley; "ACE"; Theproline-rich domains of CPRF1 and 4 activate transcription;CPRF1-containing bZIP heterodimer interacts with ACE in vivo; BoxIICPRFbZIPleafshootCHSACElightbZIP Parsley (Petroselinum crispum)cWeisshaar B, Armstrong GA, Block A, da Costa e Silva O, HahlbrockK.Sprenger-Haussels M, Weisshaar B�Light-inducible and constitutively expressed DNA-binding proteinsrecognizing a plant promoter element with functional relevance inlight responsivenessTransactivation properties of parsley proline-rich bZIPtranscription factors2EMBO J 10: 1777-1786 (1991)Plant J 22: 1-8 (2000)!PubMed: 2050115;PubMed: 10792815;
CCACGTGGCC CRTDREHVCBF2S000411!22-June-2006 (last modified) kehi� Preferred sequence for AP2 transcriptional activator HvCBF2 ofbarley; "Core CRT/DRE motif"; HvCBF2 bound to a (G/a)(T/c)CGACcore motif (Xue, 2003); DNA binding is regulated by temperature;This motif was erroneously ID-labeled in PLACEdb as CDTDREHVCBF2,and was corrected on 22 June, 2006;coldAP2CRT/DRECBFHordeum vulgare (barley)Xue GP�The DNA-binding activity of an AP2 transcriptional activatorHvCBF2 involved in regulation of low-temperature responsive genesin barley is modulated by temperature.Plant J. 33: 373-383 (2003)PubMed: 12535350; GTCGAC CTRMCAMV35SS000460"27-March-2004 (last modified) kehi�CT-rich motif (inverted GAGA) found in a 60-nucleotide region(S1) downstream of the transcription start site of the CaMV 35SRNA; Can enhance gene expression; Inverted GAGA; See alsoS000405, S000427 (GAGA); (TC)4T;CaMV 35Senhancer Cauliflower mosaic virus (CaMV)*Pauli S, Rothnie HM, Chen G, He X, Hohn T.MThe cauliflower mosaic virus 35S promoter extends into thetranscribed region. J Virol. 78: 12120-12128.(2004)PubMed: 15507598 TCTCTCTCT
CURECORECRS000493"11-April-2006 (last modified) kehi�GTAC is the core of a CuRE (copper-response element) found inCyc6 and Cpx1 genes in Chlamydomonas; Also involved inoxygen-response of these genes; For CuRE, see Quin and Merchant,1995;copperoxygenhypoxicChlamydomonas reinhardtii�Quinn JM, Barraco P, Eriksson M, Merchant S.Quinn JM, Eriksson M, Moseley JL, Merchant S.Quinn JM, Merchant S.Kropat J, Tottey S, Birkenbihl RP, Depege N, Huijser P, MerchantS.��Coordinate copper- and oxygen-responsive Cyc6 and Cpx1 expressionin Chlamydomonas is mediated by the same element.Oxygen deficiency responsive gene expression in Chlamydomonasreinhardtii through a copper-sensing signal transductionpathway.Two copper-responsive elements associated with the ChlamydomonasCyc6 gene function as targets for transcriptional activators.A regulator of nutritional copper signaling in Chlamydomonas isan SBP domain protein that recognizes the GTAC core of copperresponse element.�J Biol Chem. 275: 6080-6089 (2000).Plant Physiol. 128 :463-471 (2002).Plant Cell. 7 :623-628 (1995).Proc Natl Acad Sci U S A. 102: 18730-18735.(2005)?PubMed: 10692397PubMed: 11842150PubMed: 7780310PubMed: 16352720 GTACCYTOSITECSHPRAS000261 14-Oct-1999 (last modified) kehi�13 bp sequence of unknown function found in cucumber (C.s.)hydroxypyruvate reductase (hprA) gene promoter; Protein bindingsite; Required for cytokinin responsiveness; See S000260(AS1LIKECSHPRA) found in the same region; Also involved in lightresponsiveness; see also S000260; cytokininas-1lightcucumber (Cucumis sativus)CJin G, Davey MC, Ertl JR, Chen R, Yu Z, Daniel SG, Becker WM,Chen CInteraction of DNA-binding proteins with the 5'-flanking regionof a cytokinin-responsive cucumber hydroxypyruvate reductasegene Plant Mol Biol 38:713-724 (1998)PubMed: 9862489;
AAGATTGATTGAG D1GMAUX28S000328 20-Feb-2002 (last modified) uchi��"D1"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; D1 and D4 share a verysimilar core sequence TAGTXXCTGT and TAGTXCTGT, respectively;D1/D4-like sequence were identified in several otherauxin-responsive genes; Binding site of GmGT-2 which is the GT-2family of transcription factors; GmGT-2 are down-regulated bylight in a phytochrome-dependent manner; See 000331;AuxinAux28GT-2 phytochromeD1 hypocotylsoybean (Glycine max)WNagao RT, Goekjian VH, Hong JC, Key JLO'Grady K, Goekjian VH, Naim CJ, Nagao RT, Key JL�Identification of protein-binding DNA sequences in anauxin-regulated gene of soybeanThe transcript abundance of GmGT-2, a new member of the GT-2family of transcription factors from soybean, is down-regulatedby light in a phytochrome-dependent mannerEPlant Mol Biol 21: 1147-1162 (1993)Plant Mol Biol 47: 367-378 (2001)!PubMed: 8490133;PubMed: 11587508;
ACAGTTACTA D2GMAUX28S000329 7-Sep-2000 (last modified) seki�"D2"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; Located between -703 and-716; A/T-rich sequence;AuxinAux28soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133; ATTTATATAAAT D3GMAUX28S000330 7-Sep-2000 (last modified) seki�"D3"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; Located between -750 and-760; A/T-rich sequence;AuxinAux28soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133; TATTTGCTTAA D4GMAUX28S000331 7-Sep-2000 (last modified) seki�"D4"; DNase I protected sequence found in the soybean (G.m.)auxin responsive gene, Aux28, promoter; D1 and D4 share a verysimilar core sequence TAGTXXCTGT and TAGTXCTGT, respectively;D1/D4-like sequence were identified in several otherauxin-responsive genes; See 000328;AuxinAux28soybean (Glycine max)&Nagao RT, Goekjian VH, Hong JC, Key JLTIdentification of protein-binding DNA sequences in anauxin-regulated gene of soybean#Plant Mol Biol 21: 1147-1162 (1993)PubMed: 8490133; TAGTGCTGT DE1PSPRA2S000379 21-May-2001 (last modified) uchi�""DE1" found in the pea(P.S) pra2 gene promoter; Involved in pra2down-regulation by phytochrome A, phytochrome B and blue-lightphotoreceptors; pra2 encodes a small GTPase belonging to theYPT/rab family; DF1 has DNA-binding domain specifically binds totwo types of DNA sequences, DE1 and GT2;pra2light responsedark inductiondown regulationDF1pea (Pisum sativum)LInaba T, Nagano Y, Reid JB, Sasaki YNagano Y, Inaba T, Furuhashi H, Sasaki Y�5DE1, a 12-base pair cis-regulatory element sufficient to conferdark-inducible and light down-regulated expression to a minimalpromoter in peaTrihelix DNA-binding protein with specificities for two distinctcis-elements: both important for light down-regulated anddark-inducible gene expression in higher plantsFJ Biol Chem 275: 19723-19727 (2000)J Biol Chem 276: 22238-22243 (2001)"PubMed: 10777499;PubMed: 11301338; GGATTTTACAGT DOFCOREZMS000265 7-Sep-2000 (last modified) seki��Core site required for binding of Dof proteins in maize (Z.m.);Dof proteins are DNA binding proteins, with presumably only onezinc finger, and are unique to plants; Four cDNAs encoding Dofproteins, Dof1, Dof2, Dof3 and PBF, have been isolated frommaize; PBF is an endosperm specific Dof protein that binds toprolamin box; Maize Dof1 enhances transcription from thepromoters of both cytosolic orthophosphate kinase (CyPPDK) and anon-photosynthetic PEPC gene; Maize Dof2 supressed the C4PEPCpromoter;DofC4PEPCCyPPDKPEPCC4leafshootmaize (Zea mays)$Yanagisawa S, Schmidt RJYanagisawa S�Diversity and similarity among recognition sequences of Doftranscription factorsDof1 and Dof2 transcription factors are associated withexpression of multiple genes involved in carbon metabolism inmaize3Plant J 17:209-214 (1999)Plant J 21:281-288 (2000)"PubMed: 10074718;PubMed: 10758479; AAAG
DPBFCOREDCDC3S000292 7-Sep-2000 (last modified) seki��A novel class of bZIP transcription factors, DPBF-1 and 2 (Dc3promoter-binding factor-1 and 2) binding core sequence; Found inthe carrot (D.c.) Dc3 gene promoter; Dc3 expression is normallyembryo-specific, and also can be induced by ABA; The Arabidopsisabscisic acid response gene ABI5 encodes a bZIP transcriptionfactor; abi5 mutant have a pleiotropic defects in ABA response;ABI5 regulates a subset of late embryogenesis-abundant genes;GIA1 (growth-insensitivity to ABA) is identical to ABI5; Dc3lea class geneembryoABADPBF-1, DPBF-2bZIPGIA1ABI5seed-carrot (Daucus carota); Arabidopsis thaliana;JKim SY, Chung HJ, Thomas TLFinkelstein RR, Lynch TJLopez-Molina L, Chua NH�kIsolation of a novel class of bZIP transcription factors thatinteract with ABA-responsive and embryo-specification elements inthe Dc3 promoter using a modified yeast one-hybrid systemThe Arabidopsis abscisic acid response gene ABI5 encodes a basicleucine zipper transcription factorA null mutation in a bZIP factor confers ABA-insensitivity inArabidopsis thaliana^Plant J 11: 1237-1251 (1997)Plant Cell 12: 599-609 (2000)Plant Cell Physiol 41: 541-547 (2000)WPubMed: 9225465 GenBank: AF061870, AF001454, AF001453PubMed: 10760247;PubMed: 10929936; ACACNNGDR5GMGH3S000337 7-Sep-2000 (last modified) seki�"DR5"; A highly active synthetic auxin response element; Createdby site-directed mutations in a natural composite AuxRE found inthe soybean GH3 promoter; The DR5 showed greater auxinresponsiveness; Binding site of ARF1; See S000270;Aux/IAADR5AuxinARF1AUXRESoybean (Glycine max)+Ulmasov T, Murfett J, Hagen G, Guilfoyle TJ{Aux/IAA proteins repress expression of reporter genes containingnatural and highly active synthetic auxin response elements Plant Cell 9: 1963-1971 (1997)PubMed: 9401121; CCTTTTGTCTCDRE1COREZMRAB17S000401 27-Aug-2002 (last modified) uchi�3"DRE1" core found in maize (Z.M.) rab17 gene promoter; "DRE1" wasprotected, in in vivo footprinting, by a protein in embryosspecifically, but in leaves, was protected when was treated withABA and drought; rab17 is expressed during late embryogenesis,and is induced by ABA; See S000150, S000200 and S000402;rab17ABAdrought responsemaize (Zea mays)+Busk PK, Jensen AB, Pages MKizis D, Pages M�Regulatory elements in vivo in the promoter of the abscisic acidresponsive gene rab17 from maizeMaize DRE-binding proteins DBF1 and DBF2 are involved in rab17regulation through the drought-responsive element in anABA-dependent pathway8Plant J. 11: 1285-1295 (1997)Plant J. 30 :679-689 (2002)!PubMed: 9225468;PubMed: 12061899; ACCGAGADRE2COREZMRAB17S000402 03-Jun-2003 (last modified) kehi�"DRE2" core found in maize (Z.M.) rab17 gene promoter; "DBF1" and"DBF2" bound to "DRE2"; rab17 is expressed during lateembryogenesis, and is induced by ABA; See S000150, S000200 andS000401;rab17ABAdrought responseDBF1DBF2maize (Zea mays)�Busk PK, Jensen AB, Pages MKizis D, Pages MDubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S,Seki M, Shinozaki K, Yamaguchi-Shinozaki K.�yRegulatory elements in vivo in the promoter of the abscisic acidresponsive gene rab17 from maizeMaize DRE-binding proteins DBF1 and DBF2 are involved in rab17regulation through the drought-responsive element in anABA-dependent pathwayOsDREB genes in rice, Oryza sativa L., encode transcriptionactivators that function in drought-, high-salt- andcold-responsive gene expression.SPlant J. 11: 1285-1295 (1997)Plant J. 30 :679-689 (2002)Plant J. 33: 751-763 (2003)2PubMed: 9225468;PubMed: 12061899;PubMed: 12609047; ACCGAC DRECRTCOREATS000418$30-January-2006 (last modified) kehi��Core motif of DRE/CRT (dehydration-responsive element/C-repeat)cis-acting element found in many genes in Arabidopsis and inrice; R=G/A; Os DREB1A bound to GCCGAC more preferentially thanto ACCGAC whereas At DREB1A bound to both GCCGAC and ACCGACefficiently; See S000402 (ACCGAC); Maize ZmDREB1A bound to DRE(Qin et al. 2004); HaDREB2 in Helianthus annuus(sunflower)(Diaz-Martin et al. 2005); HaDREB2 physically interactwith HaHSFA9 in vitro (Diaz-Martin et al. 2005);DRE/CRTdrought
high-lightcoldDREBDREB1DREB2CBFDOryza sativa (rice); Zea mays (maize); Helianthus annuus(sunflower);��Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S,Seki M, Shinozaki K, Yamaguchi-Shinozaki K.Qin F, Sakuma Y, Li J, Liu Q, Li YQ, Shinozaki K,Yamaguchi-Shinozaki K.Diaz-Martin J, Almoguera C, Prieto-Dapena P, Espinosa JM, JordanoJSuzuki M, Ketterling MG, McCarty DR.Skinner JS, von Zitzewitz J, Szucs P, Marquez-Cedillo L,Filichkin T, Amundsen K, Stockinger EJ, Thomashow MF, Chen TH,Hayes PM.�qOsDREB genes in rice, Oryza sativa L., encode transcriptionactivators that function in drought-, high-salt- andcold-responsive gene expression.Cloning and functional analysis of a novel DREB1/CBFtranscription factor involved in cold-responsive gene expressionin Zea mays L.Functional Interaction between Two Transcription Factors Involvedin the Developmental Regulation of a Small Heat Stress ProteinGene PromoterQuantitative statistical analysis of cis-regulatory sequences inABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis.Structural, functional, and phylogenetic characterization of alarge CBF gene family in barley.�Plant J. 33: 751-763 (2003)Plant Cell Physiol. 45: 1042-1052 (2004).Plant Physiology, 139: 1483-1494 (2005)Plant Physiol.139: 437-447 (2005)Plant Mol Biol. 59: 533-551 (2005)QPubMed: 12609047;PubMed: 15356330PubMed: 16244139PubMed: 16113229PubMed: 16244905 in silicoRCCGACDREDR1ATRD29ABS000152!23-June-2006 (last modified) kehi��Related to responsiveness to drought, low-temperature orhigh-salt stress; See S000153, S000157; Binding site of DREB1 andDREB2: Binding site of Arabidopsis CBF1(C-repeat/DRE bindingfactor); Overexpression of DREB1A activated the expression ofstress tolerance genes; CBF1 overexpression induces COR genes andenhances freezing tolerance; Heterologous CBF1 expressionenhances oxidative stresses tolerance; DRE and ABRE areinterdependent in the ABA-responsive expression of the rd29A inArabidopsis;DREdrought water stressoxidative stresslow temperature high saltstressLREDREBC-repeatCBF1AP2cold dehydrationCRTleafshoot#Arabidopsis thaliana; Populus spp.;��Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki KSuzuki M, Ketterling MG, McCarty DR.Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, AbeH, Narusaka M, Shinozaki K, Yamaguchi-Shinozaki K.Benedict C, Skinner JS, Meng R, Chang Y, Bhalerao R, Huner NPA,Finn CE, Chen THH, Hurry VPandey GK, Grant JJ, Cheong YH, Kim BG, Li L, Luan S.Nakashima K, Shinwari ZK, Sakuma Y, Seki M, Miura S, Shinozaki K,Yamaguchi-Shinozaki KHsieh TH, Lee JT, Yang PT, Chiu LH, Charng YY, Wang YC, Chan MT��Improving plant drought, salt, and freezing tolerance by genetransfer of a single stress-inducible transcription factorQuantitative statistical analysis of cis-regulatory sequences inABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis.Interaction between two cis-acting elements, ABRE and DRE, inABA-dependent expression of Arabidopsis rd29A gene in response todehydration and high-salinity stresses.The CBF1-dependent low temperature signalling pathway, regulonand increase in freeze tolerance are conserved in Populus spp.ABR1, an APETALA2-Domain Transcription Factor That Functions as aRepressor of ABA Response in Arabidopsis.Organization and expression of two Arabidopsis DREB2 genesencoding DRE-binding proteins involved in dehydration- andhigh-salinity-responsive gene expressionHeterology expression of the Arabidopsis C-repeat/dehydrationresponse element binding factor 1 gene confers elevated toleranceto chilling and oxidative stresses in transgenic tomato�Nat Biotechnol 17: 287-291 (1999)Plant Physiol.139: 437-447 (2005)Plant J. 34: 137-148 (2003)Plant, Cell and Environment 29:1259-1272 (2006)Plant Physiol. 139: 1185-1193 (2005)Plant Mol Biol 42: 657-665 (2000)Plant Physiol. 129: 1086-1094 (2002)dPubMed: 10096298;PubMed: 16113229PubMed: 12694590;PubMed: 16227468PubMed: 10809011;PubMed: 12114563; in silico TACCGACAT
E2F1OSPCNAS000396 21-May-2002 (last modified) uchi�"re2f-1" found in the promoter of rice PCNA gene; Located between-142 and -135; "te2f-1" found in the promote of Tobacco PCBAgene; Located between -122 and -115; Binding site of OsE2F1 andOsE2F2; Involved in transcriptional activation in activelydividing cells and tissue;E2FPCNAmeristematic tissue
cell cycle0rice (Oryza sativa); tobacco (Nicotiana tabacum)Kosugi S, Ohashi Y�E2F sites that can interact with E2F proteins cloned from riceare required for meristematic tissue-specific expression of riceand tobacco proliferating cell nuclear antigen promotersPlant J 29: 45-59 (2002)PubMed: 12060226; GCGGGAAA E2FANTRNRS000366!23-June-2006 (last modified) kehi�"E2Fa element" found in the tobacco (N.t.) RNR (Ribonucleotidereductase) gene promoter and in the Arabidopsis thaliana (A.t.)CDC6 gene promoter; Binding site of tobacco and Arabidopsis E2F;Involved in upregulation of the promoter at G1/S transition; SeeS000367;E2FaRNRG1/S transitionCDC6
Cell-division
Cell cycleS-phasecell suspension culture2tobacco (Nicotiana tabacum); Arabidopsis thaliana;�Chaboute ME, Clement B, Sekine M, Philipps G, Chaubet-Gigot Nde Jager SM, Menges M, Bauer UM, Murra JASozzani R, Maggio C, Varotto S, Canova S, Bergounioux C, AlbaniD, Cella R�sCell cycle regulation of the tobacco ribonucleotide reductasesmall subunit gene is mediated by E2F-like elementsArabidopsis E2F1 binds a sequence present in the promoter ofS-phase-regulated gene AtCDC6 and is a member of a multigenefamily with differential activitiesInterplay between Arabidopsis Activating Factors E2Fb and E2Fa inCell Cycle Progression and Development.ePlant Cell 12: 1987-2000 (2000)Plant Mol Biol 47: 555-568 (2001)Plant Physiol. 140: 1355-1366 (2006)"PubMed: 11041892;PubMed: 11669580; TTTCCCGCE2FATS000417 03-Jun-2003 (last modified) kehi�"E2F-binding site" found in many potential E2F target genes; mostpotential E2F targets identified in silico show a cellcycle-regulated expression; Y=T/C; see S000366;E2F
cell cycleArabidopsis thaliana'Ramirez-Parra E, Frundt C, Gutierrez C.BA genome-wide identification of E2F-regulated genes inArabidopsis.Plant J. 33: 801-811 (2003)PubMed: 12609051; TYTCCCGCC E2FBNTRNRS000367%29-November-2004 (last modified) kehi�="E2Fb" found in the tobacco (N.t.) RNR (Ribonucleotide reductase)gene promoter; Binding site of tobacco E2F; Involved inupregulation of the promoter at G1/S transition; See S000366;"dE2F (distal reverse E2F element)" important for regulatingspecific RNR1a gene expression in respsonse to UV-C irradiation;See S000455;E2FbRNRG1/S transitiondE2FUV-C
ceel cycletobacco (Nicotiana tabacum)`Chaboute ME, Clement B, Sekine M, Philipps G, Chaubet-Gigot NLincker F, Philipps G, Chaboute ME.� Cell cycle regulation of the tobacco ribonucleotide reductasesmall subunit gene is mediated by E2F-like elementsUV-C response of the ribonucleotide reductase large subunitinvolves both E2F-mediated gene transcriptional regulation andprotein subcellular relocalization in tobacco cells.HPlant Cell 12: 1987-2000 (2000)Nucleic Acids Res. 32: 1430-1438. (2004).!PubMed: 11041892;PubMed: 14990748 GCGGCAAA E2FCONSENSUSS000476%05-November-2005 (last modified) kehi�"E2F consensus sequence" of all different E2F-DP-binding motifsthat were experimentally verified in plants (Vandepoele et al.,2005); See also S000417, S000397, S000396, S000367, S000366;W=A/T; S=C/G;E2F]Arabidopsis thaliana; Nicotiana tabacum (tobacco); Oryza sativa(rice); Nicotiana benthamiana;kVandepoele K, Vlieghe K, Florquin K, Hennig L, Beemster GT,Gruissem W, Van de Peer Y, Inze D, De Veylder L.?Genome-wide identification of potential plant E2F target genes."Plant Physiol.139: 316-328. (2005)PubMed: 16126853 WTTSSCSS
EBOXBNNAPAS000144#02-August-2006 (last modified) kehi�E-box of napA storage-protein gene of Brassica napus (B.n.); SeeS000042 (CACGTGMOTIF); see S000407 (Myc consensus: CANNTG); Thissequence is also known as RRE (R response element)(Hartmann etal., 2005);napAstorage proteinABREE-boxseedBrassica napus;nStalberg K, Ellerstom M, Ezcurra I, Ablov S, Rask LHartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B.�ZDisruption of an overlapping E-box/ABRE motif abolished hightranscription of the napA storage-protein promoter in transgenicBrassica napus seeds.Differential combinatorial interactions of cis-acting elementsrecognized by R2R3-MYB, BZIP, and BHLH factors controllight-responsive and tissue-specific activation ofphenylpropanoid biosynthesis genes.<Planta 199:515-519 (1996)Plant Mol Biol. 57: 155-171 (2005). PubMed: 8818291;PubMed: 15821875 CANNTG EECCRCAH1S000494"24-April-2006 (last modified) kehi�� "EEC"; Consensus motif of the two enhancer elements, EE-1 andEE-2, both found in the promoter region of the Chlamydomonas Cah1(encoding a periplasmic carbonic anhydrase); Binding site of Mybtranscription factor LCR1 (see Yoshioka et al, 2004); N=A/G/C/T;low-CO2Chlamydomonas reinhardtiiwKucho K, Yoshioka S, Taniguchi F, Ohyama K, Fukuzawa H.Yoshioka S, Taniguchi F, Miura K, Inoue T, Yamano T, Fukuzawa H.�ECis-acting elements and DNA-binding proteins involved inCO2-responsive transcriptional activation of Cah1 encoding aperiplasmic carbonic anhydrase in Chlamydomonas reinhardtii.The novel Myb transcription factor LCR1 regulates theCO2-responsive gene Cah1, encoding a periplasmic carbonicanhydrase in Chlamydomonas reinhardtii.CPlant Physiol. 133: 783-793 (2003).Plant Cell. 16: 1466-1477.(2004) PubMed: 14555782PubMed: 15155888 GANTTNC
EIN3ATERF1S000332 7-Sep-2000 (last modified) seki��EIN3 (Ethylene-insensitive 3) binding site found in the promoterof the Arabidopsis (A.t.) ERF1 (Ethylene-Response-Factor 1); EIN3recognizes its target as a homodimer; EIN3 is necessary andsufficient for ERF1 expression; Consititutive expression of ERF1results in the activation of a variety of ethylene response genesand phenotype; ERF1 is a GCC-box binding site; ERF1 actsdownstream of EIN3;EIN3ERF1EthyleneArabidopsis thaliana'Solano R, Stepanova A, Chao Q, Ecker JR~Nuclear events in ethylene signaling: a transcriptional cascademediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1 Genes Dev. 12: 3703-3714 (1998)-PubMed: 9851977; GenBank: AF076277; AF076278; GGATTCAAGGGGCATGTATCTTGAATCCELEMENT1GMLBC3S000319 7-Sep-2000 (last modified) seki� "Element 1" found in the promoter of soybean (G.m.)leghaemoglobin lbc3 gene; Binding site of nuclear extract fromsoybean nodules; Located at -223 to -246; Element 1 and Element 2(S000320) bind to the same nodule specific factor; Element 1 andElement 2 share a common motif; See S000320;noduleleghaemoglobinlbc3rootSoybean (Glycine max),Jensen EO, Marcker KA, Schell J, de Bruijn J�Interaction of a nodule specific, trans-acting factor withdistinct DNA elements in the soybean leghaemoglobin lbc3 5'upstream regionEMBO J 7:1265-1271 (1988) GATATATTAATATTTTATTTTATAELEMENT2GMLBC3S000320 7-Sep-2000 (last modified) seki�B"Element 2" found in the promoter of soybean (G.m.)leghaemoglobin lbc3 gene; Binding site of nuclear extract fromsoybean nodules; Located at -161 to -176; Element 1(S000319) andElement 2 (S000320) bind to the same nodule specific factor;Element 2 is highly conserved in other soybean lb gene promoterregions; See S000319;noduleleghaemoglobinlbc3rootSoybean (Glycine max),Jensen EO, Marcker KA, Schell J, de Bruijn J�Interaction of a nodule specific, trans-acting factor withdistinct DNA elements in the soybean leghaemoglobin lbc3 5'upstream regionEMBO J 7:1265-1271 (1988) CTTAAATTATTTATTT ELRE1PCPAL1S000306 10-Feb-2000 (last modified) seki�� One of two elicitor (ELRE) and light response elements (LRE)found in the parsley (P.c.) phenylalanine ammonia-lyase (PAL-1)gene promoter; Involved in UV light and elicitor responsiveness;Conserved in several elicitor or light-responsive genes; SeeS000307;!phenylalanine ammonia-lyase (PAL)UVelicitorlightleafshoot parsley (Petroselinum crispum)(Lois R, Dietrich A, Hahlbrok K, Schulz W�A phenylalanine ammonia-lyase gene from parsley: structure,regulation and identification of elicitor and light responsivecis-acting elementsEMBO J 8: 1641-1648 (1989)(PubMed: 2767049; GenBank: X15473, X16772 CTCCAACAAACCCCTTC ELRE2PCPAL1S000307 10-Feb-2000 (last modified) seki�� One of two elicitor (ELRE) and light response elements (LRE)found in the parsley (P.c.) phenylalanine ammonia-lyase (PAL-1)gene promoter; Involved in UV light and elicitor responsiveness;Conserved in several elicitor or light-responsive genes; SeeS000306;!phenylalanine ammonia-lyase (PAL)UVelicitorlightleafshoot parsley (Petroselinum crispum)(Lois R, Dietrich A, Hahlbrok K, Schulz W�A phenylalanine ammonia-lyase gene from parsley: structure,regulation and identification of elicitor and light responsivecis-acting elementsEMBO J 8: 1641-1648 (1989)(PubMed: 2767049; GenBank: X15473, X16772 ATTCTCACCTACCA
ELRECOREPCRP1S000142!22-June-2006 (last modified) kehi��ElRE (Elicitor Responsive Element) core of parsley (P.c.) PR1genes; consensus sequence of elements W1 and W2 of parsley PR1-1and PR1-2 promoters; Box W1 and W2 are the binding site of WRKY1and WRKY2, respectively; ERE; "WA box"; One of the W boxes foundin the Parsley (P.c.) WRKY1 gene promoter; Required for elicitorresponsiveness; See S000310; "WC box" WB box (S000310) and WC boxconstitute a palindrome; WRKY1 protein binding site; W-box foundin thioredoxin h5 gene in Arabidopsis (Laloi et al.);
ElicitorPR1ElREELREEREW boxWRKY1
palindromesalicylic acidTMV<Petroselinum crispum (parsley); Nicotiana tabacum (tobacco);�.Rushton PJ, Torres JT, Parniske M, Wernert P, Hahlbrock K,Somssich IEEulgem T, Rushton PJ, Schmelzer E, Hahlbrock K, Somssich IEEulgem T, Rushton PJ, Robatzek S, Somssich IEChen C, Chen ZRushton PJ, Reinstadler A, Lipka V, Lippok B, Somssich IELaloi C, Mestres-Ortega D, Marco Y, Meyer Y, Reichheld JP.��Interaction of elicitor-induced DNA-binding proteins withelicitor response elements in the promoters of parsley PR1genes.Early nuclear events in plant defence signalling: rapid geneactivation by WRKY transcription factorsThe WRKY superfamily of plant transcription factorsIsolation and characterization of two pathogen- and salicylicacid-induced genes encoding WRKY DNA-binding proteins fromtobaccoSynthetic plant promoters containing defined regulatory elementsprovide novel insights into pathogen- and wound-inducedsignalingThe Arabidopsis cytosolic thioredoxin h5 gene induction byoxidative stress and its W-box-mediated response to pathogenelicitor.�EMBO J 15:5690-5700 (1996)EMBO J 18: 4689-4699 (1999)Trends Plant Sci 5: 199-206 (2000)Plant Mol Biol 42: 387-396 (2000)Plant Cell. 14: 749-762 (2002)Plant Physiol. 134:1006-1016 (2004).}PubMed: 8896462; GenBank: U48862, U48863;PubMed: 10469648;PubMed: 10785665;PubMed: 10794538;PubMed: 11971132;PubMed: 14976236ReviewTTGACC ELRENTCHN50S000155 17-May-1998 (last modified) kehiaElicitor-responsive element (ElRE); Found in tobacco (N. t.)basic class I chitinase gene (CHN50);ELREelicitor chitinase tobacco (Nicotiana tabacum);Fukuda Y{Interaction of tobacco nuclear protein with anelicitor-responsive element in the promoter of a basic class Ichitinase gene. Plant Mol Biol 34:81-87 (1997)PubMed: 9177314; GGTCANNNAGTC EMBP1TAEMS000119 16-Feb-2001 (last modified) seki�lBinding site of trans-acting factor EMBP-1; wheat (T.a.) Em gene;See S000015; Binding site of ABFs; ABFs (ABRE binding factors)were isolated from Arabidopsis by a yeast one-hybrid screeningsystem; Expression ABFs is induced by ABA and various stresstreatment; ABFs belongs to a distinct subfamily of bZIP proteins;Involved in ABA-mediated stress-signaling pathway;EMBP-1EmABAABFABREbZIPseed0wheat (Triticum aestivum); Arabidopsis thaliana;�Guiltinan MJ, Marcotte WR Jr, Quatrano RSVasil V, Marcotte Jr. WR, Rosenkrans L, Cocciolone SM, Vasil IK,Quatrano RS, McCarty DRChoi H, Hong J, Ha J, Kang J, Kim SY�"A plant leucine zipper protein that recognizes an abscisic acidresponse element.Overlap of viviparous1 (VP1) and abscisic acid response elementsin the EM promoter: G-Box elements are sufficient but notnecessary for VP1 transactivationABFs, a family of ABA-responsive element binding factorsYScience 250:267-270 (1990)Plant Cell 7: 1511-1518 (1995)J Biol Chem 275: 1723-1730 (2000)IPubMed: 2145628; GenBank: M62893, M63999;PubMed: 8589631PubMed: 10636868; CACGTGGC EMHVCHORDS000452%29-November-2004 (last modified) kehi�"Endosperm motif (EM)" found in the promoter of barley (H.v.)c-hordein gene; Involved in the nitrogen response of c-hordeinpromoter;EM endospermhordeinnitrogenHordeum vulgare (barley)Muller M, Knudsen S.�The nitrogen response of a barley C-hordein promoter iscontrolled by positive and negative regulation of the GCN4 andendosperm box.Plant J. 4: 343-355 (1993).PubMed: 8220485 TGTAAAGTEREGCCS000036 03-Jun-2003 (last modified) kehi��"GCC box" in "ERE (ethylene responsive element)";Ethylene-responsive region of tobacco (N.t.) chitinase genecontains two copies of the GCC-box; ERF2 and ERF4 enhanced theGCC box-mediated transcription; ERF3 reduced the transcription ofthe reporter gene in tobacco protoplasts; Binding site of AtEBP;Pti4/5/6 proteins from tomato which belong to the ERF familyactivate the expression of "GCC box"-containing PR genes; ERF3was found to interact with NtUBC2, a ubiquitin-conjugatingenzyme;EthyleneEREBPGCC boxG-boxCHNEREERFxylanaseTvXOBFbZIPEBPpathogenocsleafshootPti4/5/6 ubiquitinUBC22tobacco (Nicotiana tabacum); Arabidopsis thaliana;�Koyama T, Okada T, Kitajima S, Ohme-Takagi M, Shinshi H, Sato F.Gu YQ, Wildermuth MC, Chakravarthy S, Loh YT, Yang C, He X, HanY, Martin GBYamamoto S, Suzuki K, Shinshi HOhta M, Ohme-Takagi M, Shinshi HOhme-Takagi M, Shinshi HButtner M, Singh KBOhme-Takagi M, Suzuki K, Shinshi H�YIsolation of tobacco ubiquitin-conjugating enzyme cDNA in a yeasttwo-hybrid system with tobacco ERF3 as bait and itscharacterization of specific interaction.Tomato transcription factors pti4, pti5, and pti6 activatedefense responses when expressed in ArabidopsisElicitor-responsive, ethylene-independent activation of GCCbox-mediated transcription that is regulated by both proteinphosphorylation and dephosphorylaton in cultured tobacco cellsThree ethylene-responsive transcription factors in tobacco withdistinct transactivation functionsEthylene-inducible DNA binding proteins that interact with anethylene-responsive elementArabidopsis thaliana ethylene-responsive element binding protein(AtEBP), an ethylene-inducible, GCC box DNA-binding proteininteracts with an ocs element binding proteinRegulation of Ethylene-Induced Transcription of Defense Genes�J Exp Bot. 54: 1175-1181 (2003)Plant Cell 14: 817-831 (2002)Plant J 20: 571-579 (1999)Plant J 22:29-38 (2000)Plant Cell 7: 173-182 (1995)Proc Natl Acad Sci USA 94: 5961-5966 (1997)Plant Cell Physiol 41: 1187-1192 (2000)�PubMed: 12654868;PubMed: 11971137;PubMed: 10652129;PubMed: 10792818;PubMed: 7756828;PubMed: 9159183; GenBank: Y09942;PubMed: 11092902; TAAGAGCCGCCERELEE4S000037#02-August-2006 (last modified) kehi�"ERE (ethylene responsive element)" of tomato (L.e.) E4 andcarnation GST1 genes; GST1 is related to senescence; Found in the5'-LTR region of TLC1.1 retrotransposon family in Lycopersiconchilense (Tapia et al.); ERE motifs mediate ethylene-inducedactivation of the U3 promoter region;EthyleneE4GST1
senescenceEREfruitZtomato (Lycopersicon esculentum); carnation (Dianthuscaryophyllus); Lycopersicon chilense;�Itzhaki H, Maxson JM, Woodson WRMontgomery J, Goldman S, Deikman J, Margossian L, Fischer RLTapia G, Verdugo I, Yanez M, Ahumada I, Theoduloz C, Cordero C,Poblete F, Gonzalez E, Ruiz-Lara S.Rawat R, Xu ZF, Yao KM, Chye ML.��An ethylene-responsive enhancer element is involved in thesenescence-related expression of the carnationglutathione-S-transferase (GSTI) gene.Identification of an ethylene-responsive region in the promoterof a fruit ripening gene.Involvement of Ethylene in Stress-Induced Expression of theTLC1.1 Retrotransposon from Lycopersicon chilense Dun.Identification of cis-elements for ethylene and circadianregulation of the Solanum melongena gene encoding cysteineproteinase.�Proc Natl Acad Sci USA 91:8925-8929 (1994)Proc Natl Acad Sci USA 90:5939-5943 (1993)Plant Physiol. 138:2075-2086 (2005)Plant Mol Biol. 57: 629-643 (2005).@PubMed: 8090746;PubMed: 8327464;PubMed: 16040666PubMed: 15988560 AWTTCAAA ESPASGL01S000509$04-January-2007 (last modified) kehik"ESP (endosperm specificity palindrome)" element found in thepromoter of oat (A.s.) globulin gene (AsGlo1); endospermglobulinAvena sativa (oat) Vickers CE, Xue G, Gresshoff PM.tA novel cis-acting element, ESP, contributes to high-levelendosperm-specific expression in an oat globulin promoter.!Plant Mol Biol. 62:195-214 (2006)PubMed: 16915522 ACATGTCATCATGT EVENINGATS000385$26-October-2005 (last modified) kehi�d"Evening element" found 46 times in the promoters of 31 cyclinggenes in Arabidopsis thaliana (Harmer et al. 2000); Required forcircadian control of gene expression; "EE (evening element)motif"; Also found in the promoter of the Solanum melongena geneencoding cysteine protease, and identified as cis-element for itscircadian regulation (Rawat et al. 2005);evening circadianclockEE(Arabidopsis thaliana; Solanum melongena;sHarmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, WangX, Kreps JA, Kay SARawat R, Xu ZF, Yao KM, Chye ML.�Orchestrated transcription of key pathways in Arabidopsis by thecircadian clockIdentification of cis-elements for ethylene and circadianregulation of the Solanum melongena gene encoding cysteineproteinase.AScience 290: 2110-2113 (2000)Plant Mol Biol. 57: 629-643 (2005).!PubMed: 11118138;PubMed: 15988560 AAAATATCTGADOWNATS000438#01-August-2006 (last modified) kehi�Sequence present in 24 genes in the GA-down regulated d1 cluster(106 genes) found in Arabidopsis seed germination; This motif issimilar to ABRE (Busk and Pages 1998);Gaseed germainationArabidopsis thaliana;�Ogawa M, Hanada A, Yamauchi Y, Kuwahara A, Kamiya Y, YamaguchiS.Nakashima K, Fujita Y, Katsura K, Maruyama K, Narusaka Y, Seki M,Shinozaki K, Yamaguchi-Shinozaki K.�Gibberellin biosynthesis and response during Arabidopsis seedgermination.Transcriptional regulation of ABI3- and ABA-responsive genesincluding RD29B and RD29A in seeds, germinating embryos, andseedlings of Arabidopsis.@Plant Cell 15: 1591-1604 (2003)Plant Mol Biol. 60: 51-68 (2006).!PubMed: 12837949;PubMed: 16463099 ACGTGTC GAGA8HVBKN3S000427 29-Sep-2003 (last modified) kehi�"GA octodinucleotide repeat" found in intron IV of the barley(H.v.) gene Bkn3; Binding site for GAGA-binding factor BBR; SeeS000405 (GAGA element in the soy bean Gsa1 gene);GAGAGBPBBRHordeum vulgare (barley)iSanti L, Wang Y, Stile MR, Berendzen K, Wanke D, Roig C, Pozzi C,Muller K, Muller J, Rohde W, Salamini F.zThe GA octodinucleotide repeat binding factor BBR participates inthe transcriptional regulation of the homeobox gene Bkn3.Plant J. 34:813-826 (2003)PubMed: 12795701; GAGAGAGAGAGAGAGA
GAGAGMGSA1S000405 21-Nov-2002 (last modified) uchi�"GAGA element" found in the promoter of the heme and chlorophyllsynthesis gene Gsa1 in soybean (G.m.); GAGA binding protein (GBP)binds to (GA)n/(CT)n DNA;Dinucleotide repeat GAGA elementGBPGsa1Glycine max (soybean)Sangwan I, O'Brian MR[Identification of a Soybean Protein That Interacts with GAGAElement Dinucleotide Repeat DNA$Plant Physiol. 129: 1788-1794 (2002)PubMed: 12177492; GAGAGAGAGAGAGAGAGA GARE1OSREP1S000419%28-November-2004 (last modified) kehi}"Gibberellin-responsive element (GARE)" found in the promoterregion of a cystein proteinase (REP-1) gene in rice; SeeS000020;aleuroneGARE gibberellinseedOryza sativa (rice)Sutoh K, Yamauchi D.oTwo cis-acting elements necessary and sufficient forgibberellin-upregulated proteinase expression in rice seedsPlant J. 34: 636-645 (2003)PubMed: 12787245; TAACAGAGARE2S000165 17-May-1998 (last modified) kehi{Putative gibberellin responsive element; Consensus sequence of GAinducible alpha-amylase genes from rice, barley and wheat; gibberellinGAREseedHrice (Oryza sativa); barley (Hordeum vulgare); wheat (Triticumaestivum);?Huang N, Sutliff TD, Litts JC, Rodriguez RLRogers JC, Rogers SW�Classification and characterization of the rice alpha-amylasemultigene family.Definition and functional implications of gibberellin andabscisic acid cis-acting hormone response complexes=Plant Mol Biol 14:655-668 (1990)Plant Cell 4:1443-1451 (1992)1PubMed: 2102847; GenBank: X16509;PubMed: 1477557;&Consensus sequence of GA-induced genesRTAACARANTCYGG GARE2OSREP1S000420%28-November-2004 (last modified) kehi}"Gibberellin-responsive element (GARE)" found in the promoterregion of a cystein proteinase (REP-1) gene in rice; SeeS000020;aleuroneGARE gibberellinseedOryza sativa (rice)Sutoh K, Yamauchi D.oTwo cis-acting elements necessary and sufficient forgibberellin-upregulated proteinase expression in rice seedsPlant J. 34: 636-645 (2003)PubMed: 12787245; TAACGTA GARE4HVEPB1S000297 10-Feb-2000 (last modified) seki�"GARE-4" found in the barley (H.v.) EPB-1 (cysteine proteinase)gene promoter; Located between -142 to -156; Required for GAinduction; Putative binding site of transcription factor, GAMyB;See S000298;EPBcysteine proteinaseGAABAGAREpyrimidine boxseedaleuronebarley (Hordeum vulgare)!Cercos M, Gomez-Cadenas A, Ho THD�Hormonal regulation of a cysteine proteinase gene, EPB-1, inbarley aleurone layers: cis- and trans-acting elements involvedin the co-ordinated gene expression regulated by gibberellins andabscisic acidPlant J 19: 107-118 (1999)PubMed: 10476058 GTAACAGAATGCTGGGAREATS000439 27-Jan-2004 (last modified) kehi�GARE (GA-responsive element); Occurrence of GARE in GA-inducible,GA-responsible, and GA-nonresponsive genes found in Arabidopsisseed germination was 20, 18, and 12%, respectively; see S000181;GAREGAArabidopsis thaliana;@Ogawa M, Hanada A, Yamauchi Y, Kuwahara A, Kamiya Y, YamaguchiS.IGibberellin biosynthesis and response during Arabidopsis seedgermination. Plant Cell 15: 1591-1604 (2003)PubMed: 12837949; TAACAAR
GAREHVAMY1S000038 17-May-1998 (last modified) kehia"GARE (gibberellic acid responsive element)" of barley (H.v.)alpha-amylase gene (Amy 1/6-4); GA3;gibberellic acidGAGA3amylaseAmy1/6-4GAREbarley (Hordeum vulgare)TSkriver K, Olsen FL, Rogers JC, Mundy JGilmartin PM, Sarokin L, Memelink J, Chua N-H{Cis-acting DNA elements responsive to gibberellin and itsantagonist abscisic acid.Molecular light switches for plant genes.EProc Natl Acad Sci USA 88:7266-7270 (1991)Plant Cell 2:369-378 (1990) PubMed: 1831269;PubMed: 2152164; GGCCGATAACAAACTCCGGCCGATABOXS000039#01-August-2006 (last modified) kehi�0"GATA box"; GATA motif in CaMV 35S promoter; Binding with ASF-2;Three GATA box repeats were found in the promoter of Petunia(P.h.) chlorophyll a/b binding protein, Cab22 gene; Required forhigh level, light regulated, and tissue specific expression;Conserved in the promoter of all LHCII type I Cab genes;ASF-2GATA boxCab chlorophyll a/b binding proteinleafshootdCaMV; Cauliflower mosaic virus; Petunia hybrida (petunia);Arabidopsis thaliana; Oryza sativa (rice);�Lam E, Chua NHGilmartin PM, Sarokin L, Memelink J, Chua N-HBenfey PN, Chua NHGidoni D, Brosio P, Bond-Nutter D, Bedbrook J, Dunsmuir PTeakle GR, Manfield IW, Graham JF, Gilmartin PMReyes JC, Muro-Pastor MI, Florencio FJ.Rubio-Somoza I, Martinez M, Abraham Z, Diaz I, Carbonero P.�9ASF-2: A factor that binds to the cauliflower mosaic virus 35Spromoter and a conserved GATA motif in cab promoters.Molecular light switches for plant genes.The cauliflower mosaic virus 35S promoter: combinatorialregulation of transcription in plantsNovel cis-acting elements in Petunia Cab gene promotersArabidopsis thaliana GATA factors: organisation, expression andDNA-binding characteristicsThe GATA family of transcription factors in Arabidopsis andrice.Ternary complex formation between HvMYBS3 and other factorsinvolved in transcriptional control in barley seeds.�Plant Cell 1:1147-1156 (1989)Plant Cell 2:369-378 (1990)Science 250:959-966 (1990)Mol Gen Genet 215: 337-344 (1989)Plant Mol Biol. 50 :43-57 (2002)Plant Physiol. 134: 1718-1732 (2004).Plant J. 47: 269-281 (2006)aPubMed: 2535536;PubMed: 2152164;PubMed: 2651885;PubMed: 12139008;PubMed: 15084732PubMed: 16762033 GATAGBOX10NTS000272 15-Oct-1999 (last modified) kehi�One of 11 G-box sequences in tobacco (N.t.); Required forhigh-level constitutive expression in seed, leaf, root, axillarybud, almost all parts of flower buds and pollen;G-boxG-box 10tetramerseedrootleaf axillary budpollentobacco (Nicotiana tabacum)/Ishige F, Takaichi M, Foster R, Chua NH, Oeda KiA G-box motif (GCCACGTGCC) tetramer confers high-levelconstitutive expression in dicot and monocot plantsPlant J 18:443-448 (1999)
GCCACGTGCC
GBOXLERBCSS000041 7-Sep-2000 (last modified) seki�"G box"; Conserved sequence upstream of light-regulated genes;Sequence found in the promoter region of rbcS of tomato (L.e.)and Arabidopsis; Binding with GBF; M=A/C; See S000345;G boxrbcStomatoG-boxleafshoot7tomato (Lycopersicon esculentum); Arabidopsis thaliana;�Giuliano G, Pichersky E, Malik VS, Timko MP, Scolnik PA, CashmoreARDonald RGK, Cashmore ARVasil V, Marcotte Jr. WR, Rosenkrans L, Cocciolone SM, Vasil IK,Quatrano RS, McCarty DR�fAn evolutionarily conserved protein binding sequence upstream ofa plant light-regulated gene.Mutation of either G box or I box sequences profoundly affectsexpression from the Arabidopsis rbcS-1A promoter.Overlap of viviparous1 (VP1) and abscisic acid response elementsin the EM promoter: G-Box elements are sufficient but notnecessary for VP1 transactivationaProc Natl Acad Sci USA 85:7089-7093 (1988)EMBO J 9:1717-1726 (1990)Plant Cell 7: 1511-1518 (1995)/PubMed: 2902624;PubMed: 2347304;PubMed: 8589631 MCACGTGGCGBOXPCS000324 7-Sep-2000 (last modified) seki�G"G box"; Binding site of parsley (P.c.) cytosolic G-box bindingfactors (cytosolic GBFs); Cytosolic G-Box binding activity ismodulated by light; DNA binding activity of cytosolic GBFs isregulated by cytosolic phosphorylation/dephospholylationactivities; Cytosolic GBFs are translocated to the nucleus in alight-regulated manner;G-boxlightcytosolic GBFsbZIPleafshoot parsley (Petroselinum crispum)=Harter K, Kircher S, Frohnmeyer H, Krenz M, Nagy F, Schafer EcLight-regulated modification and nuclear translocation ofcytosolic G-box binding factors in parsley Plant Cell 6: 545-559 (1994)PubMed: 8205004;
ACCACGTGGC
GBOXRELOSAMY3S000206 29-Sep-1999 (last modified) kehiWG box-related element found in Amy3D (amylase) promoter of rice(O.s.); Similar to ABRE;amylaseG boxG box-like elementrice (Oryza sativa);DHwang YS, Karrer EE, Thomas BR, Chen L, Rodriguez RLBusk PK, Pages M�Three cis-elements required for rice alpha-amylase Amy3Dexpression during sugar starvationRegulation of abscisic acid-induced transcription@Plant Mol Biol 36:331-341 (1998)Plant Mol Biol 37:425-435 (1998) PubMed: 9484474;PubMed: 9617810;Review CTACGTGGCCA GBOXSORBCS1S000380 23-Aug-2001 (last modified) uchi�"G-box" found in the spinach(S.O.) RBCS-1 gene promoter; Locatedbetween -219 and -212; G-box trimer confers relatively high levelexpression in roots;RBCS-1G-boxrootspinach (Spinacia oleracea)ELubberstedt T, Bolle CE, Sopory S, Flieger K, Herrmann RG,Oelmuller RoPromoters from genes for plastid proteins possess regions withdifferent sensitivities toward red and blue light"Plant Physiol 104: 997-1006 (1994)PubMed: 8165263;
TCCACGTGGTGCAACREPEATZMZEINS000027 17-May-1998 (last modified) kehi�"GCAAC repeat" found in the 22bp recognition site for beta-1factor in the promoter of beta-zein (prolamin type) gene of maize(Z.m.); GCAAC is the core recognition sequence of the proteinencoded by the retroviral oncogene myb (Biedenkapp et al. Nature335:835-837 (1988)); beta-zeinGCAACrepeatmybseed endospermmaize (Zea mays)So J-S, Larkins BAwBinding of an endosperm-specific nuclear protein to a maizebeta-zein gene correlates with zein transcriptional activity Plant Mol Biol 17:309-319 (1991)PubMed: 1883992;
GCAACGCAAC GCBP2ZMGAPC4S000351 16-Feb-2001 (last modified) seki�Binding site of tobacco nuclear factor (GCBP-2) found in themaize (Z.m.) GapC4 (Glyceraldehyde-3-phosphate dehydrogenase 4)gene promoter; Located between -293 and -285; See S000350; anaerobicGapC4GCBP-2maize (Zea mays)Geffers R, Cerff R, Hehl RuAnaerobiosis-specific interaction of tobacco nuclear factors withcis-regulatory sequences in the maize GapC4 promoter Plant Mol Biol 43: 11-21 (2000)PubMed: 10949370; GTGGGCCCGGCCCORES000430 28-Jan-2004 (last modified) kehi��Core of GCC-box found in many pathogen-responsive genes such asPDF1.2, Thi2.1, and PR4; Has been shown to function asethylene-responsive element; See S000036, S000232, S000332;Appears to play important roles in regulatingjasmonate-responsive gene expression; Tomato Pti4 (ERF) regulatesdefence-related gene expression via GCC box and non-GCC box ciselements (Myb1 (GTTAGTT) and G-box(CACGTG));GCCGCC-boxEREJAPti4ERFPR7Arabidopsis thaliana; Lycopersicon esculentum (tomato);{Brown RL, Kazan K, McGrath KC, Maclean DJ, Manners JM.Chakravarthy S, Tuori RP, DAscenzo MD, Fobert PR, Despres C,Martin GB�A role for the GCC-box in jasmonate-mediated activation of thePDF1.2 gene of Arabidopsis.The tomato transcription factor Pti4 regulates defence-relatedgene expression via GCC box and non-GCC box cis elementsBPlant Physiol. 132:1020-1032 (2003)Plant Cell 15: 3033-3050 (2003)"PubMed: 12805630;PubMed: 14630974; GCCGCC GCN4OSGLUB1S000277 21-May-2002 (last modified) uchi��"GCN4 motif" found in GluB-1 gene in rice (O.s.); Required forendosperm-specific expression; See S000276; AACA and ACGT motifswas found sufficient to confer a detectable level of endospermexpression; See S000353, S000354; This motif is the recognitionsite for a basic leucine zipper transcription factor that belongsto the group of maize Opaque-2 (O2)-like proteins; Although allthe RISBZ proteins are able to interact with the GCN4 motif, onlyRISBZ1 is capable of activating the gene expression;GluB-1glutelin endospermseedstorage protein
GCN4 motifRISBZ proteinsO2rice (Oryza sativa)�Washida H, Wu CY, Suzuki A, Yamanouchi U, Akihama T, Harada K,Takaiwa FWu C, Washida H, Onodera Y, Harada K, Takaiwa FOnodera Y, Suzuki A, Wu CY, Washida H, Takaiwa F��Identification of cis-regulatory elements required for endospermexpression of the rice storage protein glutelin gene GluB-1Quantitative nature of the Prolamin-box, ACGT and AACA motifs ina rice glutelin gene promoter: minimal cis-element requirementsfor endosperm-specific gene expressionA rice functional transcriptional activator, RISBZ1, responsiblefor endosperm-specific expression of storage protein genesthrough GCN4 motifYPlant Mol Biol 40:1-12 (1999)Plant J 23: 415-421 (2000)J Biol Chem 27: 14139-14152 (2001)3PubMed: 10394940;PubMed: 10929134;PubMed: 11133985; TGAGTCAGGTCCCATGMSAURS000360 16-Feb-2001 (last modified) seki�Sequence found in NDE element in Soybean (G.m.) SAUR (SmallAuxin-Up RNA) 15A gene promoter; Involved in auxinresponsiveness; See S000270, S000359;SAURNDEAuxinSoybean (Glycine max)Xu N, Hagen G, Guilfoyle T@Multiple auxin response modules in the soybean SAUR 15A promoter Plant Sci 126: 193-201 (1997) GGTCCCAT
GLMHVCHORDS000451%29-November-2004 (last modified) kehi�a"GLM (GCN4-like motif)" found in the promoter of barley (H.v.)B1- and c-hordein gene; Involved in the nitrogen response ofc-hordein promoter; R=A/G; S=C/G; See also S000277 (GCN4OSGLUB1);SPA, a seed-specific basic leucine zipper protein from wheat, canactivate transcription from the GCN4-like motif (GLM) of -326LMWG-1D1 promoter (Albani et al., 1997);GLMGCN4hordeinGLM4Hordeum vulgare (barley); Triticum aestivum (wheat);�Muller M, Knudsen S.Albani D, Hammond-Kosack MC, Smith C, Conlan S, Colot V,Holdsworth M, Bevan MW.Onate L, Vicente-Carbajosa J, Lara P, Diaz I, Carbonero P.��The nitrogen response of a barley C-hordein promoter iscontrolled by positive and negative regulation of the GCN4 andendosperm box.The wheat transcriptional activator SPA: a seed-specific bZIPprotein that recognizes the GCN4-like motif in the bifactorialendosperm box of prolamin genes.Barley BLZ2, a seed-specific bZIP protein that interacts withBLZ1 in vivo and activates transcription from the GCN4-like motifof B-hordein promoters in barley endosperm.\Plant J. 4: 343-355 (1993).Plant Cell. 9: 171-184 (1997).J Biol Chem. 274: 9175-9182 (1999)..PubMed: 8220485PubMed: 9061949PubMed: 10092589 RTGASTCAT
GLUTAACAOSS000045 17-May-1998 (last modified) kehib"glutelin common motif"; "AACA motif"; Conserved in all member ofrice (0.s.) glutelin; -74 to -64;AACAglutelinseed endospermrice (Oryza sativa)Takaiwa F, Oono KpInteraction of an immature seed-specific trans-acting factor withthe 5' upstream region of a rice glutelin gene. Mol Gen Genet 224:289-293 (1990)PubMed: 2277646; AACAAACTCTATGLUTEBOX1OSGT2S000046 17-May-1998 (last modified) kehi]"Box 1" of rice (O.s.) glutelin Gt2 gene family promoter regions;nuclear factor binding site;glutelinBox 1Gt2seed endospermrice (Oryza sativa) Kim SY, Wu R@Multiple protein factors bind to a rice glutelin promoterregion.%Nucleic Acids Res 18:6845-6852 (1990)!PubMed: 2263449; GenBank: X52153; ATATCATGAGTCACTTCAGLUTEBOX1OSGT3S000128 17-May-1998 (last modified) kehiW"Box 1" of rice (O.s.) glutelin Gt3 gene family promoter region;See S000128 GLUTEBOX2A;Box 1glutelinGt3seed endospermrice (Oryza sativa);Croissant-Sych Y, Okita TWaIdentification of positive and negative regulatory cis-elementsof the rice glutelin Gt3 promoter. Plant Science 116:27-35 (1996) TATCTAGTGAGTCACTTCAGLUTEBOX2OSGT2S000047 17-May-1998 (last modified) kehiM"Box II" of rice (O.s.) glutelin Gt2 gene family; nuclear factorbinding site;glutelinBox IIGt2seed endospermrice (Oryza sativa) Kim SY, Wu R@Multiple protein factors bind to a rice glutelin promoterregion.%Nucleic Acids Res 18:6845-6852 (1990)!PubMed: 2263449; GenBank: X52153; TCCGTGTACCAGLUTEBOX2OSGT3S000129 17-May-1998 (last modified) kehiW"Box 2" of rice (O.s.) glutelin Gt3 gene family promoter region;See S000128 GLUTEBOX1A;Box 2glutelinGt3seed endospermrice (Oryza sativa);Croissant-Sych Y, Okita TW.aIdentification of positive and negative regulatory cis-elementsof the rice glutelin Gt3 promoter. Plant Science 116:27-35 (1996) CTTTTGTGTACCTTA
GLUTEBP1OSS000048 17-May-1998 (last modified) kehi�"Glutelin BP-1"; Binding site in the promoter region of glutelinGt3 gene family of nuclear factor (PB-1); PB-1 is observed onlyin nuclear extract of developing seeds;glutelinnuclear factorseed endospermBP-1PB-1rice (Oryza sativa)&Zhao, OkitaCroissant-Sych Y, Okita TW.aIdentification of positive and negative regulatory cis-elementsof the rice glutelin Gt3 promoter.S(in press; cited by Croissant-Sych Y, Okita TW, 1996)Plant Science 116:27-35 (1996) AAGCAACACACAAC
GLUTEBP2OSS000049 17-May-1998 (last modified) kehiC"Glutelin BP-2"; Binding with nuclear factors from developingseeds;glutelinnuclear factorseed endospermGt3 gene familyrice (Oryza sativa)&Zhao, OkitaCroissant-Sych Y, Okita TW.aIdentification of positive and negative regulatory cis-elementsof the rice glutelin Gt3 promoter.S(in press; cited by Croissant-Sych Y, Okita TW, 1996)Plant Science 116:27-35 (1996) ATGCTCAATAGATATAAGT GLUTECOREOSS000050 17-May-1998 (last modified) kehi�Core site required for binding of the trans-acting factor in thepromoter region of rice (O.s.) glutelin (type 2 glutelin genefamily);riceglutelintype 2 glutelinseed endospermrice (Oryza sativa)Takaiwa F, Oono KpInteraction of an immature seed-specific trans-acting factor withthe 5' upstream region of a rice glutelin gene. Mol Gen Genet 224:289-293 (1990)PubMed: 2277646; CTTTCGTGTAC GMHDLGMVSPBS000372 31-Jul-2001 (last modified) uchi�Binding site of the soybean homeodomein leucine zipper proteins(GmHdl56, GmHdl57); Found in the phosphate response domain of thesoybean VspB promoter; Located between -536 and -527; VspBencodes vacuolar glycoprotein acid phosphatase that serve asvegetative storage protein;VspBHD-ZIPSphosphate responsehomeotic domainsoybean (Glycine max)(Tang Z, Sadka A, Morishige DT, Mullet JEpHomeodomain leucine zipper proteins bind to the phosphateresponse domain of the soybean VspB tripartite promoter!Plant Physiol 125: 797-809 (2001)PubMed: 11161037;
CATTAATTAG
GRAZMRAB17S000150 29-Sep-1999 (last modified) kehi�"GRA"; GC-rich rab activator; Found in the promoter of ABAresponsive rab17 gene from maize (Z.m.); Important fortranscription in leaves but not in embryos; See S000200, S000401and S000402;GRAABArab17rableafembryoseedmaize (Zea mays)+Busk PK, Jensen AB, Pages MBusk PK, Pages M�Regulatory elements in vivo in the promoter of the abscisic acidresponsive gene rab17 from maize.Regulation of abscisic acid-induced transcription;Plant J 11:1258-1295 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 9225468;PubMed: 9617810;Review CACTGGCCGCCC
GRAZMRAB28S000220 11-May-2006 (last modified) kehi�"GRA"; "GC-rich rab activator"; Found in the promoter of ABAresponsive rab28 gene from maize (Z.m.); Similar (seven of 12bases) to the GRA element from the maize rab17 promoter (S000150;GRAZMRAB17); Found at -138 to -130;GRAABArab28rabseedmaize (Zea mays) Busk PK, Pages MBusk PK, Pages M�Protein binding to the abscisic acid-responsive element isindependent of VIVIPAROUS1 in vivoRegulation of abscisic acid-induced transcription=Plant Cell 9:2261-2270 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 11407411PubMed: 9617810;Review CATGCCGCCGREGIONNTPRB1BS000364 16-Feb-2001 (last modified) seki�$"G region" found in tobacco (N.t.) PRB-1b gene promoter; Locatedat -201 to -178; Binding site of nuclear protein; Required forethylene induction; Contains an 11bp sequence, TAAGAGCCGCC, whichis highly conserved in the promoter of ethylene-induced PR genes;Contains a G box motif; See S000365;PR-1PRB-1bethyleneGG boxTobacco (Nicotiana tabacum)"Meller Y, Sessa G, Eyal Y, Fluhr RNDNA-protein interactions on a cis-DNA element essential forethylene regulation!Plant Mol Biol 23: 453-463 (1993)PubMed: 8219081; TGGCGGCTCTTATCTCACGTGATG GT1CONSENSUSS000198 11-May-2006 (last modified) kehi��Consensus GT-1 binding site in many light-regulated genes, e.g.,RBCS from many species, PHYA from oat and rice, spinach RCA andPETA, and bean CHS15; R=A/G; W=A/T; For a compilation of relatedGT elements and factors, see Villain et al. (1996); GT-1 canstabilize the TFIIA-TBP-DNA (TATA box) complex; The activationmechanism of GT-1 may be achieved through direct interactionbetween TFIIA and GT-1; Binding of GT-1-like factors to the PR-1apromoter influences the level of SA-inducible gene expression;
GT-1lightTATATFIIATBPHRSARTMVleafshoot�pea (Pisum sativum); oat (Avena sativa); rice (Oryza sativa);tobacco (Nicotiana tabacum); Arabidopsis thaliana; spinach(Spinacia oleracea); bean;�Terzaghi WB, Cashmore ARVillain P, Mache R, Zhou DXLe Gourrierec J, Li YF, Zhou DXBuchel AS, Brederode FT, Bol JF, Linthorst HJMZhou DX��Light-regulated transcriptionThe mechanism of GT element-mediated cell type-specifictranscriptional controlTranscriptional activation by Arabidopsis GT-1 may be throughinteraction with TFIIA-TBP-TATA complexMutation of GT-1 binding sites in the Pr-1A promoter influencesthe level of inducible gene expression in vivoRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)J Biol Chem 271:32593-32598 (1996)Plant J 18:663-668 (1999)Plant Mol Biol 40:387-396 (1999)Trends in Plant Science 4:210-214 (1999)APubMed: 8955086;PubMed: 10417717PubMed: 10437823;PubMed: 10366876 ReviewReviewGRWAAWGT1CORES000125 15-Oct-1999 (last modified) kehi�Critical for GT-1 binding to box II of rbcS; See S000051GT1MOTIF1; For a compilation of related GT elements and factors,see Villain et al. (1996);rbcSbox IIGT-1rbcS-3leafshootpea (Pisum sativum);�Green PJ, Yong M-H, Cuozzo M, Kano-Murakami Y, Silverstein P,Chua N-HGilmartin PM, Sarokin L, Memelink J, Chua N-HTerzaghi WB, Cashmore ARVillain P, Mache R, Zhou DXZhou DX��Binding site requirements for pea nuclear protein factor GT-1correlate with sequences required for light-dependenttranscriptional activation of the rbcS-3A gene.Molecular light switches for plant genes.Light-regulated transcriptionThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�EMBO J 7:4035-4044 (1988)Plant Cell 2:369-378 (1990)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)0PubMed: 3243271;PubMed: 2152164;PubMed: 8955086;ReviewGGTTAA
GT1GMSCAM4S000453%29-November-2004 (last modified) kehi�"GT-1 motif" found in the promoter of soybean (Glycine max) CaMisoform, SCaM-4; Plays a role in pathogen- and salt-inducedSCaM-4 gene expression; See also S000198 (GT-1 consensus);GT-1 boxGlycine max (soybean)�Park HC, Kim ML, Kang YH, Jeon JM, Yoo JH, Kim MC, Park CY, JeongJC, Moon BC, Lee JH, Yoon HW, Lee SH, Chung WS, Lim CO, Lee SY,Hong JC, Cho MJ.�Pathogen- and NaCl-induced expression of the SCaM-4 promoter ismediated in part by a GT-1 box that interacts with a GT-1-liketranscription factor.%Plant Physiol. 135: 2150-2161 (2004).PubMed: 15310827 GAAAAAGT1MOTIFPSRBCSS000051 15-Oct-1999 (last modified) kehi�"GT-1 motif"; "Consensus sequence of rbcS BOX II, III, II',III'"; "GT-1 box"; 5' upstream region (-151) of pea (P.s.) rbcSgene; binding with trans factor GT-1; See S000125 GT1CORE; K=G/T;W=A/T; R=A/G; For a compilation of related GT elements andfactors, see Villain et al. (1996);RBCSBOX 2Box IIGT-1PEAleafshootpea (Pisum sativum)�Green PJ, Yong M-H, Cuozzo M, Kano-Murakami Y, Silverstein P,Chua N-HGilmartin PM, Sarokin L, Memelink J, Chua N-HVillain P, Mache R, Zhou DXZhou DX�eBinding site requirements for pea nuclear protein factor GT-1correlate with sequences required for light-dependenttranscriptional activation of the rbcS-3A gene.Molecular light switches for plant genes.The mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorsEMBO J 7:4035-4044 (1988)Plant Cell 2:369-378 (1990)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)0PubMed: 3243271;PubMed: 2152164;PubMed: 8955086;Review KWGTGRWAAWRW GT2OSPHYAS000207 11-May-2006 (last modified) kehi�7GT-2 (a rice nuclear protein) binding site in a rice (O.s.) phyApromoter; phyA gene are transcriptionaly repressed in response tolight; One of GT elements; For a compilation of related GTelements and factors, see Villain et al. (1996); The HMG-1/Yprotein PF1 stimulates binding of the GT-2 to PHYA genepromoter;GT-2phyAGTlightHMG-1/Y proteinPF1leafshoot(rice (Oryza sativa); oat (Avena sativa);ZDehesh K, Bruce WB, Quail PHVillain P, Mache R, Zhou DXMartinez-Garcia JF, Quail PHZhou DX�PA trans-acting factor that binds to a GT-motif in a phytochromegene promoterThe mechanism of GT element-mediated cell type-specifictranscriptional controlThe HMG-I/Y protein PF1 stimulates binding of the transcriptionalactivator GT-2 to the PHYA gene promoterRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�Science 250:1397-1399 (1990)J Biol Chem 271:32593-32598 (1996)Plant J 18:173-183 (1999)Trends in Plant Science 4:210-214 (1999)BPubMed: 2255908;PubMed: 8955086;PubMed: 10363369;PubMed: 10366876Review GCGGTAATT GTGANTG10S000378 23-Aug-2001 (last modified) uchi�"GTGA motif" found in the promoter of the tobacco (N.t.) latepollen gene g10 which shows homology to pectate lyase and is theputative homologue of the tomato gene lat56; Located between -96and -93; See S000280;g10pollen
pectate lyasetabacco(Nicotiana tabacum)ORogers HJ, Bate N, Combe J, Sullivan J, Sweetman J, Swan C,Lonsdale DM, Twell DeFunctional analysis of cis-regulatory elements within thepromoter of the tobacco late pollen gene g10!Plant Mol Biol 45: 577-585 (2001)PubMed: 11414616; GTGAHBOXCONSENSUSPVCHSS000200 27-Aug-2002 (last modified) uchi��"H-box"; Consensus sequence of H-boxes found in bean (Phaseolusvulgaris) chs15 gene promoter; Essential for both lightregulation and elicitor induction; Similar sequence was found intobacco Tnt1 retrotransposon promoter (LTR); Tnt1 is induced bywounding and by abiotic stress; "KAP-2" binds to the H-box andstimulates transcription from a promoter harboring the H-box;"KAP-2" shares sequence similarity to the large subunit ofmammalian Ku autoantigen; See S000150, S000402 and S000401;H-boxH boxCHSchslight regulationlightelicitorstress
transposonwoundingleafshootKu autoantigenKAP-2#bean (Phaseolus vulgaris); tobacco;�Loake GJ, Faktor O, Lamb CJ, Dixon RATerzaghi WB, Cashmore ARMhiri C, Morel JB, Vernhettes S, Casacuberta JM, Lucas H,Grandbastien MALindsay WP, McAlister FM, Zhu Q, He XZ, Droge-Laser W, Hedrick S,Doerner P, Lamb C, Dixon RA��Combination of H-box [CCTACC(N)7CT] and G-box (CACGTG) ciselements is necessary for feed-forward stimulation of a chalconesynthase promoter by the phenypropanoid-pathway intermediatep-coumaric acidLight-regulated transcriptionThe promoter of the tobacco Tnt1 retrotransposon is induced bywounding and by abiotic stressKAP-2, a protein that binds to the H-box in a bean chalconesynthase promoter, is a novel plant transcription factor withsequence identity to the large subunit of human Ku autoantigen�Proc Natl Acad Sci USA 89:9230-9234(1992)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)Plant Mol Biol 33:257-266 (1997)Plant Mol Biol 49: 503-514 (2002)1PubMed: 1409628;PubMed: 9037144;PubMed: 12090626;ReviewCCTACCNNNNNNNCT HBOXPVCHS15S000361 16-Feb-2001 (last modified) seki�Binding site of two bean protein factors, KAP-1 and KAP-2; KAP-1is a 97 kDa polypeptide; KAP-2 comprises two polypeptides of 76kDa and 56 kDa; Elicitation of bean cell with glutathione causesa rapid increase in specific activities of KAP-1 and KAP2;H-boxKAP-1KAP-2elicitor glutathionebean (Phaseolus vulgaris)Yu LM, Lamb CJ, Dixon RA�Purification and biochemical characterization of proteins whichbind to the H-box cis-element implicated in transcriptionalactivation of plant defense genesPlant J 3: 805-816 (1993)PubMed: 8401613; CCTACCNNNNNNNCTNNNNA HDMOTIFPCPR2S000233 17-May-1998 (last modified) kehi{HD (homeodomain) protein target site in parsley (P.c.)pathogenesis-related protein 2 (PR2); A potential in vivo targetsite;HD homeodomainPR2 parsley (Petroselinum crispum):Korfhage U, Trezzini GF, Meier I, Hahlbrock K, Somssich IEbPlant homeodomain protein involved in transcriptional regulationof a pathogen defense-related genePlant Cell 6:695-708 (1994)PubMed: 7913642; CTAATTGTTTA
HDZIP2ATATHB2S000373 31-Jul-2001 (last modified) uchi�
Binding site of the Arabidopsis (A.T.) homeobox gene (ATHB-2)found in its own promoter; Located between -72 and -80; Similarto the HD-ZIP-2 binding consensus sequence; ATHB-2 is regulatedby light signals which function as a negative autoregulator ofits own gene; M=C/A;ATHB-2HAT4HD-ZIPshade avoidance responsesArabidopsis thaliana0Ohgishi M, Oka A, Morelli G, Ruberti I, Aoyama T?Negative autoregulation of the Arabidopsis homeobox gene ATHB-2Plant J 25: 389-398 (2001)PubMed: 11260495; TAATMATTA
HDZIPIIIATS000475%05-November-2005 (last modified) kehi�Ath b-9 HD-Zip (HD-Zip-9), a member of a small family of HD-Zipproteins (HD-ZIP III), in Arabidopsis recognize this sequence;See also S000371; S=G/C;HomeoboxHD-ZIPArabidopsis thalianaTSessa G, Steindler C, Morelli G, Ruberti I.Ohashi-Ito K, Kubo M, Demura T, Fukuda H.�The Arabidopsis Athb-8, -9 and -14 genes are members of a smallgene family coding for highly related HD-ZIP proteins.Class III Homeodomain Leucine-Zipper Proteins Regulate Xylem CellDifferentiation.JPlant Mol Biol. 38: 609-622.(1998)Plant Cell Physiol. 46: 1646-1656 (2005) PubMed: 9747806PubMed: 16081527 GTAATSATTAC HEXAMERATH4S000146 10-May-1998 (last modified) kehi@hexamer motif of Arabidopsis thaliana (A.t.) histone H4promoter;hexamerhistoneH4meristemArabidopsis thaliana;2Chaubet N, Flenet M, Clement B, Brignon P, Gigot CZIdentification of cis-elements regulating the expression of anArabidopsis histone H4 gene.Plant J 10:425-435 (1996)PubMed: 8811858; CCGTCGHEXATS000334 7-Sep-2000 (last modified) seki�"Hex motif"; Binding site of Arabidopsis (A.t.) bZIP protein TGA1and G box binding factor GBF1; TGA1 and members of the GBF familydiffer in their DNA binding properties; G-Box-like element;TGA1GBFG-boxbZIP Hex motifArabidopsis thaliana$Schindler U, Beckmann H, Cashmore AR�TGA1 and G-box binding factors: two distinct classes ofArabidopsis leucine zipper proteins compete for the G-box-likeelement TGACGTGG Plant Cell 4: 1309-1319 (1992) PubMed: 1446171; GenBank: X68053 TGACGTGGHEXMOTIFTAH3H4S000053 11-May-2006 (last modified) kehi��"hexamer motif" found in promoter of wheat (T.a.) histone genesH3 and H4; CaMV35S; NOS; Binding with HBP-1A and HBP-1B; Bindingsite of wheat (T.a.) nuclear protein HBP-1 (histone DNA bindingprotein-1); HBP-1 has a leucine zipper motif; "hexamer motif" intype 1 element may play important roles in regulation ofreplication- dependent but not of replication-independentexpression of the wheat histone H3 gene; See S000076, S000267;Rice OBF1-homodimer-binding site (Shimizu et al.);hexamerHBP-1AHBP-1B
histone H3CaMV35SNOSHBP-1Leucine zipper motifmeristemOBF1bZIPlip19LIP195wheat (Triticum aestivum); CaMV; Oryza sativa (rice);�0Mikami K, Tabata T, Kawata T, Nakayama T, Iwabuchi MMikami K, Nakayama T, Kawata T, Tabata T, Iwabuchi MTabata T, Takase H, Takayama S, Mikami K, Nakatsuka A, Kawata T,Nakayama T, Iwabuchi MTerada R, Nakayama T, Iwabuchi M, Shimamoto KShimizu H, Sato K, Berberich T, Miyazaki A, Ozaki R, Imai R,Kusano T.��Nuclear protein(s) binding to the conserved DNA hexamericsequence postulated to regulate transcription of wheat histonegenes.Specific interaction of nuclear protein HBP-1 with the conservedhexameric sequence ACGTCA in the regulatory region of wheathistone genes.A protein that binds to a cis-acting element of wheat histonegenes has a leucine zipper motifA type I element composed of the hexamer (ACGTCA) and octamer(CGCGGATC) motifs plays a role(s) in meristematic expression of awheat histone H3 gene in transgenic rice plantsLIP19, a Basic Region Leucine Zipper Protein, is a Fos-likeMolecular Switch in the Cold Signaling of Rice Plants.�FEBS Lett 223: 273-278 (1987)Plant Cell Physiol 30:107-119 (1989).Science 245: 965-967 (1989)Plant Mol Biol 27: 17-26 (1995)Plant Cell Physiol. 46 :1623-34. (2005)NPubMed: 2822486;PubMed: 2772648;PubMed: 2772648PubMed: 7865787PubMed: 16051676 ACGTCAHSES000054 16-Feb-2001 (last modified) seki��"HSE (heat shock response element)"; consensus sequence found inthe promoter regions of heat shock protein genes; HSF bindingsite; HsfA3, a new member of the Hsf (heat stress transcriptionfactor) family; was isolated by yeast two-hybrid screening, usingHsfA1 as a bait; HsfA3 is a single copy gene with all conservedsequence elements characteristic of a heat stress transcriptionfactor;
heat shockHSPHSE<animal; plant; Drosophila; tomato (Lycopersicon peruvianum);EPelham HBharti K, Schmidt E, Lyck R, Heerklotz D, Bublak D, Scharf KD�Activation of heat-shock genes in eukaryotes.Isolation and characterization of HsfA3, a new heat stresstranscription factor of Lycopersicon peruvianum5Trends Genet 1:31-35 (1985)Plant J (2000) 22: 355-365PubMed: 10849352;ReviewCTNGAANNTTCNAGHSELIKENTACIDICPR1S000056 17-May-1997 (last modified) kehi`"HSE-like motif" in -56 region of acidic PR1 gene of tobacco(N.t.); not found in basic PR1 gene;tobacco
PR-proteinhsetobacco (Nicotiana tabacum)%Pfitzner UM, Pfitzner AJP, Goodman HMyDNA sequence analysis of a PR-1a gene from tobacco: Molecularrelationship of heat shock and pathogen responses in plants. Mol Gen Genet 211:290-295 (1988) CNNGAANNNTTCNNG
HSELIKENTGLN2S000057 17-May-1998 (last modified) kehi]"HSE-like sequence" in 5' upstream region of beta-1,3-glucanasegene (GLN2) of tobacco (N.t.);tobaccobeta-1,3-glucanase group 2
PR-proteinhsepromoter
heat shocktobacco (Nicotiana tabacum)Ohme-Takagi M, Shinshi H>Structure and expression of a tobacco beta-1,3-glucanase gene. Plant Mol Biol 15:941-946 (1990)!PubMed: 2103484; GenBank: X53600;
AGGAATTCCT
HSRENTHSR203JS000466"24-April-2005 (last modified) kehi�"HSRE(HSR203 responsive element)" in tobacco (N.t.) responsiblefor the marked induction of the HSR203J gene during the HR(hypersensitive response); HSR203J is specifically activatedduring the early steps of incompatible plant/pathogeninteractions;HRNicotiana tabacum (tobacco)HPontier D, Balague C, Bezombes-Marion I, Tronchet M, Deslandes L,Roby D.�Identification of a novel pathogen-responsive element in thepromoter of the tobacco gene HSR203J, a molecular marker of thehypersensitive response. Plant J. 26: 495-507 (2001).PubMed: 11439136 CAAAATTTTGTAHY5ATS000345 16-Feb-2001 (last modified) seki��"G box"; Binding site of Arabidopsis bZIP protein HY5; HY5 isconstitutively nuclear localized and is involved in lightregulation of transcriptional activity of the promoterscontaining the G-box; See S000041, S000042, S000229; HY5abundance peaks in early seedling development, consistent withits role in promoting photomorphogenesis; HY5 stability andactivity is regulated by phosphorylation in its COP1 bindingdomain; HY5 regulates stimulus-induced development of root andhypocotyl; bZIPHY5LREG boxCOP1bZIPstimulus-responseroot hypocotylleafshootArabidopsis thaliana�Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei NHardtke CS, Gohda K, Osterlund MT, Oyama T, Okada K, Deng XWOyama T, Shimura Y, Okada K�NArabidopsis bZIP protein HY5 directly interacts withlight-responsive promoters in mediating light control of geneexpressionHY5 stability and activity in arabidopsis is regulated byphosphorylation in its COP1 binding domainThe Arabidopsis HY5 gene encodes a bZIP protein that regulatesstimulus-induced development of root and hypocotylUPlant Cell 10:673-683 (1998)EMBO J 19: 4997-5006 (2000)Genes Dev (1997) 11: 2983-29951PubMed: 9596629;PubMed: 10990463;PubMed: 9367981; TGACACGTGGCAIBOXS000124 7-Sep-2000 (last modified) seki�&"I box"; "I-box"; Conserved sequence upstream of light-regulatedgenes; Sequence found in the promoter region of rbcS of tomatoand Arabidopsis; I box (Giuliano et al. 1988); Binding site ofLeMYB1, that is a member of a novel class of myb-like proteins;LeMYBI act as a transcriptional activator; I boxI-boxrbcSlight regulationlightLeMYB1, Myb-likeproteinleafshoot7tomato (Lycopersicon esculentum); Arabidopsis thaliana;tGiuliano G, Pichersky E, Malik VS, Timko MP, Scolnik PA, CashmoreARDonald RGK, Cashmore ARRose A, Meier I, Wienand U�#An evolutionarily conserved protein binding sequence upstream ofa plant light-regulated gene.Mutation of either G box or l box sequences profoundly affectsexpression from the Arabidopsis rbcS-1A promoter.The tamato I-box binding factor LeMYBI is a member of a novelclass of Myb-like proteins]Proc Natl Acad Sci USA 85:7089-7093 (1988)EMBO J 9:1717-1726 (1990)Plant J 20: 641-652 (1999)1PubMed: 2902624;PubMed: 2347304;PubMed: 10652136; GATAAGIBOXCORES000199 2-May-1998 (last modified) kehi�"I box"; "I-box"; Conserved sequence upstream of light-regulatedgenes; Conserved sequence upstream of light-regulated genes ofboth monocots and dicots; See IBOX (S000124);I boxI-boxrbcSlight regulationlightleafshoot Terzaghi WB, Cashmore AR Light-regulated transcription7Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995) ReviewGATAA
IBOXCORENTS000424 29-Sep-2003 (last modified) kehi�"I-box core motif" in the CAMs (conserved DNA modular arrays)associated with light-responsive promoter regions; See S000124(GATAAG), S000199 (GATAA), S000213;I-boxCAMlight#Nicotiana plumbaginifolia (tobacco)KMartinez-Hernandez A, Lopez-Ochoa L, Arguello-Astorga G,Herrera-Estrella L.�Functional properties and regulatory complexity of a minimal RBCSlight-responsive unit activated by phytochrome, cryptochrome, andplastid signals.#Plant Physiol. 128:1223-1233 (2002)PubMed: 11950971; GATAAGRIBOXLSCMCUCUMISINS000423 29-Sep-2003 (last modified) kehi�"I-box-like sequence" found in the region (from -254 to -215) ofcucumisin (a subtilisin-like serine protease) in the fruit ofmelon (Cucumis melo L.); I-box-like sequence functions as anegative regulatory element; See S000199 (I-box, GATAA), S000124(I-box, GATAAG); cucumisinfruitCucumis melo L. (melon))Yamagata H, Yonesu K, Hirata A, Aizono Y.tTGTCACA motif is a novel cis-regulatory enhancer element involvedin fruit-specific expression of the cucumisin gene.#J Biol Chem. 277:11582-11590 (2002)PubMed: 11782472;
AGATATGATAAAA
IDE1HVIDS2S000463"24-April-2005 (last modified) kehi�IDE1 (iron-deficiency-responsive element 1) found at -153/-136 ofbarley IDS2 (iron deficiency specific clone 2) gene promoter; Seealso S000464;ironrootHordeum vulgare (barley)�Kobayashi T, Nakayama Y, Itai RN, Nakanishi H, Yoshihara T, MoriS, Nishizawa NK.Kobayashi T, Suzuki M, Inoue H, Itai RN, Takahashi M, NakanishiH, Mori S, Nishizawa NK.�OIdentification of novel cis-acting elements, IDE1 and IDE2, ofthe barley IDS2 gene promoter conferringiron-deficiency-inducible, root-specific expression inheterogeneous tobacco plants.Expression of iron-acquisition-related genes in iron-deficientrice is co-ordinately induced by partially conservediron-deficiency-responsive elements.<Plant J. 36: 780-793 (2003).J Exp Bot. 56: 1305-1316. (2005) PubMed: 14675444PubMed: 15781441 ATCAAGCATGCTTCTTGC
IDE2HVIDS2S000464"24-April-2005 (last modified) kehi�IDE2 (iron-deficiency-responsive element 2) found at -262/-236 ofbarley IDS2 (iron deficiency specific clone 2) gene promoter; Seealso S000463;ironrootHordeum vulgare (barley)�Kobayashi T, Nakayama Y, Itai RN, Nakanishi H, Yoshihara T, MoriS, Nishizawa NK.Kobayashi T, Suzuki M, Inoue H, Itai RN, Takahashi M, NakanishiH, Mori S, Nishizawa NK.�OIdentification of novel cis-acting elements, IDE1 and IDE2, ofthe barley IDS2 gene promoter conferringiron-deficiency-inducible, root-specific expression inheterogeneous tobacco plants.Expression of iron-acquisition-related genes in iron-deficientrice is co-ordinately induced by partially conservediron-deficiency-responsive elements.<Plant J. 36: 780-793 (2003).J Exp Bot. 56: 1305-1316. (2005) PubMed: 14675444PubMed: 15781441 TTGAACGGCAAGTTTCACGCTGTCACT
IDRSZMFER1S000445#04-August-2006 (last modified) kehi�."IDRS" (Iron-Dependent Regulatory Sequence) found in maize andArabidopsis ferritin genes (Fer1); IDRS is responsible fortranscriptional repression of ZmFer1 gene under low iron supplyconditions; S=C/G; K=G/T; IDRS is not involved in theFe-regulated expression of the AtAPX1 gene (Fourcroy et al.,2004);ironferritinAPX1AtFer1Fer'Zea mays (maize); Arabidopsis thaliana;�Petit JM, van Wuytswinkel O, Briat JF, Lobreaux S.Fourcroy P, Vansuyt G, Kushnir S, Inze D, Briat JF.Tarantino D, Petit JM, Lobreaux S, Briat JF, Soave C, Murgia I.Arnaud N, Murgia I, Boucherez J, Briat JF, Cellier F, Gaymard F.�Characterization of an iron-dependent regulatory sequenceinvolved in the transcriptional control of AtFer1 and ZmFer1plant ferritin genes by iron.Iron-regulated expression of a cytosolic ascorbate peroxidaseencoded by the APX1 gene in Arabidopsis seedlings.Differential involvement of the IDRS cis-element in thedevelopmental and environmental regulation of the AtFer1 ferritingene from Arabidopsis.An iron-induced nitric oxide burst precedes ubiquitin-dependentprotein degradation for arabidospsis atfer1 ferritin geneexpression.�J Biol Chem. 276:5584-5590. (2001)Plant Physiol. 134: 605-613 (2004). .Planta. 217: 709-716 (2003)J Biol Chem. 2006 Jun 16; [Epub ahead of print]@PubMed: 11092880PubMed: 14739345PubMed: 12728319PubMed: 16782706 CACGAGSCCKCCAC
INRNTPSADBS000395 21-May-2002 (last modified) uchi�"Inr (initiator)" elements found in the tobacco psaDb genepromoter without TATA boxes; Light-responsive transcription ofpsaDb depends on Inr, but not TATA box; initiater light-responsive transcriptionTATA-less promoterpsaDb Inr elementtobacco (Nicotiana tabacum) Nakamura M, Tsunoda T, Obokata JzPhotosynthesis nuclear genes generally lack TATA-boxes: a tobaccophotosystem I gene responds to light through an initiaterPlant J 29: 1-10 (2002)PubMed: 12060222 ; YTCANTYY INTRONLOWERS000086 17-May-1998 (last modified) kehid"3' intron-exon splice junctions"; Plant intron lower sequence;Consensus sequence for plant introns;intronsplice junctionmaize (Zea mays) Brown JWSSA catalog of splice junction and putative branch point sequencesfrom plant introns.%Nucleic Acids Res 14:9549-9559 (1986)PubMed: 3808952;ReviewTGCAGG INTRONUPPERS000085 17-May-1998 (last modified) kehiu"5' exon-intron splice junctions" of plant introns; Plant intronupper sequence; Consensus sequence for plant introns;intronsplice junctionmaize (Zea mays) Brown JWSSA catalog of splice junction and putative branch point sequencesfrom plant introns.%Nucleic Acids Res 14:9549-9559 (1986)PubMed: 3808952;Review MAGGTAAGTIRO2OSS000505&15-September-2006 (last modified) kehiqOsIRO2-binding core sequence; "G-box plus G"; Transcriptionfactor OsIRO2 is induced exclusively by Fe deficiency;rootshootFeironOryza sativa (rice)^Ogo Y, Itai RN, Nakanishi H, Inoue H, Kobayashi T, Suzuki M,Takahashi M, Mori S, Nishizawa NK.oIsolation and characterization of IRO2, a novel iron-regulatedbHLH transcription factor in graminaceous plants. J Exp Bot. 57:2867-2878. (2006)PubMed: 16887895 CACGTGG JASE1ATOPR1S000388 20-Feb-2002 (last modified) uchi�"JASE1"found in promoter of Arabidopsis thaliana12-oxo-phytodienoic acid-10,11-reductase (OPR1) gene; Locatedbetween -179 and -170; Involved in up-regulation by bothsenescence and JA;OPR1
senescence
Jasmonic acidJASE1JASE2leafArabidopsis thaliana He Y, Gan SuIdentical promoter elements are involved in regulation of theOPR1 gene by senescence and jasmonic acid in Arabidopsis"Plant Mol Biol 47: 595-605 (2001)PubMed: 11725945;
CGTCAATGAA JASE2ATOPR1S000389 20-Feb-2002 (last modified) uchi�"JASE2"found in promoter of Arabidopsis thaliana12-oxo-phytodienoic acid-10,11-reductase (OPR1) gene; Locatedbetween -112 and -100; Involved in up-regulation by bothsenescence and JA; JASE2 contains a mixed A/C box-like motif;OPR1
senescence
Jasmonic acidJASE1JASE2leafArabidopsis thaliana He Y, Gan SuIdentical promoter elements are involved in regulation of theOPR1 gene by senescence and jasmonic acid in Arabidopsis"Plant Mol Biol 47: 595-605 (2001)PubMed: 11725945;
CATACGTCGTCAA JERECRSTRS000384 21-Nov-2002 (last modified) uchi�e"JERE" (jasmonate- and elicitor-responsive element) found in theperiwinkle(C.R.) strictosidine synthase(Str) gene promoter;Located between -100 and -58; ORCA1, ORCA2 and ORCA3 bindspecifically to the JERE of the Str promoter; Elicitor and MeJArapidly induce Orca2, but not Orca1 mRNA levels; ORCA3 mRNAaccumulation was rapidly induced by the metyljasmonate; JEREJA jasmonateelicitorstrictosidine synthase(Str)ORCA1ORCA2ORCA3
AP2 domain periwinkle(Catharanthus roseus)}Menke FL, Champion A, Kijne JW, Memelink Jvan der Fits L, Memelink JRushton PJ, Reinstadler A, Lipka V, Lippok B, Somssich IE��A novel jasmonate- and elicitor-responsive element in theperiwinkle secondary metabolite biosynthetic gene Str interactswith a jasmonate- and elicitor-inducible AP2-domain transcriptionfactor, ORCA2The jasmonate-inducible AP2/ERF-domain transcription factor ORCA3activates gene expression via interaction with ajasmonate-responsive promoter elementSynthetic plant promoters containing defined regulatory elementsprovide novel insights into pathogen- and wound-inducedsignalingQEMBO J 18: 4455-4463 (1999)Plant J 25: 43-53 (2001)Plant Cell. 14: 749-762 (2002)3PubMed: 10449411;PubMed: 11169181;PubMed: 11971132; CTCTTAGACCGCCTTCTTTGAAAG L1BOXATPDF1S000386%05-November-2005 (last modified) kehi�|"L1 box" found in promoter of Arabidopsis thaliana (A.t.)PROTODERMAL FACTOR1 (PDF1) gene; Located between -134 and -127;Involved in L1 layer-specific expression; L1-specific homeodomainprotein ATML can bind to the "L1 box"; Y=C/T; A cotton fibergene, RD22-like 1 (RDL1), contains a homeodomain binding L1 boxand a MYB binding motif (Wang et al., 2004); HDZip IV; See alsoS000371; PDF1L1 box L1 layer-specific expression Shoot apicalmeristemSAMorgan primordia cotton fiberHDZip homeodomainleucine zipper-Arabidopsis thaliana; Gossypium spp (cotton);�)Abe M, Takahashi T, Komeda YWang S, Wang JW, Yu N, Li CH, Luo B, Gou JY, Wang LJ, Chen XY.Henriksson E, Olsson AS, Johannesson H, Johansson H, Hanson J,Engstrom P, Soderman E.Abe M, Katsumata H, Komeda Y, Takahashi T.Ohashi Y, Oka A, Rodrigues-Pousada R, Possenti M, Ruberti I,Morelli G, Aoyama T.��Identification of a cis-regulatory element for L1 layer-specificgene expression, which is targeted by an L1-specific homeodomainproteinControl of plant trichome development by a cotton fiber MYBgene.Homeodomain leucine zipper class I genes in Arabidopsis.Expression patterns and phylogenetic reRegulation of shoot epidermal cell differentiation by a pair ofhomeodomain proteins in Arabidopsis.Modulation of phospholipid signaling by GLABRA2 in root-hairpattern formation.�Plant J 26: 487-494 (2001)Plant Cell 16: 2323-2334 (2004)Plant Physiol. 139: 509-518. (2005)Development. 130: 635-643.(2003)Science. 300: 1427-1430 (2003).QPubMed: 11439135;PubMed: 15316114PubMed: 16055682PubMed: 12505995PubMed: 12775839 TAAATGYAL1DCPAL1S000504&15-September-2006 (last modified) kehi�"L1" element, found in PAL1 promoter in carrot (Daucus carota),is a protoplastization (dilution) responsive element; L1 containsBox L-like sequence (ACCTACCC); see also S000492 (BOXL CORE of DCPAL1);L1Daucus carota (carrot)"Takeda J, Ito Y, Maeda K, Ozeki Y.�Assignment of UVB-responsive cis-element andprotoplastization-(dilution-) and elicitor-responsive ones in thepromoter region of a carrot phenylalanine ammonia-lyase gene(gDcPAL1).'Photochem Photobiol. 76:232-238 (2002).PubMed: 12194222 ATTCACCTACCCL4DCPAL1S000503&15-September-2006 (last modified) kehi�"L4" element, found in PAL1 promoter in carrot (Daucus carota),is a UV-B responsive element; L4 contains Box L-like sequence(TCCAACCA); see also S000492 (BoxL core of DC PAL);L4PALDaucus carota (carrot)"Takeda J, Ito Y, Maeda K, Ozeki Y.�Assignment of UVB-responsive cis-element andprotoplastization-(dilution-) and elicitor-responsive ones in thepromoter region of a carrot phenylalanine ammonia-lyase gene(gDcPAL1).'Photochem Photobiol. 76:232-238 (2002).PubMed: 12194222 AATCTCCAACCA
LBOXLERBCSS000126 17-May-1998 (last modified) kehi^"L box"; Conserved sequence found in rbcS upstream sequences ofboth tomato (L.e.) and tobacco;L boxrbcSleafshoot>tomato (Lycopersicon esculentum); tobacco (Nicotiana tabacum);ZGiuliano G, Pichersky E, Malik VS, Timko MP, Scolnik PA, CashmoreARDonald RGK, Cashmore AR�An evolutionarily conserved protein binding sequence upstream ofa plant light-regulated gene.Mutation of either G box or l box sequences profoundly affectsexpression from the Arabidopsis rbcS-1A promoter.CProc Natl Acad Sci USA 85:7089-7093 (1988)EMBO J 9:1717-1726 (1990) PubMed: 2902624;PubMed: 2347304; AAATTAACCAA LEAFYATAGS000432 27-Jan-2004 (last modified) kehiqTarget sequence of LEAFY in the intron of AGAMOUS gene inArabidopsis; See Lohmann et al. Cell 105:793-803 (2003);LEAFYAGAMOUS*Oryza sativa (rice); Arabidopsis thaliana;5Kamiya N, Nagasaki H, Morikami A, Sato Y, Matsuoka M.�Isolation and characterization of a rice WUSCHEL-tyope homoeboxgene that is specifically expressed in the central cells of aquiescent center in the root apical meristem.Plant J. 35: 429-441 (2003)PubMed: 12904206; CCAATGT
LECPLEACS2S000465"24-April-2005 (last modified) kehiaCore element in LeCp (tomato Cys protease) binding cis-element(from -715 to -675) in LeAcs2 gene;cysteine proteaseethylenexylanaseACS Lycopersicon esculentum (tomato) Matarasso N, Schuster S, Avni A.�A novel plant cysteine protease has a dual function as aregulator of 1-aminocyclopropane-1-carboxylic Acid synthase geneexpression.!Plant Cell. 17: 1205-1216. (2005)PubMed: 15749766 TAAAATATLEGUMINBOXLEGA5S000060 17-May-1998 (last modified) kehi:"legumin box" in legA 5' legumin gene promoter in legumin;leguminpeatobaccopromoterseed=pea (Pisum sativum); tobacco (Nicotiana tabacum); Vicia faba;QBaumlein H, Wobus U, Pustell J, Kafatos FCShirsat A, Wilford N, Croy R, Boulter D�The legumin gene family: structure of a B type gene of Vicia fabaand a possible legumin gene specific regulatory element.Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco.ENucleic Acids Res 14:2707-2720 (1986)Mol Gen Genet 215:326-331 (1989)1PubMed: 3960730; GenBank: X03677;PubMed: 2710102; TCCATAGCCATGCAWRCTGMAGAATGTCLREBOX2PSRBCS3S000061 11-May-2006 (last modified) kehi�R"LRE (light-responsive element) Box II" of pea (P.s.) rbcS-3Agene; GT-1 binding; "GT-motif"; "GT1 motif"; Some similarity toSV40 enhancer core sequence; For a compilation of related GTelements and factors, see Villain et al. (1996); "BoxII" Bindingsite of transcriptional factor GTI; Located at -152 to -138;Confers light responsiveness; lightrbcSGT-1GT1enhancercoreBox IILRE
GT elementleafshoot*pea (Pisum sativum); Arabidopsis thaliana;�Green PJ, Kay SA, Chua N-HKuhlemeier C, Green PJ, Chua N-HVillain P, Mache R, Zhou DXChattopadhyay S, Puente P, Deng X-W, Wei NZhou DXLam E, Chua NH�'Sequence-specific interactions of a pea nuclear factor withlight-responsive elements upstream of the rbcS-3A gene.Regulation of gene expression in higher plantsThe mechanism of GT element-mediated cell type-specifictranscriptional controlCombinatorial interaction of ligth-responsive elements plays acritical role in determining the response characteristics ofligth-regulated promoters in ArabidopsisRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorsGT-1 binding site confers light responsive expression intransgenic tobacco�EMBO J 6:2543-2549 (1987)Ann Rev Plant Physiol 38:221-257 (1987)J Biol Chem 271:32593-32598 (1996)Plant J 15:69-77 (1998)Trends in Plant Science 4:210-214 (1999)Science 248: 471-474 (1990)@PubMed: 3678200;PubMed: 8955086;PubMed: 9744096;PubMed: 2330508 ReviewReviewTGTGTGGTTAATATGLREBOX3PSRBCS3S000062 17-May-1998 (last modified) kehi�"LRE (light-responsive element) Box III" of pea (P.s.) rbcS-3Agene; GT-1 binding; For a compilation of related GT elements andfactors, see Villain et al. (1996);lightrbcSGT-1leafshootpea (Pisum sativum)5Green PJ, Kay SA, Chua N-HVillain P, Mache R, Zhou DX�Sequence-specific interactions of a pea nuclear factor withlight-responsive elements upstream of the rbcS-3A gene.The mechanism of GT element-mediated cell type-specifictranscriptional control;EMBO J 6:2543-2549 (1987)J Biol Chem 271:32593-32598 (1996) PubMed: 3678200;PubMed: 8955086; ACTATTTTCACTATCLREBOXIIPCCHS1S000303 10-Feb-2000 (last modified) seki�"BoxII"; Light responsive element (LRE) found in the parsley(P.c.) CHS-1 (chalcone synthase-1) gene promoter; Required forlight responsiveness; nuclear protein binding site; Highlyconserved in various light inducible gene promoters; SeeS000302;chalcone synthaseCHSlightBox IILREleafshoot parsley (Petroselinum crispum)@Schulze-Lefert P, Dangl JL, Becker-Andre M, Hahlbrock K, SchulzWvInducible in vivo DNA footprints define sequences necessary forUV light activation of the parsley chalcon sythase geneEMBO J 8: 651-656 (1989)PubMed: 2566481
TCCACGTGGC
LREBOXIPCCHS1S000302 16-Feb-2001 (last modified) seki�N"BoxI"; Light responsive element (LRE) found in the parsley(P.c.) CHS-1 (chalcone synthase-1) gene promoter; Required forlight responsiveness; nuclear protein binding site; See S000303;"MRECHS" (MRE=Myb Recognition Element)Recognition site of MYB305and a novel factor PcMYB1 (Myb1 from P. crispum); PcMYB1 containsonly one MYB repeat;
chalcone synthaseCHSlightBox ILREPcMYB1MRECHSMYBleafshoot parsley (Petroselinum crispum)rSchulze-Lefert P, Dangl JL, Becker-Andre M, Hahlbrock K, SchulzWFeldbrugge M, Sprenger M, Hahlbrock K, Weisshaar B� Inducible in vivo DNA footprints define sequences necessary forUV light activation of the parsley chalcone synthase genePcMYB1, a novel plant protein containing a DNA-binding domainwith one MYB repeat, interacts in vivo with a light-regulatorypromoter unit4EMBO J 8: 651-656 (1989)Plant J (1997) 11: 1079-1093 PubMed: 2566481PubMed: 9193077;
AACCTAACCT LRENPCABES000231 17-May-1998 (last modified) kehi^"LRE"; A positive light regulatory element in tobacco (N.p.) CAB(cab-E) gene; Located at -241;CABcabcab-ECABElightleafshoot#tobacco (Nicotiana plumbaginifolia)=Castresana C, Garcia-Luque I, Alonso E, Malik VS, Cashmore AR|Both positive and negative regulatory elements mediate expressionof a photoregulated CAB gene from Nicotiana plumbaginifoliaEMBO J 7:1929-1936 (1988)!PubMed: 2901343; GenBank: X12512; ACGTGGCALS5ATPR1S000323$04-January-2007 (last modified) kehi��"LS5"; A negative regulatory element found in the Arabidopsis(A.t.) PR-1 gene promoter; Binding site of TGA2; NPR1 increasedthe binding of TGA2 to the element; NPR1 is essential inactivating systemic, inducible plant defense response; SeeS000322; TGA6 expressed in roots in young seedlings; TGA2.1 is adirect transcriptional activator; TGA2.2 stabilizes TGA2.1binding; NOTE: The motif sequence previously shown was that ofLS7. The correction was made. TGA2LS5LS7SANPR1TGA6auxinsalicylic acidroot2Arabidopsis thaliana; tobacco (Nicotiana tabacum);�Despres C, DeLong C, Glaze S, Liu E, Fobert PRXiang C, Miao Z, Lam ENiggeweg R, Thurow C, Weigel R, Pfitzner U, Gatz CThurow C, Schiermeyer A, Krawczyk S, Butterbrodt T, Nickolov K,Gatz C.�The Arabidopsis NPR1/NIM1 protein enhances the DNA bindingactivity of a subgroup of the TGA family of bZIP transcriptionfactorsDNA-binding properties, genomic organization and expressionpattern of TGA6,a new member of the TGA family of bZIPtranscription factors in Arabidopsis thalianaTobacco TGA factors differ with respect to interaction with NPR1,activation potential and DNA-binding properties.Tobacco bZIP transcription factor TGA2.2 and related factorTGA2.1 have distinct roles in plant defense responses and plantdevelopment.yPlant Cell 12: 279-290 (2000)Plant Mol Biol 34: 403-415 (1997)Plant Mol Biol 42: 775-788 (2000)Plant J. 44:100-113 (2005)APubMed: 10662863;PubMed: 9225852PubMed: 10809449;PubMed: 16167899
TCTACGTCACLS7ATPR1S000322$04-January-2007 (last modified) kehi��"LS7"; A positive salicylic acid-inducible element found in theArabidopsis (A.t.) PR-1 gene promoter; Binding site of TGA1; NPR1increased the binding of TGA2 to the element; NPR1 is essentialin activating systemic, inducible plant defense responses; SeeS000323; TGA6 expressed in roots in young seedlings; TGA2.1 is adirect transcriptional activator; TGA2.2 stabilizes TGA2.1binding; NOTE: The motif sequence previously shown was that ofLS5. The correction was made. We are very sorry. TGA2LS5LS7SANPR1TGA6auxinsalicylic acidroot2Arabidopsis thaliana; tobacco (Nicotiana tabacum);�Despres C, DeLong C, Glaze S, Liu E, Fobert PRXiang C, Miao Z, Lam ENiggeweg R, Thurow C, Weigel R, Pfitzner U, Gatz CJohnson C, Boden E, Arias J.Thurow C, Schiermeyer A, Krawczyk S, Butterbrodt T, Nickolov K,Gatz C.��The Arabidopsis NPR1/NIM1 protein enhances the DNA bindingactivity of a subgroup of the TGA family of bZIP transcriptionfactorsDNA-binding properties, genomic organization and expressionpattern of TGA6,a new member of the TGA family of bZIPtranscription factors in Arabidopsis thalianaTobacco TGA factors differ with respect to interaction with NPR1,activation potential and DNA-binding propertiesSalicylic acid and NPR1 induce the recruitment oftrans-activating TGA factors to a defense gene promoter inArabidopsis.Tobacco bZIP transcription factor TGA2.2 and related factorTGA2.1 have distinct roles in plant defense responses and plantdevelopment.�Plant Cell 12: 279-290 (2000)Plant Mol Biol 34: 403-415 (1997)Plant Mol Biol 42: 775-788 (2000)Plant Cell. 15:1846-1858 (2003)Plant J. 44:100-113 (2005)QPubMed: 10662863;PubMed: 9225852PubMed: 10809449;PubMed: 12897257PubMed: 16167899
ACGTCATAGA LTRE1HVBLT49S000250 11-Oct-1999 (last modified) kehi�"LTRE-1" (low-temperature-responsive element) in barley (H.v.)blt4.9 gene promoter; A new LTRE; A previously known LTRE isCCGAC;low temperatureLTREbarley (Hordeum vulgare)%Dunn MA, White AJ, Vural S, Hughes MApIdentification of promoter elements in alow-temperature-responsive gene (blt4.9) from barley (Hordeumvulgare L.)!Plant Mol Biol 38:551-564 (1998)PubMed: 9747801; CCGAAA LTREATLTI78S000157 17-May-1998 (last modified) kehi��Putative low temperature responsive element (LTRE); Found inArabidopsis thaliana (A.t.) low-temperature-induced (lti) genes,lti78 and lti65; Repeated four times in lti78 which is alsoknown as cor78 and rd29A (see S000152)(Baker et al., Plant MolBiol 24:701(1994)); Found also in barley low temperatureresponsive genes, blt4.2, blt4.6, blt4.9 (lipid transfer genes);cold inducible; See LTRECORE (S000153); Also present in rab18,kin1, and kin2 (Nordin et al., 1993);"low temperature responsive elementLTREcoldleafshoot/Arabidopsis thaliana; barley (Hordeum vulgare);ANordin K, Vahala T, Palva ETWhite AJ, Dunn MA, Brown K, Hughes MA�Differential expression of two related, low-temperature-inducedgenes in Arabidopsis thaliana (L.) Heynh.Comparative analysis of genomic sequence and expression of alipid transfer protein gene family in winter barley.=Plant Mol Biol 21:641-653 (1993)J Exp Bot 45:1885-1892 (1994))PubMed: 8448363; GenBank: X67670, X67671;!Consensus sequence among 2 genes;ACCGACALTRECOREATCOR15S000153$8-February-2006 (last modified) kehi��Core of low temperature responsive element (LTRE) of cor15a genein Arabidopsis (A.t.); A portion of repeat-C (C-repeat),TGGCCGAC, which is repeated twice in cor15a promoter (Baker etal., 1994); ABA responsiveness; Involved in cold induction ofBN115 gene from winter Brassica napus; LTRE; See S000157,S000152; Light signaling mediated by phytochrome is necessary forcold- or drought- induced gene expression through the C/DRE inArabidopsis; See S000152;
low temperaturecoldLTREdroughtABAcor15aBN115leafshoot phytochrome$Arabidopsis thaliana; Brassica napusfBaker SS, Wilhelm KS, Thomashow MFJiang C, Iu B, Singh JBusk PK, Pages MKim HJ, Kim YK, Park JY, Kim J��The 5'-region of Arabidopsis thaliana cor15a has cis-actingelements that confer cold-, drought- and ABA-regulated geneexpression.Requirement of a CCGAC cis-acting element for cold induction ofthe BN115 gene from winter Brassica napusRegulation of abscisic acid-induced transcriptionLight signalling mediated by phytochrome plays an important rolein cold-induced gene expression through the C-repeat/dehydrationresponsive element (C/DRE) in Arabidopsis thalianazPlant Mol Biol 24:701-713 (1994)Plant Mol Biol 30:679-684 (1996)Plant Mol Biol 37:425-435 (1998)Plant J 29: 693-704 (2002)RPubMed: 8193295; GenBank: U01377;PubMed: 8605318;PubMed: 9617810;PubMed: 12148528;ReviewCCGACMARABOX1S000063 13-Feb-2001 (last modified) kehiR"A-box" found in SAR(scaffold attachment region; or matrixattachment region, MAR);MARSARmatrixA-boxscaffoldDrosophila; fly;-Gasser SM, Amati BB, Cardenas ME, Hofmann JFXJStudies on scaffold attachment sites and their relation to genomefunction."Intnatl Rev Cyto 119:57-96 (1989)PubMed: 2695485;Review
AATAAAYAAAMARARSS000064 16-Jan-1998 (last modified) kehi("ARS element"; Motif found in SAR (MAR);MARSARARSyeast-Gasser SM, Amati BB, Cardenas ME, Hofmann JFXJStudies on scaffold attachment sites and their relation to genomefunction."Intnatl Rev Cyto 119:57-96 (1989)PubMed: 2695485;Review WTTTATRTTTWMARCEN3S000065 16-Jan-1998 (last modified) kehi@"CEN III element"; Motif found in SAR (MAR); centromere element;MARSARARSCEN
centromereyeast-Gasser SM, Amati BB, Cardenas ME, Hofmann JFXJStudies on scaffold attachment sites and their relation to genomefunction.!Intnatl Rev Cyto 119:57-96 (1989)PubMed: 2695485;ReviewTGTTTWTGNTTTCCGAAANNNNWWWMARTBOXS000067 13-Feb-2001 (last modified) kehiZ"T-Box"; Motif found in SAR (scaffold attachment region; ormatrix attachment region, MAR);MARSART-boxscaffoldmatrixDrosophila; fly;-Gasser SM, Amati BB, Cardenas ME, Hofmann JFXJStudies on scaffold attachment sites and their relation to genomefunction.!Intnatl Rev Cyto 119:57-96 (1989)PubMed: 2695485;Review
TTWTWTTWTT MEJARELELOXS000151 17-May-1998 (last modified) kehi�MeJa-responsive element (MeJaRE) in tomato (L. e.) lipoxygenase(LOX) gene; Related to tomato lipoxygenase gene expression duringdevelopment and for MeJa (methyl jasmonate)-responsiveness; lipoxygenaseloxmethyl jasmonateshootleaf!tomato (Lycopersicon esculentum);Beaudoin N, Rothstein SJ^Developmental regulation of two tomato lipoxygenase promoters intransgenic tobacco and tomato. Plant Mol Biol 33:835-846 (1997))PubMed: 9106507; GenBank: U63117, U63118; GATACANNAATNTGATG
MNF1ZMPPC1S000251 11-Oct-1999 (last modified) kehiu"MNF1" binding site in maize (Z.m.) Ppc1 (phosphoenolpyruvatecarboxylase) gene promoter; Involved in light induction;MNF1Ppc1lightleafshootmaize (Zea mays) Morishima A�Identification of preferred binding sites of a light-inducibleDNA-binding factor (MNF1) within 5'-upstream sequence of C4-typephosphoenolpyruvate carboxylase gene in maize!Plant Mol Biol 38:633-646 (1998)PubMed: 9747808; GTGCCCTTMREATCHSS000356#02-August-2006 (last modified) kehi�"MREAtCHS (MRE = Myb Recognition Element)" found in the LRU(light-responsive unit) in Arabidopsis (A.t.) chalcone synthase(CHS) gene promoter; Required for UV-B and UV-A/blue lightresponsiveness; See S000355; CHSACEMYBlightUV-AUV-BleafshootMREArabidopsis thaliana�Hartmann U, Valentine WJ, Christie JM, Hays J, Jenkins GI,Weisshaar BHartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B.�iIdentification of UV/blue light-response elements in theArabidopsis thaliana chalcone synthase promoter using ahomologous protoplast transient expression systemDifferential combinatorial interactions of cis-acting elementsrecognized by R2R3-MYB, BZIP, and BHLH factors controllight-responsive and tissue-specific activation ofphenylpropanoid biosynthesis genes.DPlant Mol Biol (1998) 36: 741-754Plant Mol Biol. 57: 155-171 (2005). PubMed: 9526507;PubMed: 15821875 TCTAACCTACCA MRNA3ENDTAH3S000069 17-May-1998 (last modified) kehi�Cis element in 3' end region of wheat (T.a.) histone H3 mRNA; 3'end formation; Also found in histone genes of other plants,yeast, etc;
histone H3mRNA3' end formationmeristem!wheat (Triticum aestivum); yeast;Ohtsubo N, Iwabuchi M�The conserved 3'-flanking sequence, AATGGAAATG, of the wheathistone H3 gene is necessary for the accurate 3'-end formation ofmRNA.%Nucleic Acids Res 22:1052-1058 (1994)PubMed: 8152910;
AATGGAAATGMRNASTA1CRPSBDS000274 15-Oct-1999 (last modified) kehi�mRNA stability determinant found in 5'-UTR of psbD mRNA ofChlamydomonas reinhardtii (C.r.); Required for the stableaccumulation; Located within the first 12 nucleotides of theleader region;mRNA stability chloroplast5'-UTRpsbDChlamydomonas reinhardtii<Nickelsen J, Fleischmann M, Boudreau E, Rahire M, Rochaix JDnIdentification of cis-acting RNA leader elements required forchloroplast psbD gene expression in Chlamydomonas Plant Cell 11:957-970 (1999)PubMed: 10330479; CUCUUTGUTTUUMRNASTA2CRPSBDS000275 15-Oct-1999 (last modified) kehi�mRNA stability determinant found in 5'-UTR of psbD mRNA ofChlamydomonas reinhardtii (C.r.); Required for the stableaccumulation; Located near position -30 relative to the AUGinitiation codon;mRNA stability chloroplast5'-UTRpsbDChlamydomonas reinhardtii<Nickelsen J, Fleischmann M, Boudreau E, Rahire M, Rochaix JDnIdentification of cis-acting RNA leader elements required forchloroplast psbD gene expression in Chlamydomonas Plant Cell 11:957-970 (1999)PubMed: 10330479; UGAGUUGMSACRCYMS000236 17-May-1998 (last modified) kehi�"MSA (M-specific activator)" motif in Catharanthus roseus (C.r.)B-type cyclin (CYM) promoter; Essential for M phase-specificexpression; Found at -66 to -58;M phasecyclinCYMmeristemCatharanthus roseusRIto M, Iwase M, Kodama H, Lavisse P, Komamine A, Nishihama R,Machida Y, Watanabe AlA novel cis-acting element in promoters of plant B-type cyclingenes activates M phase-specific transcription Plant Cell 10:331-341 (1998)PubMed: 9501108; AGACCGTTGMYB1ATS000408 03-Jun-2003 (last modified) kehi}MYB recognition site found in the promoters of thedehydration-responsive gene rd22 and many other genes inArabidopsis; W=A/T;MYBrd22BP1ABAleafseedstressArabidopsis thaliana@Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-ShinozakiK.lArabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function astranscriptional activators in abscisic acid signaling.Plant Cell 15: 63-78 (2003)PubMed: 12509522; WAACCAMYB1LEPRS000443 28-Jan-2004 (last modified) kehi�Tomato Pti4(ERF) regulates defence-related gene expression viaGCC box and non-GCC box cis elements (Myb1(GTTAGTT), G box(CACGTG));Pti4ERFPRMYB7Arabidopsis thaliana; Lycopersicon esculentum (tomato);EChakravarthy S, Tuori RP, DAscenzo MD, Fobert PR, Despres C,Martin GBvThe tomato transcription factor Pti4 regulates defence-relatedgene expression via GCC box and non-GCC box cis elements Plant Cell 15: 3033-3050 (2003)PubMed: 14630974; GTTAGTTMYB26PSS000182 17-May-1998 (last modified) kehi�Myb26 binding site; Myb26 recognizes the c-Myb and P-box-likebinding sites representing cis-elements in the promoter regionsof several phenylpropanoid biosynthetic genes; Identical to P-boxin maize, and to Myb305 binding site in snapdragon;MYBmybMybmyb26P-boxP boxflowerpea (Pisum sativum)Uimari A, Strommer J\Myb26: a MYB-like protein of pea flowers with affinity forpromoters of phenylpropanoid genesPlant J 12:1273-1284 (1997)PubMed: 9450341; GTTAGGTTMYB2ATS000177 16-May-2001 (last modified) uchi�`Binding site for ATMYB2, an Arabidopsis MYB homolog; ATMYB2binds oligonucleotides that contained a consensus MYB recognitionsequence (TAACTG), such as is in the SV40 enhancer and the maizebronze-1 promoter (Urao et al., Plant Cell 5:1529 (1993)); ATMYB2is involved in regulation of genes that are responsive to waterstress in Arabidopsis; See S000355;MYBmybSV40enhancerbronzebronze-1leafshootArabidopsis thaliana;2Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki KAn Arabidopsis myb homolog is induced by dehydration stress andits gene product binds to the conserved MYB recognition sequence Plant Cell 5:1529-1539 (1993)!PubMed: 8312738; GenBank: D14712; TAACTGMYB2CONSENSUSATS000409 03-Jun-2003 (last modified) kehi�MYB recognition site found in the promoters of thedehydration-responsive gene rd22 and many other genes inArabidopsis; Y=C/T; K=G/T; See S000177 (MYB2), S000175(MYBATRD22);MYBrd22BP1ABAleafseedstressArabidopsis thaliana@Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-ShinozakiK.lArabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function astranscriptional activators in abscisic acid signaling.Plant Cell 15: 63-78 (2003)PubMed: 12509522; YAACKG MYBATRD22S000175 16-May-2001 (last modified) uchi�Binding site for MYB (ATMYB2) in dehydration-responsive gene,rd22; MYB binding site in rd22 gene of Arabidopsis thaliana;ABA-induction; Located at ca. -141 of rd22 gene; Also MYC at ca.-200 of rd22 gene; See S000174 (MYCATRD22); See S000355; Dehydration Water stressABAMYCleafshootArabidopsis thalianaWAbe H, Yamaguchi-Shinozaki k, Urao T, Iwasaki T, Hosokawa D,Shinozaki KBusk PK, Pages M�Role of Arabidopsis MYC and MYB homologs in drought- and abscisicacid-regulated gene expression.Regulation of abscisic acid-induced transcription=Plant Cell 9:1859-1868 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 9368419;PubMed: 9617810;ReviewCTAACCAMYBCORES000176 16-May-2001 (last modified) uchi�WBinding site for all animal MYB and at least two plant MYBproteins ATMYB1 and ATMYB2, both isolated from Arabidopsis;ATMYB2 is involved in regulation of genes that are responsive towater stress in Arabidopsis; A petunia MYB protein (MYB.Ph3) isinvolved in regulation of flavonoid biosynthesis (Solano et al.EMBO J 14:1773 (1995)); See S000355;MYBmyb dehydrationwaterstressflavonoid biosynthesisleafshoot8Arabidopsis thaliana; animal; petunia (Petunia hybrida);~Luscher B, Eiseman RNUrao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki KSolano R, Nieto C, Avila J, Canas L, Diaz I, Paz-Ares J�New light on Myc and Myb. Part II. Myb.An Arabidopsis myb homolog is induced by dehydration stress andits gene product binds to the conserved MYB recognition sequenceDual DNA binding specificity of a petal epidermis-specific MYBtranscription factor (MYB.Ph3) from Petunia hybridaTGenes Dev. 4:2235-2241 (1990)Plant Cell 5:1529-1539 (1993)EMBO J 14:1773-1784 (1995)APubMed: 2279697;PubMed: 8312738; GenBank: D14712;PubMed: 7737128;ReviewCNGTTRMYBCOREATCYCB1S000502&15-September-2006 (last modified) kehi�7"Myb core" in the 18 bp sequence which is able to activatereporter gene without leading to M-phase-specific expression,found in the promoter of Arabidopsis thaliana cyclin B1:1 gene;the 18 bp sequence share homology with a sequence found in the N.sylvestris cyclin B1 promoter (Trehin et al., 1999; seeS000283):CycM phaseMybArabidopsis thalianaAPlanchais S, Perennes C, Glab N, Mironov V, Inze D, BergouniouxC.�Characterization of cis-acting element involved in cell cyclephase-independent activation of Arath;CycB1;1 transcription andidentification of putative regulatory proteins."Plant Mol Biol. 50:111-127 (2002).PubMed: 12139003 AACGGMYBGAHVS000181&15-September-2006 (last modified) kehi��Central element of gibberellin (GA) response complex (GARC) inhigh-pI alpha-amylase gene in barley (H.v.); Similar to c-myb andv-myb consensus binding site; GAmyb binds specifically to theTAACAAA box in vitro; GAmyb is the sole GA-regulatedtranscriptional factor required for transcriptional activation ofthe high-pI alpha-amylase; GARC consist of the pyrimidine,TAACAAA and TATCCAC boxes; GARE in RAmy1A gene; GARE andpyrimidine box in RAmy1A are partially involved in sugarrepression; mybMybGAmybGA gibberellinGARC alph-amylaseamylasealeuroneGAREseed.barley (Hordeum vulgare); rice (Oryza sativa);�Gubler F, Kalla R, Roberts JK, Jacobsen JVMorita A, Umemura T, Kuroyanagi M, Futsuhara Y, Perata P,Yamaguchi JGubler F, Raventos D, Keys M, Watts R, Mundy J, Jacobsen JV.�KGibberellin-regulated expression of a myb gene in barley aleuronecells: evidence for Myb transactivation of a high-plalpha-amylase gene promoterFunctional dissection of a sugar-repressed alpha-amylase gene(Ramy1A) promoter in rice embryosTarget genes and regulatory domains of the GAMYB transcriptionalactivator in cereal aleurone.MPlant Cell 7:1879-1891 (1995)FEBS Lett 423:81-85 (1998)Plant J. 17:1-9(1999).0PubMed: 8535141;PubMed: 9506846;PubMed: 10069063 TAACAAAMYBPLANTS000167 16-May-2001 (last modified) uchi�@Plant MYB binding site; Consensus sequence related to box P inpromoters of phenylpropanoid biosynthetic genes such as PAL, CHS,CHI, DFR, CL, Bz1; Myb305; M=A/C; W=A/T; See S000355; TheAmMYB308 and AmMYB330 transcription factors from Antirrhinummajus regulate phenylpropanoid and lignin biosynthesis intransgenic tobacco;MybMYBMyb305AmMYB308AmMYB330flowerPALCHSDFRCandiBz1phenylpropanoidligninleafshoot�snapdragon (Antirrhinum majus); bean (Phaseolus vulgaris);petunia (Petunia hybrida); Arabidopsis thaliana; maize (Zeamays); parsley (Petroselinum crispum);�Sablowski RWM, Moyano E, Culianez-Macia FA, Schuch W, Martin C,Bevan MTamagnone L, Merida A, Parr A, Mackay S, Culianez-Macia FA,Roberts K, Martin C�A flower-specific Myb protein activates transcription ofphenylpropanoid biosynthetic genes.The AmMYB308 and AmMYB330 transcription factors from antirrhinumregulate phenylpropanoid and lignin biosynthesis in transgenictobacco5EMBO J 13:128-137 (1994)Plant Cell 10: 135-154 (1998) PubMed: 8306956;PubMed: 9490739; MACCWAMCMYBPZMS000179 17-May-1998 (last modified) kehi�Core of consensus maize P (myb homolog) binding site; W=A/T; 6 bpcore; Maize P gene specifies red pigmentation of kernel pericarp,cob, and other floral organs; P binds to A1 gene, but not Bz1gene; Maize C1 (myb homolog) activates both A1 and Bz1 genes(Grotewold et al. 1994); W=A/T;PP gene: P-geneMYBmybseedmaize (Zea mays);-Grotewold E, Drummond BJ, Bowen B, Peterson T�The myb-homologous P gene controls phlobaphene pigmentation inmaize floral organs by directly activating a flavonoidbiosynthetic gene subsetCell 76:543-553 (1994)PubMed: 8313474; CCWACCMYBST1S000180 17-Apr-1998 (last modified) kehi�Core motif of MybSt1 (a potato MYB homolog) binding site; MybSt1cDNA clone was isolated by using CaMV 35S promoter domain A as aprobe (Baranowskij et al. 1994); The Myb motif of the MybSt1protein is distinct from the plant Myb DNA binding domaindescribed so far;MYBmybMybpotato (Solanum tuberosum);/Baranowskij N, Frohberg C, Prat S, Willmitzer L�A novel DNA binding protein with homology to Myb oncoproteinscontaining only one repeat can function as a transcriptionalactivatorEMBO J 13:5383-5392 (1994)PubMed: 7957104; GGATA MYCATERD1S000413%29-November-2004 (last modified) kehi�MYC recognition sequence (from -466 to -461) necessary forexpression of erd1 (early responsive to dehydration) indehydrated Arabidopsis; NAC protein bound specifically to theCATGTG motif (Tran et al., 2004)); NAC protein bound specificallyto the CATGTG motif (Tran et al., 2004); water-stresserdArabidopsis thaliana�Simpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K,Yamaguchi-Shinozaki K.Tran LS, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K,Fujita M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K.�ZTwo different novel cis-acting elements of erd1, a clpAhomologous Arabidopsis gene function in induction by dehydrationstress and dark-induced senescence.Isolation and functional analysis of arabidopsis stress-inducibleNAC transcription factors that bind to a drought-responsivecis-element in the early responsive to dehydration stress 1promoter.<Plant J. 33: 259-270 (2003)Plant Cell. 16: 2481-2498 (2004).!PubMed: 12535340;PubMed: 15319476 CATGTG MYCATRD22S000174 29-Sep-1999 (last modified) kehi�� Binding site for MYC (rd22BP1) in Arabidopsis (A.t.)dehydration-resposive gene, rd22; MYC binding site in rd22 geneof Arabidopsis thaliana; ABA-induction; Located at ca. -200 ofrd22 gene; Also MYB at ca. -141 of rd22 gene; See also S000175(MYBATRD22); Dehydration Water stressABAMYCmycleafshootArabidopsis thalianaWAbe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D,Shinozaki KBusk PK, Pages M�Role of Arabidopsis MYC and MYB homologs in drought- and abscisicacid-regulated gene expression.Regulation of abscisic acid-induced transcription=Plant Cell 9:1859-1868 (1997)Plant Mol Biol 37:425-435 (1998) PubMed: 9368419;PubMed: 9617810;ReviewCACATGMYCCONSENSUSATS000407$04-January-2007 (last modified) kehi�MYC recognition site found in the promoters of thedehydration-responsive gene rd22 and many other genes inArabidopsis; Binding site of ATMYC2 (previously known asrd22BP1); see S000144 (E-box; CANNTG), S000174 (MYCATRD22);N=A/T/G/C; MYC recognition sequence in CBF3 promoter; Bindingsite of ICE1 (inducer of CBF expression 1) that regulates thetranscription of CBF/DREB1 genes in the cold in Arabidopsis; ICE1(Chinnusamy et al., 2004);) This sequence is also known as RRE (Rresponse element)(Hartmann et al., 2005); MYCrd22BP1ABAleafseedstressCBF3cold CBF/DREB1ICE1RREArabidopsis thaliana��Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-ShinozakiK.Chinnusamy V, Ohta M, Kanrar S, Lee BH, Hong X, Agarwal M, ZhuJK.Chinnusamy V, Schumaker K, Zhu JK.Oh SJ, Song SI, Kim YS, Jang HJ, Kim SY, Kim M, Kim YK, Nahm BH,Kim JK.Lee BH, Henderson DA, Zhu JK.Hartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B.Agarwal M, Hao Y, Kapoor A, Dong CH, Fujii H, Zheng X, Zhu JK.� Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function astranscriptional activators in abscisic acid signaling.ICE1: a regulator of cold-induced transcriptome and freezingtolerance in Arabidopsis.Molecular genetic perspectives on cross-talk and specificity inabiotic stress signalling in plants.Arabidopsis CBF3/DREB1A and ABF3 in transgenic rice increasedtolerance to abiotic stress without stunting growth.The Arabidopsis Cold-Responsive Transcriptome and Its Regulationby ICE1.Differential combinatorial interactions of cis-acting elementsrecognized by R2R3-MYB, BZIP, and BHLH factors controllight-responsive and tissue-specific activation ofphenylpropanoid biosynthesis genes.A R2R3 type MYB transcription factor is involved in the coldregulation of CBF genes and in acquired freezing tolerance.�Plant Cell 15: 63-78 (2003)Genes Dev. 17: 1043-1054 (2003)J Exp Bot. 55: 225-236 (2004).Plant Physiology 138: 341-351 (2005)Plant Cell. 17: 3155-3175 (2005)Plant Mol Biol. 57: 155-171(2005).J Biol Chem. 281:37636-37645 (2006)rPubMed: 12509522;PubMed: 12672693;PubMed: 14673035PubMed: 15834008PubMed: 16214899PubMed: 15821875PubMed: 17015446Review.CANNTG NAPINMOTIFBNS000070 17-May-1998 (last modified) kehi�Sequence found in 5' upstream region (-6, -95, -188) of napin (2Salbumin) gene in Brassica napus (B.n.); Interact with a proteinpresent in crude nuclear extracts from developing B. napusseeds;napin
2S albuminseedstorage proteinrape (Brassica napus):Ericson ML, Muren E, Gustavsson H-O, Josefsson L-G, Rask L�Analysis of the promoter region of napin genes from Brassicanapus demonstrates binding of nuclear protein in vitro to aconserved sequence motif. Eur J Biochem 197:741-746 (1991)!PubMed: 2029903; GenBank: X58142; TACACAT NDEGMSAURS000359 16-Feb-2001 (last modified) seki�"NDE" found in Soybean (G.m.) SAUR (Small Auxin-Up RNA) 15A genepromoter; Required for auxin responsiveness; Contains twoadjacent sequences, TGTCTC (see S000270) and GGTCCCAT, which havebeen previously identified as putative auxin-responsive elements;See S000360;NDESAURAuxinSoybean (Glycine max)*Li Y, Liu ZB, Shi X, Hagen G, Guilfoyle TJ4An auxin-inducible element in soybean SAUR promoters Plant Physiol 106:37-43 (1994)PubMed: 7972520; CCATATGCCATGTCTCTCAATTGGTCCCAT NODCON1GMS000461"24-April-2005 (last modified) kehiMOne of two putative nodulin consensus sequences; See also S000462(NODCON2GM);nodulinGlycine max (soybean)^Sandal NN, Bojsen K, Marcker KA.Stougaard J, Jorgensen JE, Christensen T, Kuhle A, Marcker KA.�A small family of nodule specific genes from soybean.Interdependence and nodule specificity of cis-acting regulatoryelements in the soybean leghemoglobin lbc3 and N23 genepromoters.JNucleic Acids Res. 15:1507-1519 (1987).Mol Gen Genet. 220: 353-360 (1990). PubMed: 3822835PubMed: 2338938consesus; in silico;AAAGAT NODCON2GMS000462"24-April-2005 (last modified) kehiMOne of two putative nodulin consensus sequences; See also S000461(NODCON1GM);nodulinGlycine max (soybean)^Sandal NN, Bojsen K, Marcker KA.Stougaard J, Jorgensen JE, Christensen T, Kuhle A, Marcker KA.�A small family of nodule specific genes from soybean.Interdependence and nodule specificity of cis-acting regulatoryelements in the soybean leghemoglobin lbc3 and N23 genepromoters.JNucleic Acids Res. 15:1507-1519 (1987).Mol Gen Genet. 220: 353-360 (1990). PubMed: 3822835PubMed: 2338938consesus; in silico;CTCTT NONAMERATH4S000147 10-May-1998 (last modified) kehi@Nonamer motif of Arabidopsis thaliana (A.t.) histone H4promoter;nonamerhistoneH4meristemArabidopsis thaliana;2Chaubet N, Flenet M, Clement B, Brignon P, Gigot CZIdentification of cis-elements regulating the expression of anArabidopsis histone H4 gene.Plant J 10:425-435 (1996)PubMed: 8811858; AGATCGACGNONAMERMOTIFTAH3H4S000071 17-May-1998 (last modified) kehiI"Nonamer motif" found in promoter of wheat (T.a.) histone genesH3 and H4;HBP-1AHBP-1B
wheat histoneCaMV 35SNOSmeristem wheat (Triticum aestivum); CaMV;FNakayama T, Sakamoto A, Yang P, Minami M, Fujimoto Y, Ito T,Iwabuchi MvHighly conserved hexamer, octamer and nonamer motifs are positivecis-regulatory elements of the wheat histone H3 gene. FEBS Lett 300:167-170 (1992)!PubMed: 1563517; GenBank: S95162; CATCCAACG NRRBNEXTAS000242 11-0ct-1999 (last modified) kehi�"NRR (negative regulatory region)" in promoter region of Brassicanapus (B.n.) extA extensin gene; Removal of this region leads toexpression in all tissues within the stem internode, petiole androot;extextensinstem internodepetiolerootBrassica napusElliott KA , Shirsat AH{Promoter regions of the extA extensin gene from Brassica napuscontrol activation in response to wounding and tensile stress!Plant Mol Biol 37:675-687 (1998)PubMed: 9687071; TAGTGGAT NTBBF1ARROLBS000273 15-Oct-1999 (last modified) kehi�NtBBF1(Dof protein from tobacco) binding site in Agrobacteriumrhizogenes (A.r.) rolB gene; Found in regulatory domain B (-341to -306); Required for tissue-specific expression and auxininduction;rolBDofauxindomain BrootshootmeristemvascularAgrobacterium rhizogenes1Baumann K, De Paolis A, Costantino P, Gualberti G�The DNA binding site of the Dof protein NtBBF1 is essential fortissue-specific and auxin-regulated expression of the rolBoncogene in plants Plant Cell 11:323-333 (1999)%PubMed: 10072394; GenBank: AJ009594; ACTTTA O2F1BE2S1S000162 17-May-1998 (last modified) kehi�opaque-2 recognition site F1 in Bertholletia excelsa (Brazil nuttree) 2S storage protein gene (be2S1); O2 protein binds to F1, F2and F3 sequences of be2S1 promoter; F1 is hybrid C/G box;O2opaque-2be2S1F1seed'Brazil nut tree (Bertholletia excelsa);~Vincentz M, Leite A, Neshich G, Vriend G, Mattar C, Barros L,Weinberg D, de Almeida ER, Paes de Carvalho M, Aragao F, GanderES�ACGT and vicilin core sequences in a promoter domain required forseed-specific expression of a 2S storage protein gene arerecognized by the opaque-2 regulatory protein. Plant Mol Biol 34:879-889 (1997)!PubMed: 9290640; GenBank: X78287;
TCCACGTCGA O2F2BE2S1S000163 17-May-1998 (last modified) kehi�.opaque-2 recognition site F2 in Bertholletia excelsa (Brazil nuttree) 2S storage protein gene (be2S1); O2 protein binds to F1, F2and F3 sequences of be2S1 promoter; F2 is a new O2-bindingsequence related to the O2 target sites of the Coix alpha-coxin,the maize b-32 genes and the AP-1 pseudopalindrome;O2opaque-2be2S1seed&Brazil nut tree (Bertholletia excelsa)~Vincentz M, Leite A, Neshich G, Vriend G, Mattar C, Barros L,Weinberg D, de Almeida ER, Paes de Carvalho M, Aragao F, GanderES�ACGT and vicilin core sequences in a promoter domain required forseed-specific expression of a 2S storage protein gene arerecognized by the opaque-2 regulatory protein. Plant Mol Biol 34:879-889 (1997)!PubMed: 9290640; GenBank: X78287;
GCCACCTCAT O2F3BE2S1S000164 17-May-1998 (last modified) kehi�opaque-2 recognition site F3 in Bertholletia excelsa (Brazil nuttree) 2S storage protein gene (be2S1); O2 protein binds to F1, F2and F3 sequences of be2S1 promoter; F3 is hybrid of A/G box;O2opaque-2be2S1seed&Brazil nut tree (Bertholletia excelsa)~Vincentz M, Leite A, Neshich G, Vriend G, Mattar C, Barros L,Weinberg D, de Almeida ER, Paes de Carvalho M, Aragao F, GanderES�ACGT and vicilin core sequences in a promoter domain required forseed-specific expression of a 2S storage protein gene arerecognized by the opaque-2 regulatory protein. Plant Mol Biol 34:879-889 (1997)!PubMed: 9290640; GenBank: X78287;
TCCACGTACT
OBF5ATGST6S000304 29-Sep-2003 (last modified) kehi��"OBF5 (ocs element binding factor 5)" binding site found in theArabidopsis (A.t.) GST6 gene promoter; Similar to Ocs sequence;Located between -426 and -401; See S000305; Overexpression ofOBP3 lead to severe growth defect with altered root developmentand yellowish leaves; All OBP proteins contain transcriptionalactivation domains in their C-terminal region; Dof protein playimportant roles in plant growth and development; Binding site ofOBF4 and OBF5; See S000305, S000346; GSTOcsOBFOBPauxinSAcycloheximide, DofTGApathogenrootleafshoot"Arabidopsis (Arabidopsis thaliana)rChen W, Chao G, Singh KBKang HG, Singh KBZhang B, Foley RC, Singh KBZhang B, Chen W, Foley RC, Buttner M, Singh KB��The promoter of a H202-inducible, Arabidopsis glutathioneS-transferase gene contains closely linked OBF- and OBP1-bindingsitesCharacterization of salicylic acid-responsive, Arabidopsis Dofdomain proteins: Overexpression of OBP3 leads to growth defectsIsolation and characterization of two related Arabidopsisocs-element bZIP binding proteinsInteractions between distinct types of DNA binding proteinsenhance binding to ocs element promoter sequenceskPlant J 10: 955-966 (1996)Plant J 21: 329-339 (2000)Plant J (1993) 4: 711-716Plant Cell 7: 2241-2252 (1995)kPubMed: 9011080;PubMed: 10758484;PubMed: 8252072; GenBank: X69899; X69900;PubMed: 8718629; GenBank: X89192; ATCTTATGTCATTGATGACGACCTCC
OBP1ATGST6S000305 29-Sep-2003 (last modified) kehi��OBP1, 4, and 5 (OBF binding protein) binding site found in theArabidopsis (A.t.) GST6 gene promoter; Located between -398 and-388; OBP1 is able to stimulate the binding of OBF proteins tothe GST6 promoter; See S000304; Overexpression of OBP3 lead tosevere growth defect with altered root development and yellowishleaves; All OBP proteins contain transcriptional activationdomains in their C-term. region; Dof protein play important rolesin plant growth and development; See S000304;
GSTOcsOBFOBPauxinSAcycloheximide, Dofrootleafshoot"Arabidopsis (Arabidopsis thaliana)rChen W, Chao G, Singh KBKang HG, Singh KBZhang B, Foley RC, Singh KBZhang B, Chen W, Foley RC, Buttner M, Singh KB��The promoter of a H202-inducible, Arabidopsis glutathioneS-transferase gene contains closely linked OBF- and OBP1-bindingsitesCharacterization of salicylic acid-responsive, Arabidopsis Dofdomain proteins: Overexpression of OBP3 leads to growth defectsIsolation and characterization of two related Arabidopsisocs-element bZIP binding proteinsInteractions between distinct types of DNA binding proteinsenhance binding to ocs element promoter sequenceskPlant J 10: 955-966 (1996)Plant J 21: 329-339 (2000)Plant J (1993) 4: 711-716Plant Cell 7: 2241-2252 (1995)kPubMed: 9011080;PubMed: 10758484;PubMed: 8252072; GenBank: X69899; X69900;PubMed: 8718629; GenBank: X89192; TACACTTTTGGOCETYPEIIINTHISTONES000269 15-Oct-1999 (last modified) kehi�"Type III element"; Oct-containing composite element Type IIIfound in tobacco (N.t.) histone gene promoter; Oct (octomer)motif is paired with CCAAT-box to form Type III element; Requiredfor S-phase specific and meristematic tissue-specificexpression;histoneOctOCE CCAAT-boxType IIIS-phasemeristemtobacco (Nicotiana tabacum)9Taoka K, Kaya H, Nakayama T, Araki T, Meshi T, Iwabuchi MzIdentification of three Kinds of mutually related compositeelements conferring S phase-specific transcriptional activationPlant J 18:611-623 (1999)PubMed: 10417712; GATCCGCGNNNNNNNNNNNNNNACCAATCSOCETYPEIINTHISTONES000268 15-Oct-1999 (last modified) kehi�"Type II element"; Oct-containing composite element Type II foundin tobacco (N.t.) histone gene promoter; Oct (octomer) motif ispaired with TCA motif to form Type II element; Required forS-phase specific and meristematic tissue-specific expression;histoneOctOCE TCA-motifType IIS-phasemeristemtobacco (Nicotiana tabacum)9Taoka K, Kaya H, Nakayama T, Araki T, Meshi T, Iwabuchi MzIdentification of three Kinds of mutually related compositeelements conferring S phase-specific transcriptional activationPlant J 18:611-623 (1999)PubMed: 10417712; TCACGCGGATCOCETYPEINTHISTONES000267 15-Oct-1999 (last modified) kehi�"Type I element"; Oct-containing composite element Type I foundin tobacco (N.t.) histone gene promoter; Oct (octomer) motif ispaired with Hex motif to form Type I element; Required forS-phase specific and meristematic tissue-specific expression;histoneOctOCE Hex-motifType ImeristemS-phasetobacco (Nicotiana tabacum)9Taoka K, Kaya H, Nakayama T, Araki T, Meshi T, Iwabuchi MzIdentification of three Kinds of mutually related compositeelements conferring S phase-specific transcriptional activationPlant J 18:611-623 (1999)PubMed: 10417712; CCACGTCANCGATCCGCG OCSELEMENTATS000158 16-Feb-2001 (last modified) seki��"OCS element" in octopine synthase gene (OCS) of Ti-plasmid ofAgrobacterium (A.t.); Binding with nuclear protein isolated fromtobacco; See OCS motif (S000074); "ocs-like element"; Also foundin Arabidopsis glutathione S-transferase gene (GST6); OBF (ocselement binding factor)-binding site; See S000346; Tandem OCSTFbinding-sites are essential for the activity of the Ocs-element;The Ocs-element occures rarely in plant gene promoters; SeeS000357;octopine synthaseocsGST6glutathione S-transferase9Agrobacterium tumefaciens; tobacco; Arabidopsis thaliana;�Bouchez D, Tokuhisa JG, Llewellyn DJ, Dennis ES, Ellis JGFoley RC, Grossman C, Ellis JG, Llewellyn DJ, Dennis ES, PeacockWJ, Singh KBChen W, Chao G, Singh KBEllis JG, Tokuhisa JG, Llewellyn DJ, Bouchez D, Singh K, DennisES, Peacock WJ��The ocs-element is a component of the promoters of several T-DNAand plant viral genes.Isolation of a maize bZIP protein subfamily: candidates for theocs-element transcription factor.The promoter of a H2O2-inducible, Arabidopsis glutathioneS-transferase gene contains closely linked OBF- and OBP1-bindingsitesDoes the ocs-element occur as a functional component of thepromoters of plant genes?dEMBO J 8:4197-4204 (1989)Plant J 3: 669-679 (1993)Plant J 10:955-966 (1996)Plant J (1993) 4: 433-443@PubMed: 2591372;PubMed: 8374617;PubMed: 9011080;PubMed: 8220489; TGACGYAAGSRMTKACGYMMOCSENHANMOTIFATS000074 16-Feb-2001 (last modified) seki��"OCS enhancer element" in octopine synthase gene (OCS) ofTi-plasmid of Agrobacterium tumefaciens (A.t.); Binding withnuclear protein isolated from tobacco and maize; See S000346;Tandem OCSTF binding-sites are essential for the activity of theOcs-element; The Ocs-element occures rarely in plant genepromoters; See S000357; "OCS palindrome" found in tobacco (N.t.)OCS (Octopine synthase gene) promoter; Located at -193 to -178;Binding site of ASF-1; Confers expression of the gene;octopine synthaseocsenhancerASF-1HAgrobacterium tumefaciens; tobacco (Nicotiana tabacum); maize(Zea mays);�Singh K, Tokuhisa JG, Dennis ES, Peacock WJEllis JG, Tokuhisa JG, Llewellyn DJ, Bouchez D, Singh K, DennisES, Peacock WJFromm H, Katagiri F, Chua NHTokuhisa JG, Singh K, Dennis ES, Peacock WJ��Saturation mutagenesis of the octopine synthase enhancer:correlation of mutant phenotypes with binding of a nuclearprotein factor.Does the ocs-element occur as a functional component of thepromoters of plant genes?An octopine synthase enhancer element directs tissue-specificexpression and binds ASF-1, a factor from tobacco nuclearextractsA DNA-binding protein factor recognizes two binding domainswithin the octopine synthase enhancer element{Proc Natl Acad Sci USA 86:3733-3737 (1989)Plant J (1993) 4: 433-443Plant Cell 1: 977-984 (1989)Plant Cell 2: 215-224 (1990)@PubMed: 2726750;PubMed: 8220489;PubMed: 2562557;PubMed: 2152113; ACGTAAGCGCTTACGT OCSGMGH24S000346 16-Feb-2001 (last modified) seki�q"OCS element" found in the soybean (G.m) GH2/4 gene promoter;Required for auxin and salycylic acid responsiveness; Activatedby both active and inactive auxin and salicylic acid analogues;See S000074, S000130, S000158, S000304; Tandem OCSTFbinding-sites are essential for the activity of the Ocs-element;The Ocs-element occurs rarely in plant gene promoters; SeeS000357;OCSauxinsalicylic acidGH2/4Soybean (Glycine max)lUlmasov T, Hagen G, Guilfoyle TEllis JG, Tokuhisa JG, Llewellyn DJ, Bouchez D, Singh K, DennisES, Peacock WJ�The ocs element in the soybean GH2/4 promoter is activated byboth active and inactive auxin and salicylic acid analoguesDoes the ocs-element occur as a functional component of thepromoters of plant genes?<Plant Mol Biol 26: 1055-1064 (1994)Plant J (1993) 4: 433-443 PubMed: 7811965;PubMed: 8220489; CGGTTTACGTAATCTCTTACATCA OCSGMHSP26AS000357 16-Feb-2001 (last modified) seki�Ocs element found in soybean (Glycine max) heat shock gene(Gmhsp26-A) promoter; The element is a functional ocs-element;The element did not affect the promoter's response to heat orwounding;OcsHspSoybean (Glycine max)MEllis JG, Tokuhisa JG, Llewellyn DJ, Bouchez D, Singh K, DennisES, Peacock WJTDoes the ocs-element occur as a functional component of thepromoters of plant genes?Plant J (1993) 4: 433-443PubMed: 8220489; TGATGTAAGAGATTACGTAAOCTAMERMOTIFTAH3H4S000076 11-May-2006 (last modified) kehi�."Octamer motif" found in promoter of wheat (T.a.) histone genesH3 and H4, and corn histone genes H3 and H4; Arabidopsis histoneH4; "histone-specific octamer"; About half of the Oct motifs arepresent together with another element, HexA, TCA or CCAAT-box,forming OCES (Oct-containing composite elements);histoneOctS-phaseCaMV 35SNOSmeristemdwheat (Triticum aestivum); maize (Zea mays); CaMV; Arabidopsisthaliana; tobacco (Nicotiana tabacum);�Chaubet N, Philipps G, Chaboute M-E, Ehling M, Gigot CNakayama T, Sakamoto A, Yang P, Minami M, Fujimoto Y, Ito T,Iwabuchi MChaubet N, Flenet M, Clement B, Brignon P, Gigot CTaoka K, Kaya H, Nakayama T, Araki T, Meshi T, Iwabuchi M��Nucleotide sequences of two corn histone H3 genes. Genomicorganization of the corn histone H3 and H4 genes.Highly conserved hexamer, octamer and nonamer motifs are positivecis-regulatory elements of the wheat histone H3 gene.Identification of cis-elements regulating the expression of anArabidopsis histone H4 gene.Identification of three Kinds of mutually related compositeelements conferring S phase-specific transcriptional activationmPlant Mol Biol 6:253-263 (1986)FEBS Lett 300:167-170 (1992)Plant J 10:425-435 (1996)Plant J 18:611-623 (1999)BPubMed: 1563517; GenBank: S95162;PubMed: 8811858;PubMed: 10417712; CGCGGATC
OCTAMOTIF2S000116 17-May-1998 (last modified) kehi�Octamer motif found in histone-gene-specific consensus sequences;200 base upstream from the initiation codon ATG; Exist in all ofseven plant histone genes;octamerhistonemeristemmaize (Zea mays);6Chaubet N, Philipps G, Chaboute M-E, Ehling M, Gigot ClNucleotide sequences of two corn histone H3 genes. Genomicorganization of the corn histone H3 and H4 genes. Plant Mol Biol 6:253-263 (1986) CGCGGCAT OPAQUE2ZM22ZS000017 17-May-2001 (last modified) uchi�Opaque-2 (O2) target sequence in maize (Z.m.) 22- and 27-kD zeinpromoters; "ACGT motif"; Related to seed expression; "O2 targetsequence"; Gene: maize 22-kD zein; transacting factor: 02;O2opaque
22-kD zeinseedACGTopaque-2maize (Zea mays)�Schmidt RJ, Ketudat M, Aukerman MJ, Hoschek GThomas TLUeda T, Waverczak W, Ward K, Sher N, Ketudat M, Schmidt RJ,Messing JSingh KB�OOpaque-2 is a transcriptional activator that recognizes aspecific target site in 22-kD zein genesGene expression during plant embryogenesis and germination: Anoverview.Mutations of the 22- and 27-kD zein promoters affecttransactivation by the opaque-2 proteinTranscriptional Regulation in Plants: The Importance ofCombinatorial ComtroluPlant Cell 4:689-700 (1992)Plant Cell 5:1401-1410 (1993)Plant Cell 4:701-709 (1992)Plant Pysiol 118: 1111-1120 (1998)PPubMed: 1392590; GenBank: M86591;PubMed: 8281041;PubMed: 1392591;PubMed: 9847085 Reviewreview
TCCACGTAGA OPAQUE2ZMB32S000077 17-May-1998 (last modified) kehi�"opaque-2 binding site" of maize (Z.m.) b-32 (type Iribosome-inactivating protein gene; O2; O2S; O2S and GARE form agibberellin response complex (GARC)(Rogers and Rogers, 1992); opaque-2o2b-32O2O2Scoupling elementGARCGAREseedmaize (Zea mays)�#Muller M, Muth JR, Gallusci P, Knudsen S, Maddaloni M, Motto M,Schmitz D, Sorensen MB, Salamini F, von Wettstein D, Thompson RDCroissant-Sych Y, Okita TWLohmer S, Maddaloni M, Motto M, Di Fonzo N, Hartings H, SalaminiF, Thompson RDRogers JC, Rogers SWLanahan MB, Ho THD, Rogers SW, Rogers JC��Regulation of storage protein synthesis in cereal seeds:developmental and nutritional aspects.Identification of positive and negative regulatory cis-elementsof the rice glutelin Gt3 promoter.The maize regulatory locus Opaque-2 encodes a DNA-binding proteinwhich activates the transcription of the b-32 gene.Definition and functional implications of gibberellin andabscisic acid cis-acting hormone response complexes.A gibberellin response complex in cereal alpha-amylase genepromoters.�J Plant Physiol 145:606-613 (1995)Plant Science 116:27-35 (1996)EMBO J 10:617-624 (1991)Plant Cell 4:1443-1451 (1992)Plant Cell 4:203-211 (1992)0PubMed: 2001677;PubMed: 1477557;PubMed: 1386000;
GATGAYRTGGOSE1ROOTNODULES000467"24-April-2005 (last modified) kehi�One of the consensus sequence motifs of organ-specific elements(OSE) characteristic of the promoters activated in infected cellsof root nodules; See also S000468;
leghemoglobinLb29rootnodule arbuscule@Vicia faba; Medicago truncatula; Glycine max; Sesbania rostrata;�Vieweg MF, Fruhling M, Quandt HJ, Heim U, Baumlein H, Puhler A,Kuster H, Andreas MP.Fehlberg V, Vieweg MF, Dohmann EM, Hohnjec N, Puhler A, PerlickAM, Kuster H.��The promoter of the Vicia faba L. leghemoglobin gene VfLb29 isspecifically activated in the infected cells of root nodules andin the arbuscule-containing cells of mycorrhizal roots fromdifferent legume and nonlegume plants.The promoter of the leghaemoglobin gene VfLb29: functionalanalysis and identification of modules necessary for itsactivation in the infected cells of root nodules and in thearbuscule-containing cells of mycorrhizal roots.IMol Plant Microbe Interact. 17: 62-69 (2004).J Exp Bot. 56:799-806 (2005) PubMed: 14714869PubMed: 15668224 AAAGATOSE2ROOTNODULES000468"24-April-2005 (last modified) kehi�One of the consensus sequence motifs of organ-specific elements(OSE) characteristic of the promoters activated in infected cellsof root nodules; See also S000467;
leghemoglobinLb29rootnodule arbuscule@Vicia faba; Medicago truncatula; Glycine max; Sesbania rostrata;�Vieweg MF, Fruhling M, Quandt HJ, Heim U, Baumlein H, Puhler A,Kuster H, Andreas MP.Fehlberg V, Vieweg MF, Dohmann EM, Hohnjec N, Puhler A, PerlickAM, Kuster H.��The promoter of the Vicia faba L. leghemoglobin gene VfLb29 isspecifically activated in the infected cells of root nodules andin the arbuscule-containing cells of mycorrhizal roots fromdifferent legume and nonlegume plants.The promoter of the leghaemoglobin gene VfLb29: functionalanalysis and identification of modules necessary for itsactivation in the infected cells of root nodules and in thearbuscule-containing cells of mycorrhizal roots.IMol Plant Microbe Interact. 17: 62-69 (2004).J Exp Bot. 56:799-806 (2005) PubMed: 14714869PubMed: 15668224 CTCTTP1BSS000459"27-March-2004 (last modified) kehi�PHR1-binding sequence found in the upstream regions of phosphatestarvation responsive genes from several plant species; phr1(phosphate starvation response 1) gene codes for PHR1 proteinrelated to PSR1 gene in C. reinhardtii; phosphate
starvationMYBeArabidopsis thaliana; Lycopersicon esculentum (tomato); Medicagotruncatula; Hordeum vulgare (barley);�Rubio V, Linhares F, Solano R, Martin AC, Iglesias J, Leyva A,Paz-Ares J.Schunmann PH, Richardson AE, Smith FW, Delhaize E.Schunmann PH, Richardson AE, Vickers CE, Delhaize E.��A conserved MYB transcription factor involved in phosphatestarvation signaling both in vascular plants and in unicellularalgae.Characterization of promoter expression patterns derived from thePht1 phosphate transporter genes of barley (Hordeum vulgare L.).Promoter analysis of the barley Pht1;1 phosphate transporter geneidentifies regions controlling root expression and responsivenessto phosphate deprivation.bGenes Dev. 15: 2122-2133.(2001)J Exp Bot. 55: 855-865. (2004)Plant Physiol. 136: 4205-4214. (2004)0PubMed: 11511543PubMed: 15020637PubMed: 15542491 GNATATNC PALBOXAPCS000137$06-January-2006 (last modified) kehi��Box A; Consensus; One of three putative cis-acting elements(boxes P, A, and L) of phenylalanine ammonia-lyase (PAL; EC4.3.1.5) genes in parsley (P.c.); "None of these elements (boxesP, A, and L) alone, or the promoter region containing all of themtogether, conferred elicitor or light responsiveness. Theseelements appear to be necessary but not sufficient for elicitor-or light-mediated PAL gene activation." (Logemann et al., 1995);See also S000136 (Box P), S000138 (Box L);Box APAL parsley (Petroselinum crispum)#Logemann E, Parniske M, Hahlbrock KuModes of expression and common structural features of thecomplete phenylalanine ammonia-lyase gene family in parsley.*Proc Natl Acad Sci USA 92:5905-5909 (1995)1PubMed: 7597051; GenBank: L37355, L37356, L37357; CCGTCC PALBOXLPCS000138$06-January-2006 (last modified) kehi��Box L; Consensus; One of three putative cis-acting elements(boxes P, A, and L) of phenylalanine ammonia-lyase (PAL; EC4.3.1.5) genes in parsley (P.c.); "None of these elements (boxesP, A, and L) alone, or the promoter region containing all of themtogether, conferred elicitor or light responsiveness. Theseelements appear to be necessary but not sufficient for elicitor-or light-mediated PAL gene activation." (Logemann et al., 1995);See also S000136 (Box P), S000137 (Box A);Box LPAL parsley (Petroselinum crispum)#Logemann E, Parniske M, Hahlbrock KuModes of expression and common structural features of thecomplete phenylalanine ammonia-lyase gene family in parsley.*Proc Natl Acad Sci USA 92:5905-5909 (1995)1PubMed: 7597051; GenBank: L37355, L37356, L37357; YCYYACCWACC PALBOXPPCS000136$06-January-2006 (last modified) kehi��Box P; Consensus; One of three putative cis-acting elements(boxes P, A, and L) of phenylalanine ammonia-lyase (PAL; EC4.3.1.5) genes in parsley (P.c.); "None of these elements (boxesP, A, and L) alone, or the promoter region containing all of themtogether, conferred elicitor or light responsiveness. Theseelements appear to be necessary but not sufficient for elicitor-or light-mediated PAL gene activation." (Logemann et al., 1995);See also S000137 (Box A), S000138 (Box L);Box PPAL parsley (Petroselinum crispum)#Logemann E, Parniske M, Hahlbrock KuModes of expression and common structural features of thecomplete phenylalanine ammonia-lyase gene family in parsley.*Proc Natl Acad Sci USA 92:5905-5909 (1995)1PubMed: 7597051; GenBank: L37355, L37356, L37357; YTYYMMCMAMCMMCPALINDROMICCBOXGMS000255!23-June-2006 (last modified) kehi�Palindromic C-box in soybean (G.m.); bZIP factors, STGA1 and STFs(STF1 and STF2) found in soybean apical hypocotyl, bind to thissequence;C-boxbZIPSTGA1STF hypocotylTGASA*Glycine max(soybean); Arabidopsis thaliana�Cheong YH, Yoo CM, Park JM, Ryu GR, Goekjian VH , Nagao RT, KeyJL, Cho MJ, Hong JCThibaud-Nissen F, Wu H, Richmond T, Redman JC, Johnson C, GreenR, Arias J, Town CD�#STF1 is a novel TGACG-binding factor with a zinc-finger motif anda bZIP domain which heterodimerizes with GBF proteinsDevelopment of Arabidopsis whole-genome microarrays and theirapplication to the discovery of binding sites for the TGA2transcription factor in salicylic acid-treated plants.3Plant J 15:199-209 (1998)Plant J 47:152-162 (2006)PubMed: 9721678;>in silico based on whole-genome microarray analysis after ChIPTGACGTCA PASNTPARAS000336 7-Sep-2000 (last modified) seki�"pas"; as-1-related element found in the tobacco (N.t.) parA genepromoter; Involved in Cadmium responsiveness; Not related tocopper responsiveness; Located between -68 and -49;parApascadmiumas-1tobacco (Nicotiana tabacum) Kusaba M, Takahashi Y, Nagata TrA multiple-stimuli-responsive as-1-related element of parA geneconfers responsiveness to cadmium but not to copper#Plant Physiol 111: 1161-1167 (1996)PubMed: 8756498; TTACGCAAGCAATGACATCT
PE1ASPHYA3S000196 17-May-1998 (last modified) kehi�PE1; Positively acting element found at -381 to -348 of oat(A.s.) phyA3 promoter; A general positive element (Terzaghi &Cashmore, 1995); phytochromephyphyAphyA3leafshootoat (Avena sativa);FBruce WB, Quail PHBruce WB, Deng X-W, Quial PHTerzaghi WB, Cashmore AR�cis-Acting elements involved in photoregulation of an oatphytochrome promoter in riceA negatively acting DNA sequence element mediatesphytochrome-directed repression of phyA gene transcription.Light-regulated transcriptionnPlant Cell 2:1081-1089 (1990)EMBO J 10:3015-3024 (1991)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995) PubMed: 2152109;PubMed: 1915276;ReviewGAAATAGCAAATGTTAAAAATA PE2FNTRNR1AS000455%29-November-2004 (last modified) kehi�$"pE2F (proximal E2F elemen)" at -143bp of tobacco (N.t.) RNR1apromoter; E2F factors involved in gene induction at the G1/Stransition of the cell cycle; Important for regulating specificRNR1a (ribonucleotide reductase large subunit) gene expression inresponse to UV-C irradiation; See S000367;E2FRNR1aUV-C
cell cycleG1SNicotiana tabacum (tobacco)#Lincker F, Philipps G, Chaboute ME.�UV-C response of the ribonucleotide reductase large subunitinvolves both E2F-mediated gene transcriptional regulation andprotein subcellular relocalization in tobacco cells.*Nucleic Acids Res. 32: 1430-1438 (2004). .PubMed: 14990748 ATTCGCGC
PE3ASPHYA3S000197 17-May-1998 (last modified) kehiePE3; Positively acting element found at -111 to -81 (Bruce etal., 1991) of oat (A.s.) phyA3 promoter; phytochromephyphyAphyA3leafshootoat (Avena sativa);.Bruce WB, Quail PHBruce WB, Deng X-W, Quial PH�cis-Acting elements involved in photoregulation of an oatphytochrome promoter in riceA negatively acting DNA sequence element mediatesphytochrome-directed repression of phyA gene transcription.7Plant Cell 2:1081-1089 (1990)EMBO J 10:3015-3024 (1991) PubMed: 2152109;PubMed: 1915276; CAGCTCCCATGGCTCTCCCATCCGCGCCGGTPIATGAPBS000381 23-Aug-2001 (last modified) uchi�"PI" found in the Arabidopsis thaliana(A.T.) GAPB gene promoter;Located between -157 and -150; Mutations in the "PI" resulted inreductions of light-activated gene transcription; GAPB encodesthe B subunit of chloroplast glyceraldehyde-3-phosphatedehydrogenase(GADPH) of A.T.;GAPB(glyceraldehyde-3-phosphate dehydrogenaselight-activated
transcriptionArabidopsis thalianaChan CS, Guo L, Shih MC�Promoter analysis of the nuclear gene encoding the chloroplastglyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsisthaliana!Plant Mol Biol 46: 131-141 (2001)PubMed: 11442054; GTGATCAC PIIATGAPBS000382 23-Sep-2001 (last modified) kehi�"PII" found in the Arabidopsis thaliana(A.T.) GAPB gene promoter;Located between -69 and -50; Mutations in the "PII" resulted inreductions of light-activated gene transcription; GAPB encodesthe B subunit of chloroplast glyceraldehyde-3-phosphatedehydrogenase(GADPH) of A.T.;GAPB(glyceraldehyde-3-phosphate dehydrogenaselight-activated
transcriptionArabidopsis thalianaChan CS, Guo L, Shih MC�Promoter analysis of the nuclear gene encoding the chloroplastglyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsisthaliana!Plant Mol Biol 46: 131-141 (2001)PubMed: 11442054; TTGGTTTTGATCAAAACCAAPOLASIG1S000080%18-November-2005 (last modified) kehi�"PolyA signal"; poly A signal found in legA gene of pea, ricealpha-amylase; -10 to -30 in the case of animal genes. Nearupstream elements (NUE) in Arabidopsis (Loke et al. 2005);
poly A signalNUEFUE?pea (Pisum sativum); rice (Oryza sativa); Arabidopsis thaliana;�Heidecker G, Messing JJoshi CPO'Neill SD, Kumagai MH, Majumdar A, Huang N, Sutliff TD,Rodriguez RLLoke JC, Stahlberg EA, Strenski DG, Haas BJ, Wood PC, Li QQ.�oStructural analysis of plant genes.Putative polyadenylation signals in nuclear genes of higherplants: a compilation and analysis.The alpha-amylase genes in Oryza sativa: Characterization of cDNAclones and mRNA expression during seed germination.Compilation of mRNA polyadenylation signals in Arabidopsisrevealed a new signal element and potential secondarystructures.�Ann Rev Plant Physiol 37:439-466 (1986)Nucleic Acids Res 15:9627-9640 (1987)Mol Gen Genet 221:235-244 (1990)Plant Physiol. 138: 1457-1468. (2005)IPubMed: 3697078;PubMed: 2370848; GenBank: M24286, M24287;PubMed: 15965016Reviewin silicoAATAAAPOLASIG2S000081 17-May-1998 (last modified) kehi�"PolyA signal"; poly A signal found in rice alpha-amylase; -10 to-30 in the case of animal genes. AATAAA; AATAAT; AATTAAA;AATAAG;
poly A signal rice (Oryza sativa); animal;DO'Neill SD, Kumagai MH, Majumdar A, Huand N, Sutliff TD,Rodriguez RLtThe alpha-amylase genes in Oryza sativa: Characterization of cDNAclones and mRNA expression during seed germination. Mol Gen Genet 221:235-244 (1990))PubMed: 2370848; GenBank: M24286, M24287; AATTAAAPOLASIG3S000088 11-May-2006 (last modified) kehiI"Plant polyA signal"; Consensus sequence for plantpolyadenylation signal;poly Apolyadenylationmaize (Zea mays) Heidecker G, Messing JJoshi CP�Structural analysis of plant genes.Putative polyadenylation signals in nuclear genes of higherplants: a compilation and analysis.LAnn Rev Plant Physiol 37:439-466 (1986)Nucleic Acids Res 15:9627-9640 (1987)PubMed: 3697078;ReviewAATAATPOLLEN1LELAT52S000245$26-October-2005 (last modified) kehi�XOne of two co-dependent regulatory elements responsible forpollen specific activation of tomato (L.e.) lat52 gene; Found at-72 to -68 region; See S000246 (POLLEN2LELAT52); AGAAA andTCCACCATA (S000246) are required for pollen specific expression;Also found in the promoter of tomato endo-beta-mannanase gene(LeMAN5) gene (Filichkin et al. 2004);pollenlat52endo-beta-mannnanaseMAN Lycopersicon esculentum (tomato)HBate N, Twell DFilichkin SA, Leonard JM, Monteros A, Liu PP, Nonogaki H.� Functional architecture of a late pollen promoter:pollen-specific transcription is developmentally regulated bymultiple stage-specific and co-dependent activator elementsA novel endo-beta-mannanase gene in tomato LeMAN5 is associatedwith anther and pollen development.DPlant Mol Biol 37:859-869 (1998)Plant Physiol. 134 1080-1087 (2004) PubMed: 9678581;PubMed: 14976239 AGAAAPOLLEN2LELAT52S000246 11-Oct-1999 (last modified) kehi�One of two co-dependent regulatory elements responsible forpollen specific activation of tomato (L.e.) lat52 gene; Found at-60 to -52 region; See S000245 (POLLEN1LELAT52); AGAAA (S000245)and TCCACCATA are required for pollen specific expression;pollenlat52 tomato (Lycopersicon esculentum)Bate N, Twell D�Functional architecture of a late pollen promoter:pollen-specific transcription is developmentally regulated bymultiple stage-specific and co-dependent activator elements!Plant Mol Biol 37:859-869 (1998)PubMed: 9678581; TCCACCATAPR2GCNTS000089 10-May-1998 (last modified) kehi�"GC element" conserved in the 5' upstream regions of group 2 PRprotein genes (beta-1,3-glucanase (GLN2), chitinase (CHN17,CHN50)) of tobacco (N.t.);tobaccogroup 2
pr-protein
GC element chitinasebeta-1,3-glucanase tobacco (Nicotiana tabacum);Ohme-Takagi M, Shinshi H>Structure and expression of a tobacco beta-1,3-glucanase gene. Plant Mol Biol 15:941-946 (1990)!PubMed: 2103484; GenBank: X53600; TAARAGCCGCC
PREATPRODHS000450#04-August-2006 (last modified) kehi��"PRE (Pro- or hypoosmolarity-responsive element) found in thepromoter region of proline dehydrogenase (ProDH) gene inArabidopsis; Core of 9-bp sequence ACTCATCCT which is necessaryfor the efficient expression of ProDH in response to L-Pro andhypoosmolarity (Satoh et al., 2002); ATB2-binding site; Similarto GCN4 motif (ATGA(C/G)TCAT); ATB2 subgroup of bZIPtranscription factors function as transcriptional activator forhypoosmolarity-inducible ProDH (Satoh et al., 2004);prolineProDHhypoosomolaritybZIPArabidopsis thaliana�Satoh R, Nakashima K, Seki M, Shinozaki K, Yamaguchi-ShinozakiK.Satoh R, Fujita Y, Nakashima K, Shinozaki K, Yamaguchi-ShinozakiK.Weltmeier F, Ehlert A, Mayer CS, Dietrich K, Wang X, Schutze K,Alonso R, Harter K, Vicente-Carbajosa J, Droge-Laser W.��ACTCAT, a novel cis-acting element for proline- andhypoosmolarity-responsive expression of the ProDH gene encodingproline dehydrogenase in Arabidopsis.A novel subgroup of bZIP proteins functions as transcriptionalactivators in hypoosmolarity-responsive expression of the ProDHgene in Arabidopsis.Combinatorial control of Arabidopsis proline dehydrogenasetranscription by specific heterodimerisation of bZIPtranscription factors.ePlant Physiol. 130:709-719 (2002).Plant Cell Physiol. 45: 309-317 (2004).EMBO J. 25:3133-3143. (2006)0PubMed: 12376638PubMed: 15047879PubMed: 16810321 ACTCATPRECONSCRHSP70AS000506$04-January-2007 (last modified) kehi�Consensus sequence of PRE (plastid response element) in thepromoters of HSP70A in Chlamydomonas; Involved in induction ofHSP70A gene by both MgProto and light; S=G/C; Y=C/T; R=A/G;H=T/C/A; D=A/T/G;HSP
chlorophylMgProtoChlamydomonas reinhardtii,von Gromoff ED, Schroda M, Oster U, Beck CF.nIdentification of a plastid response element that acts as anenhancer within the Chlamydomonas HSP70A promoter.&Nucleic Acids Res. 34:4767-4779 (2006)PubMed: 16971458
consensus;SCGAYNRNNNNNNNNNNNNNNNHDPREMOTIFNPCABES000230 17-May-1998 (last modified) kehi�Motif sequence repeated many times in two positive regulatoryelements, PRE1 (-1554 to -1182) and PRE2 (-747 to -516) found farupstream in the tobacco (N.p.) CAB gene (cab-E) promoter; Confermaximum levels of photoregulated expression;PREcabCABphotoregulated geneslight-regulated geneslightleafshoot#tobacco (Nicotiana plumbaginifolia)UCastresana C, Garcia-Luque I, Alonso E, Malik VS, Cashmore ARTerzaghi WB, Cashmore AR�Both positive and negative regulatory elements mediate expressionof a photoregulated CAB gene from Nicotiana plumbaginifolia.Light-regulated transcriptionPEMBO J 7:1929-1936 (1988)Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995)!PubMed: 2901343; GenBank: X12512;Review ACCGGCCCACTT PROLAMINBOXS000091 15-Oct-1999 (last modified) kehi��"Prolamin Box"; -330 consensus sequence found in all zein genes;prolamin type consensus sequence found in the 5'upstream regionsof seed storage proteins of maize (22 kDa zein); similar sequencefound in 19 kDa zein, B-hordein (barley), gamma-gliadin (wheat),high M.W. glutenin (wheat); ESBF-1 enhanced transcriptionalactivation mediated by SPA (the endosperm-specific wheat bZIPfactor);
prolamin-boxzeinhordeingliadingluteninSPAbZIPEBESBF-1 endospermWPBFDOFseedZrice (Oryza sativa); maize (Zea mays); barley (Hordeum vulgare);wheat (Triticum aestivum);�Brown JWS, Wandelt C, Feix GMaier U-G, Brown JWS, Toloczyki C, Feix GSchmidt RJ, Ketudat M, Aukerman MJ, Hoschek GConlan RS, Hammond-Kosack M, Bevan M��The upstream regions of zein genes: sequence analysis andexpression in the unicellular green alga Acetabularia.Binding of a nuclear factor to a consensus sequence in the 5'flanking region of zein genes from maize.Opaque-2 is a transcriptional activator that recognizes aspecific target site in 22-kD zein genes.Transcription activation mediated by the bZIP factor SPA on theendosperm box is modulated by ESBF-1 in vitrojEur J Cell Biol 42:161-170 (1986)EMBO J 6:17-22 (1987)Plant Cell 4:689-700 (1992)Plant J 19:173-181 (1999)2PubMed: 1392590; GenBank: M86591;PubMed: 10476064; CACATGTGTAAAGGTPROLAMINBOXOSGLUB1S000354 16-Feb-2001 (last modified) seki�"Prolamine box" found in the rice (O.s.) GluB-1 gene promoter;Involved in quantitative regulation of the GluB-1 gene; SeeS000276, S000277, S000278 (for elements in GluB-1); See S000001,S000091, S000265, S000341 (for Prolamin box);
prolamine boxGluB-1seed endospermrice (Oryza sativa)/Wu C, Washida H, Onodera Y, Harada K, Takaiwa F�Quantitative nature of the Prolamin-box, ACGT and AACA motifs ina rice glutelin gene promoter: minimal cis-element requirementsfor endosperm-specific gene expressionPlant J 23: 415-421 (2000)PubMed: 10929134; TGCAAAG PROXBBNNAPAS000263 16-Feb-2001 (last modified) seki��"prox B (proximal portion of B-box) found in napA gene ofBrassica napus (B.n.); CA-rich sequence; Found between -130 and-124; Required for seed specific expression and ABAresponsiveness; See S000262, S000264; dist B ABRE mediatedtransactivation by ABI3 adn ABI3-dependent response to ABA; atetramer of the composite RY/G complex mediated onlyABA-independent transactivation by ABI3; B2 domain of ABI3 isnecessary for ABA-independent and ABA-dependent activationthrough the dist B ABRE;ABREABAprox BB-boxseednapAnapinBrassica napus|Ezcurra I, Ellerstrom M, Wycliffe P, Stalberg K, Rask LBusk PK, Pages MEzcurra I, Wycliffe P, Nehlin L, Ellerstrom M, Rask L��Interaction between composite elements in the napA promoter: boththe B-box ABA-responsive complex and the RY/G complex arenecessary for seed-specific expressionRegulation of abscisic acid-induced transcriptionTransactivation of the Brassica napus napin promoter by ABI3requires interaction of the conserved B2 and B3 domains of ABI3with different cis-elements: B2 mediates activation through anABRE, whereas B3 interacts with an RY/G-boxYPlant Mol Biol 40:699-709 (1999)Plant Mol Biol 37:425-435 (1998)Plant J 24:57-66 (2000)1PubMed: 10480393PubMed: 9617810;PubMed: 11029704; CAAACACCPSREGIONZMZM13S000253 11-Oct-1999 (last modified) kehiSPollen specific (PS) region in maize (Z.m.) ZM13 gene promoter;Found at -84 to -53;pollenZM13maize (Zea mays)'Hamilton DA, Schwarz YH, Mascarenhas JP^A monocot pollen-specific promoter contains separablepollen-specific and quantitative elements!Plant Mol Biol 38:663-669 (1998)PubMed: 9747811; TCGGCCACTATTTCTACGGGCAGCCAGACAAAPYRIMIDINEBOXHVEPB1S000298 10-Feb-2000 (last modified) seki�"Pyrimidine box" found in the barley (H.v.) EPB-1 (cysteineproteinase) gene promoter; Located between -120 to -113; Requiredfor GA induction; See S000297, S000259;EPBcysteine proteinaseGAABAGAREpyrimidine boxseedaleuronebarley (Hordeum vulgare)!Cercos M, Gomez-Cadenas A, Ho THD�Hormonal regulation of a cysteine proteinase gene, EPB-1, inbarley aleurone layers: cis- and trans-acting elements involvedin the co-ordinated gene expression regulated by gibberellins andabscisic acidPlant J 19: 107-118 (1999)PubMed: 10476058 TTTTTTCCPYRIMIDINEBOXOSRAMY1AS000259#19-August-2004 (last modified) kehi�VPyrimidine box found in rice (O.s.) alpha-amylase (RAmy1A) gene;Gibberellin-respons cis-element of GARE and pyrimidine box arepartially involved in sugar repression; Found in the promoter ofbarley alpha-amylase (Amy2/32b) gene which is induced in thealeurone layers in response to GA; BPBF protein bindsspecifically to this site; See S000265;
alpha-amylasesugar repressionGAREpyrimidine box feed-backmetabolic repressionembryoseedDofBPBFpbf.rice (Oryza sativa); barley (Hordeum vulgare);uMorita A, Umemura T, Kuroyanagi M, Futsuhara Y, Perata P,Yamaguchi JMena M, Cejudo FJ, Isabel-Lamoneda I, Carbonero P�Functional dissection of a sugar-repressed alpha-amylase gene(Ramy1A) promoter in rice embryosA Role for the DOF Transcription Factor BPBF in the Regulation ofGibberellin-Responsive Genes in Barley Aleurone<FEBS Lett 423:81-85 (1998)Plant Physiol. 130: 111-119 (2002)!PubMed: 9506846;PubMed: 12226491; CCTTTT QARBNEXTAS000244 11-0ct-1999 (last modified) kehid"QAR (quantitative activator region)" in promoter region ofBrassica napus (B.n.) extA extensin gene;extextensinBrassica napusElliott KA , Shirsat AH{Promoter regions of the extA extensin gene from Brassica napuscontrol activation in response to wounding and tensile stress!Plant Mol Biol 37:675-687 (1998)PubMed: 9687071; AACGTGTQELEMENTZMZM13S000254 11-Oct-1999 (last modified) kehi�"Q(quantitative)-element" in maize (Z.m.) ZM13 gene promoter;Found at -107 to -102; Involved in expression enhancing activity;ZM13 is a maize homolog of tomato LAT52 gene; ZM13 is apollen-specific maize gene; enhancingZM13LAT52pollenmaize (Zea mays)'Hamilton DA, Schwarz YH, Mascarenhas JP^A monocot pollen-specific promoter contains separablepollen-specific and quantitative elements!Plant Mol Biol 38:663-669 (1998)PubMed: 9747811; AGGTCARAV1AATS000314 7-Sep-2000 (last modified) seki��Binding consensus sequence of Arabidopsis (A.t.) transcriptionfactor, RAV1; RAV1 specifically binds to DNA with bipartitesequence motifs of RAV1-A (CAACA) and RAV1-B (CACCTG); RAV1protein contain AP2-like and B3-like domains; The AP2-like andB3-like domains recognize the CAACA and CACCTG motifs,respectively; The expression level of RAV1 were relatively highin rosette leaves and roots; See S000315(CACCTG);RAV1AP2VP1B3rootleafshoot"Arabidopsis (Arabidopsis thaliana) Kagaya Y, Ohmiya K, Hattori T�RAV1, a novel DNA-binding protein, binds to bipartite recognitionsequence through two distinct DNA-binding domains uniquely foundin higher plants$Nucleic Acids Res 27: 470-478 (1999)PubMed: 9862967; CAACARAV1BATS000315 7-Sep-2000 (last modified) seki��Binding consensus sequence of an Arabidopsis (A.t.) transcriptionfactor, RAV1; RAV1 specifically binds to DNA with bipartitesequence motifs of RAV1-A (CAACA) and RAV1-B (CACCTG); RAV1protein contain AP2-like and B3-like domains; The AP2-like andB3-like domains recognize the CAACA and CACCTG motifs,respectively; The expression level of RAV1 were relatively highin rosette leaves and roots; See S000314(CAACA);RAV1AP2VP1B3rootleafshoot"Arabidopsis (Arabidopsis thaliana) Kagaya Y, Ohmiya K, Hattori T�RAV1, a novel DNA-binding protein, binds to bipartite recognitionsequence through two distinct DNA-binding domains uniquely foundin higher plants$Nucleic Acids Res 27: 470-478 (1999)PubMed: 9862967; CACCTG
RBCSBOX2PSS000094 15-Oct-1999 (last modified) kehi�G"rbcS box II"; 5' upstream region (-151) of pea (P.s.) rbcS gene;Binding with trans factor GT-1; one of GT-1 boxes; For acompilation of related GT elements and factors, see Villain etal. (1996); GT-1 may act as a molecular switch modulated bycalcium-dependent phosphorylation and dephosphorylation inresponse to light signals;rbcSbox IIGT-1 boxGT-1lightLREleafshootpea (Pisum sativum)�� Fluhr R, Kuhlemeier C, Nagy F, Chua N-HGreen PJ, Yong M-H, Cuozzo M, Kano-Murakami Y, Silverstein P,Chua N-HGilmartin PM, Sarokin L, Memelink J, Chua N-HVillain P, Mache R, Zhou DXMarechal E, Hiratsuka K, Delgado J, Nairn A, Qin J, Chait BT,Chua NHZhou DX��Organ-specific and light-induced expression of plant genes.Binding site requirements for pea nuclear protein factor GT-1correlate with sequences required for light-dependenttranscriptional activation of the rbcS-3A gene.Molecular light switches for plant genes.The mechanism of GT element-mediated cell type-specifictranscriptional controlModulation of GT-1 DNA-binding activity by calcium-dependentphosphorylationRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�Science 232:1106-1112 (1986)EMBO J 7:4035-4044 (1988)Plant Cell 2:369-378 (1990)J Biol Chem 271:32593-32598 (1996)Plant Mol Biol 40:373-386 (1999)Trends in Plant Science 4:210-214 (1999)APubMed: 3243271;PubMed: 2152164;PubMed: 8955086;PubMed: 10437822;ReviewGTGTGGTTAATATG
RBCSBOX3PSS000095 17-May-1998 (last modified) kehi�"rbcS box III"; 5' upstream region (-114) of pea (P.s.) rbcSgene; binding with trans factor GT-1; one of GT-1 boxes; For acompilation of related GT elements and factors, see Villain etal. (1996);rbcSbox IIIGT-1 boxGT-1leafshootpea (Pisum sativum)�Fluhr R, Kuhlemeier C, Nagy F, Chua N-HGreen PJ, Yong M-H, Cuozzo M, Kano-Murakami Y, Silverstein P,Chua N-HGilmartin PM, Sarokin L, Memelink J, Chua N-HVillain P, Mache R, Zhou DX�SOrgan-specific and light-induced expression of plant genes.Binding site requirements for pea nuclear protein factor GT-1correlate with sequences required for light-dependenttranscriptional activation of the rbcS-3A gene.Molecular light switches for plant genes.The mechanism of GT element-mediated cell type-specifictranscriptional controlrScience 232:1106-1112 (1986)EMBO J 7:4035-4044 (1988)Plant Cell 2:369-378 (1990)J Biol Chem 271:32593-32598 (1996)0PubMed: 3243271;PubMed: 2152164;PubMed: 8955086; ATCATTTTCACT
RBCSCONSENSUSS000127 17-May-1998 (last modified) kehi7"rbcS general consensus sequence"; AATCCAA or AATCCAAC;rbcSG boxI boxleafshoot�tomato (Lycopersicon esculentum); petunia (Petunia hybrida);tobacco (Nicotiana tabacum); pea (Pisum sativum); soybean(Glycine max);,Manzara T, Gruissem WDonald RGK, Cashmore AR�Organization and expression of the genes encodingribulose-1,5-bisphosphate carboxylase in higher plants.Mutation of either G box or l box sequences profoundly affectsexpression from the Arabidopsis rbcS-1A promoter.9Photosynth Res 16:117-139 (1988)EMBO J 9:1717-1726 (1990)PubMed: 2347304; AATCCAA
RBCSGBOXPSS000096 17-May-1998 (last modified) kehis"rbcS G-box"; 5'upstream region (-211) of pea rbcS gene; bindingwith trans factor GBF (CG-1); Light-responsiveness;rbcSG-boxG boxGBFCG-1lightleafshootpea (Pisum sativum);-Gilmartin PM, Sarokin L, Memelink J, Chua N-H)Molecular light switches for plant genes.Plant Cell 2:369-378 (1990)PubMed: 2152164; CACATGGCACTRBENTGA3S000358 16-Feb-2001 (last modified) seki�"rbe (RSG binding element)" found in the tobacco (N.t.) GA3 genepromoter; Binding site of RSG (Repression of shoot growth); RSGis a bZIP transcriptional activator; RSG regulates the morphologyof plants by controlling the endogenous amounts of GAs;RSGrberbeGA3bZIPGA3 gibberellinleafshoottobacco (Nicotiana tabacum)@Fukazawa J, Sakai T, Ishida S, Yamaguchi I, Kamiya Y, TakahashiY~Repression of shoot growth, a bZIP transcriptional activator,regulates cell elongation by controlling the level ofgibberellins Plant Cell 12: 901-915 (2000)PubMed: 10852936; TCCAACTTGGA
RE1ASPHYA3S000195 17-May-1998 (last modified) kehi�RE1 (putative repressor element) responsible for Pfr-directedrepression of oat (A.s.) phyA3 phytochrome gene; Also found inpea AS1 (asparagine synthetase) gene (Ngai, Tsai, Coruzzi: PlantJ 12:1021-1234 (1997));light
repressionphyphyAleafshoot(oat (Avena sativa); pea (Pisum sativum);5Bruce WB, Deng XW, Quail PHNgai N, Tsai FY, Coruzzi G�A negatively acting DNA sequence element mediatesphytochrome-directed repression of phyA gene transcriptionLight-induced transcriptional repression of the pea AS1 gene:identification of cis-elements and transfactors5EMBO J 10:3015-3024 (1991)Plant J 12:1021-1034 (1997) PubMed: 1915276;PubMed: 9418044; CATGGGCGCGGREALPHALGLHCB21S000362 16-Feb-2001 (last modified) seki�"REalpha" found in Lemna gibba Lhcb21 gene promoter; Located at-134 to -129; Binding site of proteins of whole-cell extracts;The DNA binding activity is high in etiolated plants but muchlower in green plants; Required for phytochrome regulation; SeeS000363;REalphaLhcb21 phytochromeREbeta Lemna gibbaDegenhardt J, Tobin EM�A DNA binding activity for one of two closely defined phytochromeregulatory elements in an Lhcb promoter is more abundant inetiolated than in green plantsPlant Cell 8: 31-41 (1996)PubMed: 8597658; AACCAAREBETALGLHCB21S000363 16-Feb-2001 (last modified) seki�"REbeta" found in Lemna gibba Lhcb21 gene promoter; Located at-114 to -109; A GATA sequence created at a position sixnucleotides upstream could replace the function of REbeta;Required for phytochrome regulation; See S000362;REalphaLhcb21 phytochromeREbeta Lemna gibbaDegenhardt J, Tobin EM�A DNA binding activity for one of two closely defined phytochromeregulatory elements in an Lhcb promoter is more abundant inetiolated than in green plantsPlant Cell 8: 31-41 (1996)PubMed: 8597658; CGGATA
REGION1OSOSEMS000300 16-Feb-2001 (last modified) seki�"region 1" ABRE-like sequence found in rice (O.s.) Osem genepromoter; Important for regulation by ABA; See S000102, S000299;TRAB1, bZIP transcription factor, interacts with VP1 and mediatesabscisic acid-induced transcritption;ABREEmOsemABAVP1seedrice (Oryza sativa);Hattori T, Terada t, Hamasuna SHobo T, Kowyama Y, Hattori T�Regulation of the Osem gene by abscisic acid and thetranscriptional activator VP1: analysis of cis-acting promoterelements required for regulation by abscisic acid and VP1A bZIP factor, TRAB1, interacts with VP1 and mediates abscisicacid-induced transcriptionFPlant J 7: 913-925 (1995)Proc Natl Acad Sci USA 96: 15348-15353 (1999)1PubMed: 7599651; GenBank: U22102PubMed: 10611387; CGGCGGCCTCGCCACGRGATAOSS000191 17-May-1998 (last modified) kehi�
R-GATA (GATA motif binding factor) binding site; GATA motif isfound at -143 to -135 of RTBV promoter; GATA motif is requiredfor phloem-specific gene expression of Rice Tungro BacilliformVirus (RTBV); See also RNFG1OS (S000188), RNFG2OS (S000189), andABFOS (S000190);GATAphloemRTBVR-GATAstemphloem9rice (Oryza sativa); RTBV; rice tungro bacilliform virus;Yin Y, Chen L, Beachy R\Promoter elements required for phloem-specific gene expressionfrom the RTBV promoter in ricePlant J 12:1179-1188 (1997)PubMed: 9418055; CAGAAGATA RHERPATEXPA7S000512$04-January-2007 (last modified) kehi�"Right part of RHEs (Root Hair-specific cis-Elements)" conservedamong the Arabidopsis thaliana A7 (AtEXPA7) orthologous (andparalogous) genes from diverse angiosperm species with differenthair distribution patterns; K=G/T; W=T/A;roothairArabidopsis thaliana@Kim DW, Lee SH, Choi SB, Won SK, Heo YK, Cho M, Park YI, Cho HT.~Functional Conservation of a Root Hair Cell-Specific cis-Elementin Angiosperms with Different Root Hair Distribution Patterns. Plant Cell. 18:2958-2970 (2006)PubMed: 17098810 KCACGWRNFG1OSS000188 17-May-1998 (last modified) kehi�RNFG1 binding site; Box I; RNFG1 is one of two Rice NuclearFactors required for phloem-specific gene expression of RiceTungro Bacilliform Virus (RTBV); Box I is found at -3 to +8 ofRTBV promoter; See also RNFG2OS (S000189);RNFG1phloemRTBVstemphloemrice (Oryza sativa);Yin Y, Beachy RN|The regulatory regions of the rice tungro bacilliform viruspromoter and interacting nuclear factors in rice (Oryza sativaL.)Plant J 7:969-980 (1995)PubMed: 7599653; GATCATCGATCRNFG2OSS000189!12-Apri-2004 (last modified) kehi�hRNFG2 binding site; Box II; RNFG2 is one of two Rice NuclearFactors required for phloem-specific gene expression of RiceTungro Bacilliform Virus (RTBV); Box II is found at -53 to -39 ofRTBV promoter; See also RNFG1OS (S000188); "Box II" is thebinding site of bZIP protein RF2a and RF2b; RF2a and RF2b arepredominantly expressed in vascular tissue (Dai et al.);
RNFG1phloemRTBVBox IIstemphloemRF2aRF2bbZIPvascularrice (Oryza sativa);IYin Y, Beachy RNYin Y, Chen L, Beachy RDai S, Zhang Z, Chen S, Beachy RN.�TThe regulatory regions of the rice tungro bacilliform viruspromoter and interacting nuclear factors in rice (Oryza sativaL.)Promoter elements required for phloem-specific gene expressionfrom the RTBV promoter in riceRF2b, a rice bZIP transcription activator, interacts with RF2aand is involved in symptom development of rice tungro disease.^Plant J 7:969-980 (1995)Plant J 12:1179-1188 (1997)Proc Natl Acad Sci U S A. 101:687-92.(2004)1PubMed: 7599653;PubMed: 9418055;PubMed: 14704272; CCAGTGTGCCCCTGGROOTMOTIFTAPOX1S000098 13-Feb-2001 (last modified) kehi&Motif found both in promoters of rolD;rootrolDAgrobacterium rhizogenes;Elmayan T, Tepfer M�Evaluation in tobacco of the organ specificity and strength ofthe rol D promoter, domain A of the 35S promoter and the 35S^2promoter Transgenic Res 4:388-396 (1995)PubMed: 7581519;Sequence similarity;ATATT RSEPVGRP1S000099 13-Feb-2001 (last modified) kehii"RSE (root-specific element)" of bean (P.v.) GRP1.8 gene;consensus sequence;See also S000288 and S000289;rootGRP1.8bean (Phaseolus vulgaris)Elmayan T, Tepfer M�Evaluation in tobacco of the organ specificity and strength ofthe rol D promoter, domain A of the 35S promoter and the 35S^2promoter. Transgenic Res 4:388-396 (1995)PubMed: 7581519; CAACTTTCATAT
RSEPVGRP18S000289 10-Feb-2000 (last modified) seki�"RSE (root-specific element)" found in bean (P.V.) grp1.8 genepromoter; Located at -98 to -73; Required also forvascular-specific expression in stem; See S000288, S000099;RSEgrp1.8vascularrootstemshootbean (Phaseolus vulgaris)Keller B, Heierli D�Vascular expression of the grp1.8 promoter is controlled by threespecific regulatory elements and one unspecific activatingsequence!Plant Mol Biol 26: 747-756 (1994)PubMed: 7948928 CATCCAACTTTCATATCCATGTGCTT RSRBNEXTAS000243 11-0ct-1999 (last modified) kehi["RSR (root specific region)" in promoter region of Brassica napus(B.n.) extA extensin gene;rootBrassica napusElliott KA , Shirsat AH{Promoter regions of the extA extensin gene from Brassica napuscontrol activation in response to wounding and tensile stress!Plant Mol Biol 37:675-687 (1998)PubMed: 9687071; CAAACTCGTATATCCAT RYREPEAT4S000010 16-Feb-2001 (last modified) seki�o"RY repeat motif"; "Sph element"; seed expression; ABA; Gene:maize C1, wheat Em, rice rab16A, maize Rab17; Transacting factor:VP1 (maize C1); See S000105 RYREPEAT2 (CATGCAT); The RY sequencemotif does not play a major role in VP1 or ABA regulation of Emgene in protoplast; VP1 gene is specifically required forexpression of the maturation program in seed development;RY motifC1EmRab17seedABAVP1 Sph element@maize (Zea mays); wheat (Triticum aestivum); rice (Oryza sativa)�Hattori T, Vasil V, Rosenkrans L, Hannah LC, McCarty DR, VasilIKThomas TLBusk PK, Pages MVasil V, Marcotte Jr. WR, Rosenkrans L, Cocciolone SM, Vasil IK,Quatrano RS, McCarty DRMcCarty DR, Hattori T, Carson CB, Vasil V, Lazar M, Vasil IK��The Viviparous-1 gene and abscisic acid activate the C1regulatory gene for anthocyanin biosynthesis during seedmaturation in maize.Gene expression during plant embryogenesis and germination: Anoverview.Regulation of abscisic acid-induced transcriptionOverlap of viviparous1 (VP1) and abscisic acid response elementsin the EM promoter: G-Box elements are sufficient but notnecessary for VP1 transactivationThe Viviparous-1 developmental gene of maize encodes a noveltranscriptional activator�Genes Dev 6:609-618 (1992)Plant Cell 5:1401-1410 (1993)Plant Mol Biol 37:425-435 (1998)Plant Cell 7: 1511-1518 (1995)Cell 66: 895-905 (1991)NPubMed: 1532784;PubMed: 8281041;PubMed: 9617810PubMed: 8589631PubMed: 1889090; ReviewReview
TCCATGCATGCACRYREPEATBNNAPAS000264 16-Feb-2001 (last modified) seki��"RY repeat" found in RY/G box (the complex containing the two RYrepeats and the G-box) of napA gene in Brassica napus (B.n.);Found between -78 and -50; Required for seed specific expression;See S000262, S000263; dist B ABRE mediated transactivation byABI3 adn ABI3-dependent response to ABA; a tetramer of thecomposite RY/G complex mediated only ABA-independenttransactivation by ABI3; B2 domain of ABI3 is necessary forABA-independent and ABA-dependent activation through the dist BABRE; RY repeatRY/G boxseednapAnapinBrassica napuslEzcurra I, Ellerstrom M, Wycliffe P, Stalberg K, Rask LEzcurra I, Wycliffe P, Nehlin L, Ellerstrom M, Rask L��Interaction between composite elements in the napA promoter: boththe B-box ABA-responsive complex and the RY/G complex arenecessary for seed-specific expressionTransactivation of the Brassica napus napin promoter by ABI3requires interaction of the conserved B2 and B3 domains of ABI3with different cis-elements: B2 mediates activation through anABRE, whereas B3 interacts with an RY/G-box8Plant Mol Biol 40:699-709 (1999)Plant J 24:57-66 (2000)"PubMed: 10480393;PubMed: 11029704; CATGCA
RYREPEATGMGY2S000105 11-May-2006 (last modified) kehi_"RY repeat motif (CATGCAT)"; Present in the 5' region of thesoybean (G.m.) glycinin gene (Gy2);glycininCATGCATGy2seedsoybean (Glycine max);%Lelievre J-M, Oliveira LO, Nielsen NC@5'-CATGCAT-3' elements modulate the expression of glyciningenes. Plant Physiol 98:387-391 (1992)PubMed: 16668640 CATGCATRYREPEATLEGUMINBOXS000100 17-May-1998 (last modified) kehii"RY repeat (CATGCAY)" or legumin box found in seed-storageprotein genes in legume such as soybean (G.m.); RY repeat legumin boxseedstorage protein legume; soybean (Glycine max);Fujiwara T, Beachy RNxTissue-specific and temporal regulation of a beta-conglyciningene: roles of the RY repeat and other cis-acting elements. Plant Mol Biol 24:261-272 (1994)PubMed: 8111031; CATGCAYRYREPEATVFLEB4S000102#01-August-2006 (last modified) kehi��"RY repeat motif"; quantitative seed expression; Gene: Vicia fabaLeB4; Soybean glycinin (Gy2); other dicot and monocot seedprotein genes; "Sph box" found in rice (O.s.) Osem gene promoter;See S000010, S000299, S000300; Binding site of ArabidopsisB3-domain-containing transcription factor FUS3; TRAB1, bZIPtranscription factor, interacts with VP1 and mediates abscisicacid-induced transcritption; FUS3 protein physically interactwith two RY elements present in the AtGA3ox promoter (Curaba etal., 2004);RY repeat motifLeB4Gy2seedSphABAVP1OsemEmABREFUS3embryoB3GAubean (Phaseolus vulgaris); soybean (Glycine max); Vicia faba;rice (Oryza sativa); Arabidopsis (Arabidopsis thaliana);�'Nag R, Maity MK, Dasgupta M.Baumlein H, Nagy I, Villarroel R, Inze D, Wobus UThomas TLHattori T, Terada t, Hamasuna SReidt W, Wohlfarth T, Ellerstrom M, Czihal A, Tewes A, Ezcurra I,Rask L, Baumlein HHobo T, Kowyama Y, Hattori TCuraba J, Moritz T, Blervaque R, Parcy F, Raz V, Herzog M, VachonG.�zDual DNA binding property of ABA insensitive 3 like factorstargeted to promoters responsive to ABA and auxin.Cis-analysis of a seed protein gene promoter: the conservative RYrepeat CATGCATG within the legumin box is essential fortissue-specific expression of a legumin gene.Gene expression during plant embryogenesis and germination: Anoverview.Regulation of the Osem gene by abscisic acid and thetranscriptional activator VP1: analysis of cis-acting promoterelements required for regulation by abscisic acid and VP1Gene regulation during late embryogenesis: the RY motif ofmaturation-specific gene promoters is a direct target of the FUS3gene productA bZIP factor, TRAB1, interacts with VP1 and mediates abscisicacid-induced transcriptionAtGA3ox2, a Key Gene Responsible for Bioactive GibberellinBiosynthesis, Is Regulated during Embryogenesis by LEAFYCOTYLEDON2 and FUSCA3 in Arabidopsis.�Plant Mol Biol. 59: 821-838 (2005).Plant J 2:233-239 (1992)Plant Cell 5:1401-1410 (1993)Plant J 7: 913-925 (1995)Plant J 21: 401-408 (2000)Proc Natl Acad Sci USA 96: 15348-15353 (1999)Plant Physiol. 136: 3660-3669. (2004)�PubMed: 16270233PubMed: 1338774;PubMed: 8281041;PubMed: 7599651; GenBank: U22102PubMed: 10758492;PubMed: 10611387;PubMed: 15516508ReviewCATGCATGS1FBOXSORPS1L21S000223 10-May-1998 (last modified) kehi� "S1F box" conserved both in spinach (S.o.) RPS1 and RPL21 genesencoding the plastid ribosomal protein S1 and L21, respectively;Negative element; Might play a role in downregulating RPS1 andRPL21 promoter activity (Lagrange et al., 1993); See S000211(SITE1SORPS1), S000215 (S1FSORPL21); S1FS1F boxS1F-boxS1plastid proteinRPS1RPL21leafnegativespinach (Spinacia oleracea)[Zhou DX, LI YF, Rocipon M, Mache RLagrange T, Franzetti B, Axelos M, Mache R, Lerbs-Mache S�(Sequence specific interaction between S1F, a spinach nuclearfactor, and a negative cis-element conserved in plastid-relatedgenesStructure and expression of the nuclear gene encoding for thechloroplast ribosomal protein L21: Developmental regulation of ahouse-keeping gene by alternative promotersCJ Biol Chem 267:23515-23519 (1992)Mol Cell Biol 13:2614-2622 (1993)1PubMed: 1429696;PubMed: 8455634; GenBank: M64682; ATGGTA
S1FSORPL21S000215#19-August-2004 (last modified) kehi�� "S1F binding site" ("S1 site") in spinach (S.o.) RPL21 geneencoding the plastid ribosomal protein L21; Negative element;Might play a role in downregulating RPL21 promoter activity(Lagrange et al., 1993); See S000211 (SITE1SORPS1), S000166(S2FSORPL21);S1FS1plastid proteinRPL21leafnegativespinach (Spinacia oleracea)�Zhou DX, LI YF, Rocipon M, Mache RLagrange T, Franzetti B, Axelos M, Mache R, Lerbs-Mache SLagrange T, Gauvin S, Yeo HJ, Mache R��Sequence specific interaction between S1F, a spinach nuclearfactor, and a negative cis-element conserved in plastid-relatedgenesStructure and expression of the nuclear gene encoding for thechloroplast ribosomal protein L21: Developmental regulation of ahouse-keeping gene by alternative promotersS2F, a leaf-specific trans-acting factor, binds to a novelcis-acting element and differentially activates the RPL21 gene`J Biol Chem 267:23515-23519 (1992)Mol Cell Biol 13:2614-2622 (1993)Plant Cell 9:1469-1479 (1997)APubMed: 1429696;PubMed: 8455634; GenBank: M64682;PubMed: 9286115; ATGGTATT
S2FSORPL21S000166 17-May-1998 (last modified) kehi��"S2F binding site" ("S2 site") in spinach RPL21 gene encoding theplastid ribosomal protein L21; S2 site (CATACAWW) is conserved inpromoter region of many nuclear genes encoding plastid proteins;Leaf-specific, light-independent regulatory element; S2 site isrelated to but different from the light-responsive GT-1 bindingsite (Lagrange et al., 1997); For a compilation of related GTelements and factors, see Villain et al. (1996);
S2FS2plastid proteinRPL21
leaf-specificlight-independentlight
GT elementleafshoot spinach (Spinacia oleracea);@Lagrange T, Gauvin S, Yeo HJ, Mache RVillain P, Mache R, Zhou DX�S2F, a leaf-specific trans-acting factor, binds to a novelcis-acting element and differentially activates the RPL21 gene.The mechanism of GT element-mediated cell type-specifictranscriptional control?Plant Cell 9:1469-1479 (1997)J Biol Chem 271:32593-32598 (1996) PubMed: 9286115;PubMed: 8955086; CCATACATTSARECAMVS000156 16-Jan-1998 (last modified) kehi�Salicylic acid responsive element found in CaMV 35S promoter;Identical to as-1; Binding with ASF-1 (Activation SequenceFactor-1); See AS1 (S000023);Salicylic acidSAREas-1 CaMV; Cauliflower mosaic virus;\Qin X-F, Holuigue L, Horvath DM, Chua N-HStange C, Ramirez I, Gomez I, Jordana X, Holuigue L�Immediate early transcription activation by salicylic acid viathe cauliflower mosaic virus as-1 element.Phosphorylation of nuclear proteins directs binding to salicylicacid-responsive elements.6Plant Cell 6:863-874 (1994)Plant J 11:1315-1324 (1997) PubMed: 8061520;PubMed: 9225470; CTGACGTAAGGGATGACGCAC SB1NPABC1S000435 27-Jan-2004 (last modified) kehi�Sclareol box1 (SB1) found at -827 of a plasma membrane ATPbinding cassette (ABC) transporter gene (NpABC1) in N.plumbaginifolia; Mutation in SB3 completely abolishedsclareolide-mediated expression; See S ; scalareol diterpeneABC transporter$Nicotiana plumbaginifolia (tobacco);8Grec S, Vanham D, de Ribaucourt J, Purnelle B, Boutry P.�Identification of regulatory sequence elements within thetranscription promoter region of NpABC1, a gene encoding a plantABC transporter induced by diterpenes.Plant J. 35: 237-250 (2003)PubMed: 12848828; CACTAACACAAAGTAA SB3NPABC1S000434 27-Jan-2004 (last modified) kehi�Sclareol box3 (SB3) found at -216 of a plasma membrane ATPbinding cassette (ABC) transporter gene (NpABC1) in N.plumbaginifolia; Mutation in SB3 completely abolishedsclareolide-mediated expression; See S ;sclareolABC transporterSB3$Nicotiana plumbaginifolia (tobacco);8Grec S, Vanham D, de Ribaucourt J, Purnelle B, Boutry P.�Identification of regulatory sequence elements within thetranscription promoter region of NpABC1, a gene encoding a plantABC transporter induced by diterpenes.Plant J. 35: 237-250 (2003)PubMed: 12848828; TTATGAACAGTAATT
SBOXATRBCSS000500#04-August-2006 (last modified) kehi�"S-box" conserved in several rbcS promoters in Arabidopsis; ABI4binding site; "Important for the sugar and ABA responsiveness ofCMA5"(Acevedo-Hernandez et al., 2005);rbcSsugarABAABI4Arabidopsis thaliana2Acevedo-Hernandez GJ, Leon P, Herrera-Estrella LR.jSugar and ABA responsiveness of a minimal RBCS light-responsiveunit is mediated by direct binding of ABI4.Plant J. 43:506-519 (2005).PubMed: 160981050in silico; Electrophoretic mobility shift assay;CACCTCCA
SE1PVGRP18S000288 10-Feb-2000 (last modified) seki�"SE1 (Stem element 1)" found in the bean (P.v.) grp1.8 genepromoter; Located between -121 and -94; Enhances the expressionstrongly but unspecifically; See S000289, S000101 (SE2);SE1grp1.8vascularstemshootbean (Phaseolus vulgaris)Keller B, Heierli D�Vascular expression of the grp1.8 promoter is controlled by threespecific regulatory elements and one unspecific activatingsequence!Plant Mol Biol 26: 747-756 (1994)PubMed: 7948928 ATAATGGGCCACACTGTGGGGCAT SE2PVGRP1S000101 17-May-1998 (last modified) kehiF"SE2 (stem element 2)" of bean (P.v.) GRP1.8 gene; part of SE2element;stemSE2GRPGRP1bean (Phaseolus vulgaris)Elmayan T, Tepfer M.�Evaluation in tobacco of the organ specificity and strength ofthe rolD promoter, domain A of the 35S promoter and the 35S2promoter. Transgenic Res 4:388-396 (1995)PubMed: 7581519; TTNNNGTAGCTAGTGTATTTGTATSEBFCONSSTPR10AS000391 20-Feb-2002 (last modified) uchi�Binding site of the potato silencing element binding factor(SEBF) gene found in promoter of pathogenesis-related gene(PR-10a); Located between -45 and -39; Similar to the auxinresponse element; W=A/T;PR-10aSEBF pathogenesis silencingSolanum tuberosum (potato)Boyle B, Brisson NTRepression of the defense gene PR-10a by the single-stranded DNAbinding protein SEBF Plant Cell 13: 2525-2537 (2001)PubMed: 11701886; YTGTCWC SEF1MOTIFS000006 17-May-1998 (last modified) kehi�"SEF1 (soybean embryo factor 1)" binding motif; sequence found in5'-upstream region (-640; -765) of soybean beta-conglicinin (7Sglobulin) gene; W=A/T;SOYBEANSTORAGE PROTEIN7SGLOBULINBETA-CONGLICININseedsoybean (Glycine max)lAllen RD, Bernier F, Lessard PA, Beachy RNLessard PA, Allen RD, Bernier F, Crispino JD, Fujiwara T, BeachyRN�Nuclear factors interact with a soybean beta-conglycininenhancer.Multiple nuclear factors interact with upstream sequences ofdifferentially regulated beta-conglycinin genes.;Plant Cell 1:623-631 (1989)Plant Mol Biol 16:397-413 (1991) PubMed: 2535514;PubMed: 1893110; ATATTTAWW SEF3MOTIFGMS000115 17-May-1998 (last modified) kehi�"SEF3 binding site"; Soybean (G.m.) consensus sequence found inthe 5' upstream region of beta-conglycinin (7S globulin) gene;AACCCA(-27bp-)AACCCA; SEF=soybean embryo factor; SEF2; SEF3;SEF4;SEF3beta-conglycinin7Sglobulinseedsoybean (Glycine max);lAllen RD, Bernier F, Lessard PA, Beachy RNLessard PA, Allen RD, Bernier F, Crispino JD, Fujiwara T, BeachyRN�Nuclear factors interact with a soybean beta-conglycininenhancer.Multiple nuclear factors interact with upstream sequences ofdifferentially regulated beta-conglycinin genes.;Plant Cell 1:623-631 (1989)Plant Mol Biol 16:397-413 (1991) PubMed: 2535514;PubMed: 1893110; AACCCA
SEF4MOTIFGM7SS000103 17-May-1998 (last modified) kehi�"SEF4 binding site"; Soybean (G.m.) consensus sequence found in5'upstream region (-199) of beta-conglycinin (7S globulin) gene(Gmg17.1); "Binding with SEF4 (soybean embryo factor 4)"; R=A/G;soybeanseedstorage protein7Sglobulinbeta-conglycininSEFsoybean (Glycine max);lAllen RD, Bernier F, Lessard PA, Beachy RNLessard PA, Allen RD, Bernier F, Crispino JD, Fujiwara T, BeachyRN�Nuclear factors interact with a soybean beta-conglycininenhancer.Multiple nuclear factors interact with upstream sequences ofdifferentially regulated beta-conglycinin genes.;Plant Cell 1:623-631 (1989)Plant Mol Biol 16:397-413 (1991) PubMed: 2535514;PubMed: 1893110; RTTTTTR
SGBFGMGMAUX28S000287 10-Feb-2000 (last modified) sekiabZIP proteins SGBF-1 and SGBF-2 binding site in soybean (G.m.)GmAux28 gene promoter; see S000042;Aux28G boxauxinbZIPSGBF-1SGBF-2soybean (Glycine max)5Hong JC, Cheong YH, Nagao RT, Bahk JD, Key JL, Cho MJoIsolation of two soybean G-box binding factors which interactwith a G-box sequences of an auxin-responsive genePlant J 8: 199-211 (1995)0PubMed: 7670504; GenBank: L01447, L01448, L01449
TCCACGTGTC SITE1SORPS1S000211 11-May-2006 (last modified) kehi��Site 1 in the spinach (S.o.) rps1 promoter; S1F binding site;Nuclear genes encoding plastid ribosomal proteins are more highlyexpressed in leaves than in root; Involved in leaf-specificinduction; Seems to be light-independent; Involved in negativeregulation; Related to the light-responsive Box II of the pearbcs-3A promoter; Related to GT elements; For a compilation ofrelated GT elements and factors, see Villain et al. (1996); SeeS000215 (S1FSORPL21); S1 box=ATGGTA;Site 1rps1ribosomal proteinS1Fleaf
leaf-specific
repressionnegative spinach (Spinacia oleracea);kZhou DX, Li YF, Rocipon M, Mache RVillain P, Clabault G, Mache R, Zhou DXVillain P, Mache R, Zhou DXZhou DX��Sequence-specific interaction between S1F, a spinach nuclearfactor, and a negative cis-element conserved in plastid-relatedgenesS1F binding site is related to but different from thelight-responsive GT-1 binding site and differentially repressesthe spinach rps1 promoter in transgenic tobaccoThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors�J Biol Chem 267:23515-23519 (1992)J Biol Chem 269:16626-16630 (1994)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)@PubMed: 1429696;PubMed: 8206981;PubMed: 8955086;PubMed: 10366876ReviewTCATGGTAACAATT SITE3SORPS1S000212 11-May-2006 (last modified) kehi�Site 3 of spinach (S.o.) rps1 promoter; S1F binding site; For acompilation of related GT elements and factors, see Villain etal. (1996);Site 3rps1S1Fspinach (Spinacia oleracea)IVillain P, Clabault G, Mache R, Zhou DXVillain P, Mache R, Zhou DXZhou DX�>S1F binding site is related to but different from thelight-responsive GT-1 binding site and differentially repressesthe spinach rps1 promoter in transgenic tobaccoThe mechanism of GT element-mediated cell type-specifictranscriptional controlRegulatory mechanism of plant gene transcription by GT-elementsand GT-factorsmJ Biol Chem 269:16626-16630 (1994)J Biol Chem 271:32593-32598 (1996)Trends in Plant Science 4:210-214 (1999)0PubMed: 8206981;PubMed: 8955086;PubMed: 10366876ReviewAGTTAGTTAAAAGA
SITEIIAOSPCNAS000216 11-May-2006 (last modified) kehi�h"Site IIa" of rice (O.s.) PCNA (proliferating cell nuclearantigen) gene; Found at -197 to -188; Binding site for twonuclear proteins, PCF1 and PCF2 (Kosugi and Ohashi, 1997);Suggested to be involved in meristematic tissue-specificexpression; Resemble the conserved motif (T/GGTCCCAT) found inpromoter regions of auxin-regulated genes; See S000026(AUXREPSIAA4);PCNASite IIameristemtissue-specificrice (Oryza sativa)5Kosugi S, Suzuka I, Ohashi YKosugi S, Ohashi YZhou DX�FTwo of three promoter elements identified in a rice gene forproliferating cell nuclear antigen are essential for meristematictissue-specific expressionPCF1 and PCF2 specifically bind to cis elements in the riceproliferating cell nuclear antigen geneRegulatory mechanism of plant gene transcription by GT-elementsand GT-factors^Plant J 7:877-886 (1995)Plant Cell 9:1607-1619 (1997)Trends in Plant Science 4:210-214 (1999)0PubMed: 7599648;PubMed: 9338963;PubMed: 10366876Review TGGGCCCGT SITEIIATCYTCS000474#01-August-2006 (last modified) kehi��"Site II element" found in the promoter regions of cytochromegenes (Cytc-1, Cytc-2) in Arabidopsis; Located between -147 and-156 from the translational starts sites (Welchen et al., 2005);Y=C/T; See also S000308; Overrepresented in the promoters ofnuclear genes encoding components of the oxidativephosphorylation (OxPhos) machinery from both Arabidopsis and rice(Welchen and Gonzalez, 2006);)
cytochrome
TCP-domainmeristemoxidative phosphorylation*Arabidopsis thaliana; Oryza sativa (rice);.Welchen E, Gonzalez DH.Welchen E, Gonzalez DH.��Differential expression of the Arabidopsis cytochrome c genesCytc-1 and Cytc-2. Evidence for the involvement of TCP-domainprotein-binding elements in anther- and meristem-specificexpression of the Cytc-1 gene.Overrepresentation of Elements Recognized by TCP-DomainTranscription Factors in the Upstream Regions of Nuclear GenesEncoding Components of the Mitochondrial OxidativePhosphorylation Machinery.APlant Physiol.139: 88-100 (2005)Plant Physiol. 141:540-545 (2006) PubMed: 16113211PubMed: 16760496 in silicoTGGGCY
SITEIIBOSPCNAS000217 10-May-1998 (last modified) kehi�b"Site IIb" of rice PCNA (proliferating cell nuclear antigen)gene; Found at -178 to -169; Binding site for two nuclearproteins, PCF1 and PCF2 (Kosugi and Ohashi, 1997); Suggested tobe involved in meristematic tissue-specific expression; Resemblethe conserved motif (T/GGTCCCAT) found in promoter regions ofauxin-regulated genes; See S000026 (AUXREPSIAA4);PCNASite IIbmeristemtissue-specificrice (Oryza sativa).Kosugi S, Suzuka I, Ohashi YKosugi S, Ohashi Y�Two of three promoter elements identified in a rice gene forproliferating cell nuclear antigen are essential for meristematictissue-specific expressionPCF1 and PCF2 specifically bind to cis elements in the riceproliferating cell nuclear antigen gene5Plant J 7:877-886 (1995)Plant Cell 9:1607-1619 (1997) PubMed: 7599648;PubMed: 9338963; TGGTCCCAC SITEIOSPCNAS000224 10-May-1998 (last modified) kehi�"Site I" of rice (O.s.) PCNA (proliferating cell nuclear antigen)gene; Found at -201 to -194; Resemble G-box; May contribute inpart to transcriptional activation;PCNASite IG-boxmeristemrice (Oryza sativa) Kosugi S, Suzuka I, Ohashi Y�Two of three promoter elements identified in a rice gene forproliferating cell nuclear antigen are essential for meristematictissue-specific expressionPlant J 7:877-886 (1995)PubMed: 7599648; CCAGGTGG SORLIP1ATS000482%18-November-2005 (last modified) kehi��one of "Sequences Over-Represented in Light-Induced Promoters(SORLIPs) in Arabidopsis; Computationally identified phyA-inducedmotifs; SORLIP 1 is most over-represented, and most statisticallysingnificant; See also S000483, S000484, S000485, S000486 (allSORLIPs), and also S000487, S000488, S000489, S000490 (allSORLREPs); Over-represented in light-induced cotyledon and rootcommon genes and root-specific genes (Jiao et al. 2005; seeS000486);phyA phytochromelightArabidopsis thaliana8Hudson ME, Quail PH.Jiao Y, Ma L, Strickland E, Deng XW.� Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.Conservation and Divergence of Light-Regulated Genome ExpressionPatterns during Seedling Development in Rice and Arabidopsis.DPlant Physiol. 133: 1605-1616 (2003)Plant Cell. 17: 3239-3256 (2005) PubMed: 14681527PubMed: 16284311,in silico; over-represented motif;in silico;GCCAC SORLIP2ATS000483%18-November-2005 (last modified) kehi�one of "Sequences Over-Represented in Light-Induced Promoters(SORLIPs) in Arabidopsis; Computationally identified phyA-inducedmotifs; See also S000482, S000484, S000485, S000486 (allSORLIPs), and also S000487, S000488, S000489, S000490 (allSORLREPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif;GGGCC SORLIP3ATS000484%18-November-2005 (last modified) kehi�one of "Sequences Over-Represented in Light-Induced Promoters(SORLIPs) in Arabidopsis; Computationally identified phyA-inducedmotifs; See also S000482, S000483, S000485, S000486 (allSORLIPs), and also S000487, S000488, S000489, S000490 (allSORLREPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif; CTCAAGTGA SORLIP4ATS000485%18-November-2005 (last modified) kehi�one of "Sequences Over-Represented in Light-Induced Promoters(SORLIPs) in Arabidopsis; Computationally identified phyA-inducedmotifs; See also S000482, S000483, S000484, S000486 (allSORLIPs), and also S000487, S000488, S000489, S000490 (allSORLREPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif; GTATGATGG SORLIP5ATS000486%18-November-2005 (last modified) kehi�kone of "Sequences Over-Represented in Light-Induced Promoters(SORLIPs) in Arabidopsis; Computationally identified phyA-inducedmotifs; See also S000482, S000483, S000484, S000485 (allSORLIPs), and also S000487, S000488, S000489, S000490 (allSORLREPs); Over-represented in both light-inducedcotyledon-specific and root-specific genes (Jiao et al. 2005; seeS000482);phyA phytochromelightArabidopsis thaliana8Hudson ME, Quail PH.Jiao Y, Ma L, Strickland E, Deng XW.� Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.Conservation and Divergence of Light-Regulated Genome ExpressionPatterns during Seedling Development in Rice and Arabidopsis.DPlant Physiol. 133: 1605-1616 (2003)Plant Cell. 17: 3239-3256 (2005) PubMed: 14681527PubMed: 16284311,in silico; over-represented motif;in silico;GAGTGAG
SORLREP2ATS000487%18-November-2005 (last modified) kehi�� one of "Sequences Over-Represented in Light-Repressed Promoters(SORLREPs) in Arabidopsis; Computationally identifiedphyA-repressed motifs; See also S000488, S000489, S000490 (allSORLREPs); and also S000482, S000483, S000484, S000485, S000486(all SORLIPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif; ATAAAACGT
SORLREP3ATS000488%18-November-2005 (last modified) kehi�� one of "Sequences Over-Represented in Light-Repressed Promoters(SORLREPs) in Arabidopsis; Computationally identifiedphyA-repressed motifs; See also S000487, S000489, S000490 (allSORLREPs); and also S000482, S000483, S000484, S000485, S000486(all SORLIPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif; TGTATATAT
SORLREP4ATS000489%18-November-2005 (last modified) kehi�(one of "Sequences Over-Represented in Light-Repressed Promoters(SORLREPs) in Arabidopsis; Computationally identifiedphyA-repressed motifs; Common in circadian-regulated promoters;See also S000487, S000488, S000490 (all SORLREPs); and alsoS000482, S000483, S000484, S000485, S000486 (all SORLIPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif; CTCCTAATT
SORLREP5ATS000490%18-November-2005 (last modified) kehi�� one of "Sequences Over-Represented in Light-Repressed Promoters(SORLREPs) in Arabidopsis; Computationally identifiedphyA-repressed motifs; See also S000487, S000488, S000489 (allSORLREPs); and also S000482, S000483, S000484, S000485, S000486(all SORLIPs);phyA phytochromelightArabidopsis thalianaHudson ME, Quail PH.�Identification of promoter motifs involved in the network ofphytochrome A-regulated gene expression by combined analysis ofgenomic sequence and microarray data.$Plant Physiol. 133: 1605-1616 (2003)PubMed: 14681527"in silico; over-represented motif;
TTGCATGACT
SP8BFIBSP8AIBS000183 16-Feb-2001 (last modified) seki��One of SPBF binding site (SP8a); Found at -155 of gSPO-A1(sporamin) gene, and also at -880 of gB-Amy (beta-amylase) genein sweet potato (I.b.); SP8BF recognizes both SP8a and SP8bsequences; See also SP8BFIBSP8BIB (S000184); SP8BF activity isalso found in tobacco; "SP8a" found in the 5' upstream region ofthree differnt genes coding for sporamin and beta-amylase;Binding site of SPF1; SPF1 also binds to the SP8b; See S000184;SP8SP8aSP8BFsporamin beta-amylaseamylase
tuberous rootroot sweet potato (Ipomoea batatas);,Ishiguro S, Nakamura KIshiguro S, Nakamura K�FThe nuclear factor SP8BF binds to the 5'-upstream regions ofthree different genes coding for major proteins of sweet potatotuberous rootsCharacterization of a cDNA encoding a novel DNA-binding protein,SPF1, that recognizes SP8 sequences in the 5' upstream regions ofgenes coding for sporamin and beta-amylase from sweet potato@Plant Mol Biol 18:97-108 (1992)Mol Gen Genet 244: 563-571 (1994) PubMed: 1531033;PubMed: 7969025; ACTGTGTA
SP8BFIBSP8BIBS000184 16-Feb-2001 (last modified) seki��One of SPBF binding site (SP8b); Found at -330, -220, and -200 ofgSPO-B1 (sporamin) gene, and also at -80 of gB-Amy (beta-amylase)gene; SP8BF recognizes both SP8a and SP8b sequences; See alsoSP8BFIBSP8AIB (S000183); SP8BF activity is also found in tobacco;"SP8b" found in the 5' upstream region of three differnt genescoding for sporamin and beta-amylase; Binding site of SPF1; SPF1also binds to the SP8b; See S000184; SP8SP8bSP8BFsporamin beta-a,ylaseamylase
tuberous roottuberroot sweet potato (Ipomoea batatas);,Ishiguro S, Nakamura KIshiguro S, Nakamura K�FThe nuclear factor SP8BF binds to the 5'-upstream regions ofthree different genes coding for major proteins of sweet potatotuberous rootsCharacterization of a cDNA encoding a novel DNA-binding protein,SPF1, that recognizes SP8 sequences in the 5' upstream regions ofgenes coding for sporamin and beta-amylase from sweet potato@Plant Mol Biol 18:97-108 (1992)Mol Gen Genet 244: 563-571 (1994) PubMed: 1531033;PubMed: 7969025; TACTATT SPHCOREZMC1S000154 16-Feb-2001 (last modified) seki�nCore of Sph element; Core motif of Sph element in maize (Z.m.) C1gene to which maize VP1 (viviparous 1) protein binds;VP1-responsive element; see RYREPEAT4 (S000010); VP1 gene isspecifically required for expression of the maturation program inseed development; VP1 is a novel transcription factor possiblyinvolved in potentiation of a seed-specific hormone response; Sph motifC1VP1ABAseedmaize (Zea mays);XSuzuki M, Kao CY, McCarty DRMcCarty DR, Hattori T, Carson CB, Vasil V, Lazar M, Vasil IK�The conserved B3 domain of VIVIPAROUS1 has a cooperative DNAbinding activity.The Viviparous-1 developmental gene of maize encodes a noveltranscriptional activator2Plant Cell 9:799-807 (1997)Cell 66: 895-905 (1991) PubMed: 9165754;PubMed: 1889090; TCCATGCATSPHZMC1S000293 16-Feb-2001 (last modified) seki�R"Sph element" found in the maize (Z.m.) C1 gene promoter; Locatedbetween -142 and -132; Essential for VP1 activation; See S000154,S000294; VP1 gene is specifically required for expression of thematuration program in seed development; VP1 is a noveltranscription factor possibly involved in potentiation of aseed-specific hormone response;C1anthocyanin pathwayABAVP1lightSphseedmaize (Zea mays)gKao CY, Cocciolone SM, Vasil IK, McCarty DRMcCarty DR, Hattori T, Carson CB, Vasil V, Lazar M, Vasil IK�Localization and interaction of the cis-acting elements forabscisic acid, VIVIPAROUS1, and light activation of the C1 geneof maizeThe Viviparous-1 developmental gene of maize encodes a noveltranscriptional activator5Plant Cell 8: 1171-1179 (1996)Cell 66: 895-905 (1991) PubMed: 8768375PubMed: 1889090; CGTCCATGCATSREATMSDS000470#13-August-2005 (last modified) kehi�"sugar-repressive element (SRE)" found in 272 of the 1592down-regulated genes after main stem decapitation in Arabidopsis;See also S000471, S000472;Axillary bud outgrowthArabidopsis thaliana3Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E.wIdentification of cis-elements that regulate gene expressionduring initiation of axillary bud outgrowth in Arabidopsis.$Plant Physiology 138: 757-766 (2005)PubMed: 15908603 TTATCC SRENTTTO1S000271 15-Oct-1999 (last modified) kehi� Stress responsive element (SRE) in tobacco (N.t.) retrotransposonTto1; A 13 bp cis-regulatory element in the LTR promoter of thetobacco retrotransposon Tto1; Involved in responsiveness totissue culture, wounding, methyl jasmonate and fungal elicitors;Contains a conserved motif, Box L; retrotransposonLTRTto1woundingstresstissue culturemethyl jasmonatefungal elicitorBox Ltobacco (Nicotiana tabacum)+Takeda S, Sugimoto K, Otsuki H, Hirochika H�A 13-bp cis-regulatory element in the LTR promoter of the tobaccoretrotransposon Tto1 is involved in responsiveness to tissueculture, wounding, methyl jasmonate and fungal elicitorsPlant J 18:383-393 (1999)PubMed: 10406122;
TGGTAGGTGAGAT SURE1STPAT21S000186 17-May-1998 (last modified) kehi�Sucrose Responsive Element (SURE); A motif conserved among genesregulated by sucrose; See also SURE2STPAT21 (S000185); Foundbetween -184 and -156 bp in the patatin (a major tuber protein)gene promoter of potato (S.t.);SURESURE 1patatinsucrosetuberrootpotato (Solanum tuberosum);DGrierson C, Du JS, Zabala MT, Beggs K, Smith C, Holdsworth M,Bevan M|Separate cis sequences and trans factors direct metabolic anddevelopmental regulation of a potato tuber storage protein genePlant J 5:815-826 (1994)PubMed: 8054988; AATAGAAAA SURE2STPAT21S000185 17-May-1998 (last modified) kehi�Sucrose Responsive Element 2 (SURE2); A motif conserved amonggenes regulated by sucrose; See also SURE1ST (S000186); Foundbetween -184 and -156 bp in the patatin (a major tuber protein)gene promoter of potato (S.t.);SURESURE 2patatinsucrosetuberrootpotato (Solanum tuberosum);DGrierson C, Du JS, Zabala MT, Beggs K, Smith C, Holdsworth M,Bevan M|Separate cis sequences and trans factors direct metabolic anddevelopmental regulation of a potato tuber storage protein genePlant J 5:815-826 (1994)PubMed: 8054988; AATACTAAT SUREAHVISO1S000441 28-Jan-2004 (last modified) kehi�"SURE-a"; Sugar-responsive element found in barley (H. vulgare)iso1 (encoding isoamylase1) promoter at -597 to -573; Highlysimilar to SURE of potato class-1 putative promoter; SUSIBA2(WRKY transcription factor) binding site;sugarSUREpatatinWRKY
isoamylaseSUSIBA"Hordeum vulgare (barley)@Sun C, Palmqvist S, Olsson H, Boren M, Ahlandsberg S, Jansson C.�A novel WRKY transcription factor, SUSIBA2, participates in sugarsignaling in barley by binding to the sugar-responsive elementsof the iso1 promoter. Plant Cell 15: 2076-2092 (2003)PubMed: 12953112; AAAACTAAGAAAGACCGATGGAAAASURECOREATSULTR11S000499#02-August-2006 (last modified) kehi��Core of sulfur-responsive element (SURE) found in the promoter ofSULTR1;1 high-affinity sulfate transporter gene in Arabidopsis;SURE contains auxin response factor (ARF) binding sequence(GAGACA)(see S000270 ARF:TGTCTC; its complementary seq isGAGACA), and this core sequence is a part of it; this core seq isinvolved in -S response; Beware of other SURE (sucrose responsiveelement) !!;sulfate uptakesulfate transporterARF-SSArabidopsis thalianaVMaruyama-Nakashita A, Nakamura Y, Watanabe-Takahashi A, Inoue E,Yamaya T, Takahashi H.gIdentification of a novel cis-acting element conferring sulfurdeficiency response in Arabidopsis roots. Plant J. 42: 305-314 (2005).PubMed: 15842617 GAGAC
SV40COREENHANS000123 17-May-1998 (last modified) kehiB"SV40 core enhancer"; Similar sequences found in rbcS genes;W=A/T;enhancerSV40core8virus; plant; pea (Pisum sativum); Arabidopsis thaliana;KWeiher H, Konig M, Gruss PGreen PJ, Kay SA, Chua N-HDonald RGK, Cashmore AR� Multiple point mutations affecting the simian virus 40 enhancer.Sequence-specific interactions of a pea nuclear factor withlight-responsive elements upstream of the rbcs3A gene.Mutation of either G box or I box sequences profoundly affectsexpression from the Arabidopsis rbcs-1A promoter.LScience 219:626-631 (1983)EMBO J 6:2543-2549 (1987)EMBO J 9:1717-1726 (1990)0PubMed: 6297005;PubMed: 3678200;PubMed: 2347304; GTGGWWHG T/GBOXATPIN2S000458%29-November-2004 (last modified) kehi�"T/G-box" found in tomato proteinase inhibitor II (pin2) andleucine aminopeptidase (LAP) genes; Involved in jasmonate (JA)induction of these genes; bHLH-Leu zipper JAMYC2 and JAMYC10proteins specifically recognaize this motif (Boter et al.,2004);T/G-boxJApin2LAPMYCwounding7Lycopersicon esculentum (tomato); Arabidopsis thaliana;)Boter M, Ruiz-Rivero O, Abdeen A, Prat S.iConserved MYC transcription factors play a key role in jasmonatesignaling both in tomato and Arabidopsis. Genes Dev 18: 1577-1591 (2004).PubMed: 15231736 AACGTG TAAAGSTKST1S000387 20-Feb-2002 (last modified) uchi�TAAAG motif found in promoter of Solanum tuberosum (S.t.) KST1gene; Target site for trans-acting StDof1 protein controllingguard cell-specific gene expression; KST1 gene encodes a K+influx channel of guard cells; See S000265;KST1Dof
guard cellSolanum tuberosum (potato)&Plesch G, Ehrhardt T, Mueller-Roeber BqInvolvement of TAAAG elements suggests a role for Doftranscription factors in guard cell-specific gene expressionPlant J 28: 455-464 (2001)PubMed: 11737782; TAAAG TACBBFNTEAS4S000257 14-0ct-1999 (last modified) kehi�'TacBBF (TAC box binding factor) binding site in tobacco (N.t.)5-epi-aristolochene synthase (EAS4) gene; Required forelicitor-inducibility; EAS is involved in sesquiterpenephytoalexin biosynthesis; Found between -245 and -232; Appears tofunction as a silencer or repressor of EAS gene expression;EASelicitorTAC boxTacBBF
sesquiterpene phytoalexinsilencer repressortobacco (Nicotiana tabacum) Newman JD, Yin S, Chappell JiCharacterization of the TAC box, a cis-element within anelicitor-inducible sesquiterpene cyclase promoterPlant J 16:1-12 (1998) ACTCTACAGTACTCTATABOX1S000108"12-April-2004 (last modified) kehi�"TATA box"; TATA box found in the 5'upstream region of ricealpha-amylase; TATA box found in beta-phaseolin promoter (Graceet al.); sequence and spacing of TATA box elements are criticalfor accurate initiation (Grace et al.);amylasericeTATAseed phaseolin/rice (Oryza sativa); bean (Phaseolus vulgaris);0Grace ML, Chandrasekharan MB, Hall TC, Crowe AJ.oSequence and spacing of TATA box elements are critical foraccurate initiation from the beta-phaseolin promoter."J Biol Chem. 279:8102-8110 (2004).PubMed: 14660650
CTATAAATACTATABOX2S000109"12-April-2004 (last modified) kehi�"TATA box"; TATA box found in the 5'upstream region of pea legAgene; sporamin A of sweet potato; TATA box found inbeta-phaseolin promoter (Grace et al.); sequence and spacing ofTATA box elements are critical for accurate initiation (Grace etal.);TATAlegA phaseolinKpea (Pisum sativum); tobacco (Nicotiana tabacum); bean (Phaseolusvulgaris);WShirsat A, Wilford N, Croy R, Boulter DGrace ML, Chandrasekharan MB, Hall TC, Crowe AJ.�Sequences responsible for the tissue specific promoter activityof a pea legumin gene in tobacco.Sequence and spacing of TATA box elements are critical foraccurate initiation from the beta-phaseolin promoter.BMol Gen Genet 215:326-331 (1989)J Biol Chem. 279:8102-8110 (2004). PubMed: 2710102;PubMed: 14660650 TATAAATTATABOX3S000110 17-Jun-1997 (last modified) kehiS"TATA box"; TATA box found in the 5'upstream region of sweetpotato sporamin A gene;TATAsporamin sweet potato (Ipomoea batatas); TATTAATTATABOX4S000111"12-April-2004 (last modified) kehi�"TATA box"; TATA box found in the 5'upstream region of sweetpotato sporamin A gene; TATA box found in beta-phaseolin promoter(Grace et al.); sequence and spacing of TATA box elements arecritical for accurate initiation (Grace et al.);TATAsporamin phaseolin9sweet potato (Ipomoea batatas); bean (Phaseolus vulgaris)0Grace ML, Chandrasekharan MB, Hall TC, Crowe AJ.oSequence and spacing of TATA box elements are critical foraccurate initiation from the beta-phaseolin promoter."J Biol Chem. 279:8102-8110 (2004).PubMed: 14660650 TATATAATATABOX5S000203 17-May-1998 (last modified) kehi�"TATA box"; TATA box found in the 5'upstream region of pea (Pisumsativum) glutamine synthetase gene; a functional TATA element byin vivo analysis;TATA glutamine
synthetasepea (Pisum sativum); Tjaden G, Edwards JW, Coruzzi GM�cis elements and trans-acting factors affecting regulation of anonphotosynthetic light-regulated gene for chloroplast glutaminesynthetase"Plant Physiol 108:1109-1117 (1995)!PubMed: 7630938; GenBank: U22971; TTATTT TATABOXOSPALS000400 27-Aug-2002 (last modified) uchi�Binding site for OsTBP2, found in the promoter of rice pal geneencoding phenylalanine ammonia-lyase; OsTFIIB stimulated the DNAbinding and bending activities of OsTBP2 and synergisticallyenhanced OsTBP2-mediated transcription from the pal promoter;TBPTFIIBpalDNA binding and bendingOryza sativa (rice)*Zhu Q, Ordiz MI, Dabi T, Beachy RN, Lamb C�Rice TATA binding protein interacts functionally withtranscription factor IIB and the RF2a bZIP transcriptionalactivator in an enhanced plant in vitro transcription system Plant Cell 14: 795-803 (2002)PubMed: 11971135; TATTTAA
TATAPVTRNALEUS000340 21-May-2002 (last modified) uchi�"TATA-like motif"; A TATA-like sequence found in Phaseolusvulgaris tRNALeu gene promoter; Frequently observed upstream ofplant tRNA genes; Found in maize glycolyticglyceraldehyde-3-phospate dehydrogenase 4 (GapC4) gene promoter;Binding site of TATA binding protein (TBP);TATAtRNA
re-initiationGapC4MybTATA binding proteinTBP$Phaseolus vulgaris; maize (Zea mays)SYukawa Y, Sugita M, Choisne N, Small I, Sugiura MGeffers R, Sell S, Cerff R, Hehl R�The TATA motif, the CAA motif and the poly(T) transcriptiontermination motif are all important for transcriptionre-initiation on plant tRNA genesThe TATA box and a Myb binding site are essential for anaerobicexpression of a maize GapC4 minimal promoter in tobaccoCPlant J 22: 439-447 (2000)Biochim Biophys Acta 1521: 120-125 (2001)"PubMed: 10849359;PubMed: 11690643; TTTATATA
TATCCACHVAL21S000416 10-May-2006 (last modified) kehi�!"TATCCAC box" is a part of the conserved cis-acting responsecomplex (GARC) that most often contain three sequence motifs, theTAACAAA box (see S000181), or GA-responsive element (GARE); thepyrimidine box, CCTTTT (see S000259); and the TATCCAC box, whichare necessary for a full GA response; gibberellinGAGARCbarley (Hordeum vulgare)}Isabel-LaMoneda I, Diaz I, Martinez M, Mena M, Carbonero P.Martinez M, Rubio-Somoza I, Fuentes R, Lara P, Carbonero P, DiazI.�SAD: a new DOF protein from barley that activates transcriptionof a cathepsin B-like thiol protease gene in the aleurone ofgerminating seeds.The barley cystatin gene (Icy) is regulated by DOF transcriptionfactors in aleurone cells upon germination.8Plant J. 33: 329-340 (2003)J Exp Bot. 56: 547-556 (2005)!PubMed: 12535346;PubMed: 15611149 TATCCAC TATCCAOSAMYS000403&15-September-2006 (last modified) kehi�3"TATCCA" element found in alpha-amylase promoters of rice (O.s.)at positions ca.90 to 150bp upstream of the transcription startsites; Binding sites of OsMYBS1, OsMYBS2 and OsMYBS3 whichmediate sugar and hormone regulation of alpha-amylase geneexpression; See also S000021 (AMYBOX2); S000256 (TATCCAY motif);
alpha-amylase MYB proteins gibberellinGAsugar starvationOryza sativa (rice)SLu CA, Ho THD, Ho SL, Yu SMLu CA, Lim EK, Yu SM.Chen PW, Chiang CM, Tseng TH, Yu SM�fThree Novel MYB Proteins with One DNA Binding Repeat MediateSugar and Hormone Regulation of alpha-Amylase Gene ExpressionSugar response sequence in the promoter of a rice alpha-amylasegene serves as a transcriptional enhancer.Interaction between Rice MYBGA and the Gibberellin ResponseElement Controls Tissue-Specific Sugar Sensitivity ofalpha-Amylase Genes.bPlant Cell 14: 1963-1980 (2002)J Biol Chem. 273:10120-10131(1998).PLANT CELL 18: 2326-2340 (2006).0PubMed: 12172034;PubMed: 9553059PubMed: 16905658 TATCCATATCCAYMOTIFOSRAMY3DS000256#01-August-2006 (last modified) kehi�"TATCCAY motif" found in rice (O.s.) RAmy3D alpha-amylase genepromoter; Y=T/C; a GATA motif as its antisense sequence; TATCCAYmotif and G motif (see S000130) are responsible for sugarrepression (Toyofuku et al. 1998);GATAamylasesugar
repressionrice (Oryza sativa)]Toyofuku K, Umemura T, Yamaguchi JRubio-Somoza I, Martinez M, Abraham Z, Diaz I, Carbonero P.�Promoter elements required for sugar-repression of the RAmy3Dgene for alpha-amylase in riceTernary complex formation between HvMYBS3 and other factorsinvolved in transcriptional control in barley seeds.8FEBS Lett 428:275-280 (1998)Plant J. 47: 269-281 (2006) PubMed: 9654148;PubMed: 16762033 TATCCAY
TBOXATGAPBS000383 23-Aug-2001 (last modified) uchi�<"Tbox" found in the Arabidopsis thaliana (A.T.) GAPB genepromoter; Located between -94 and -89 (T1) and also between -84and -79 (T2); Mutations in the "Tbox" resulted in reductions oflight-activated gene transcription; GAPB encodes the B subunit ofchloroplast glyceraldehyde-3-phosphate dehydrogenase(GADPH) ofA.T.;GAPB(glyceraldehyde-3-phosphate dehydrogenaselight-activated
transcriptionArabidopsis thalianaChan CS, Guo L, Shih MC�Promoter analysis of the nuclear gene encoding the chloroplastglyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsisthaliana!Plant Mol Biol 46: 131-141 (2001)PubMed: 11442054; ACTTTG TCA1MOTIFS000159 17-May-1998 (last modified) kehi�STCA-1 (tobacco nuclear protein 1) binding site; Related tosalicylic acid-inducible expression of many genes; Found inbarley beta-1,3-glucanase and over 30 different plant genes whichare known to be induced by one or more forms of stress; A similarsequence (TCATTTCTT) was found in tobacco Tnt1 retrotransposonpromoter (Mhiri et al., 1997);SAsalicylic acidstressTCA-16barley (Hordeum vulgare); tobacco (Nicotiana tabacum);pGoldsbrough AP, Albrecht H, Stratford RMhiri C, Morel JB, Verbhettes S, Casacuberta JM, Lucas H,Graandbastien MA�Salicylic acid-inducible binding of a tobacco nuclear protein toa 10 bp sequence which is highly conserved amongststress-inducible genes.The promoter of the tobacco Tnt1 retrotransposon is induced bywounding and by abiotic stress8Plant J 3:563-571 (1993)Plant Mol Biol 33:257-266 (1997) PubMed: 8220463;PubMed: 9037144;
TCATCTTCTT
TDBA12NTCHN50S000266!22-June-2006 (last modified) kehi�TDBA12 binding site found in tobacco (N.t.) basic class Ichitinase gene (CHN50); Elicitor response element; TDBA12 belongsto WRKY proteins that appear to be unique to plants; TDBA12 isactivated by TMV infection in resistant tobacco plant and byplant defense signal molecule SA;TDBA12 chitinaseCHN50WRKYHRTMVSARelicitortobacco (Nicotiana tabacum)RYang P, Chen C, Wang Z, Fan B, Chen ZEulgem T, Rushton PJ, Robatzek S, Somssich IE�A pathogen- and salicylic acid-induced WRKY DNA-binding activityrecognizes the elicitor response element of the tobacco class Ichitinase gene promoterThe WRKY superfamily of plant transcription factors;Plant J 18:141-149 (1999)Trends Plant Sci 5: 199-206 (2000)PubMed: 10785665;Review TGACTTTCTGAC TE2F2NTPCNAS000397%05-November-2005 (last modified) kehi�"te2f-2" found in the promoter of tobacco PCNA gene; Locatedbetween -84 and -77; Binding site of OsE2F1 and OsE2F2; Involvedin transcriptional activation in actively dividing cells andtissue;E2FPCNAmeristematic tissue
cell cycletobacco (Nicotiana tabacum)Kosugi S, Ohashi Y�E2F sites that can interact with E2F proteins cloned from riceare required for meristematic tissue-specific expression of riceand tobacco proliferating cell nuclear antigen promotersPlant J 29: 45-59 (2002)PubMed: 12060226; ATTCCCGC TEF1BOXATA1S000311 7-Sep-2000 (last modified) seki�^"tef1 box" found in the Arabidopsis (A.t.) EF-1 alpha A1 genepromoter; Conserved in the A.t. EF-1 alpha gene promoters;Involved in the activation of EF-1 alpha gene; Involved in thetranscriptional activation of plant genes that are overexpressedin cycling cells; Conserved in the promoters of genes forproducts related to the translational apparatus; EF-1alphaA1tef1 box"Arabidopsis (Arabidopsis thaliana)�Curie C, Liboz T, Bardet C, Gander E, Medale C, Axelos M, LescureBRegad F, Herve C, Marinx O, Bergounioux C, Tremousaygue D, LescueB� Cis and Trans-acting elements involved in the activation ofArabidopsis thaliana A1 gene encoding the translation elongationfactor EF-1alphaThe tef1 box, a ubiquitous cis-acting element involved in theactivation of plant genes that are highly expressed in cyclingcellsONucleic Acids Research 19: 1305-1310 (1991)Mol. Gen. Genet. 248: 703-711 (1995) PubMed: 1840652;PubMed: 7476873; ACAGGGGCATAATGGTAATTTAAATEFBOXATEEF1AA1S000309 7-Sep-2000 (last modified) seki�"tef-box" found in the Arabidopsis (A.t.) eEF1AA1 gene promoter;An activating sequence associated with telo-box (S000308);Required for the gene expression in root primordia; Actsco-operatively with telo-box; See S000308;tef-boxtelomere motifl eEF1Aroot primordiatelo-box"Arabidopsis (Arabidopsis thaliana):Tremousayque D, Manevski A, Bardet C, Lescure N, Lescure BaPlant interstitial telomere mitifs participate in the control ofgene expression in root meristemsPlant J 20: 553-561 (1999)PubMed: 10652127; AGGGGCATAATGGTAATELOBOXATEEF1AA1S000308%05-November-2005 (last modified) kehi�p"telo-box" (telomere motif) found in the Arabidopsis (A.t.)eEF1AA1 gene promoter; Conserved in all known plant eEF1A genepromoters; Found in the 5' region of numerous genes encodingcomponents of the translational apparatus; Required for theactivation of expression in root primordia; Acts co-operativelywith tef-box; Binding site of AtPur alpha-1; See S000309,S000474;telo-boxtelomere motifeEF1Aroot primordiatef-boxPuralpha-1"Arabidopsis (Arabidopsis thaliana)�Tremousayque D, Manevski A, Bardet C, Lescure N, Lescure BAxelos M, Bardet C, Liboz T, Va Thai AL, Curie C, Lescure BWelchen E, Gonzalez DH.��Plant interstitial telomere mitifs participate in the control ofgene expression in root meristemsThe gene family encoding the Arabidopsis thaliana translationelongation factor EF-1alpha: Molecular clonig, characterizationand expression.Differential expression of the Arabidopsis cytochrome c genesCytc-1 and Cytc-2. Evidence for the involvement of TCP-domainprotein-binding elements in anther- and meristem-specificexpression of the Cytc-1 gene.[Plant J 20: 553-561 (1999)Mol Gen Genet 219: 106-112 (1989)Plant Physiol.139: 88-100 (2005)0PubMed: 10652127;PubMed: 2615757PubMed: 16113211 AAACCCTAA TGA1ANTPR1AS000247 16-Feb-2001 (last modified) seki�;TGA1a binding site in tobacco (N.t.) PR1a gene; as-1-likesequence; Contains two TGACG elements reminiscent of activationsequence-1 (as-1); See other as-1-like sequences; TGA1a ispreferentially expressed in root tip meristems; TGA1a maycontribute to the expression of GST isoenzymes, especially inroot tip meristems;TGA1aas-1PR1axenobiotic stressroottipmeristemtobacco (Nicotiana tabacum)�Strompen G, Gruner R, Pfitzner UMKlinedinst S, Pascuzzi P, Redman J, Desai M, Arias JGruner R, Strompen G, Pfitzner AJ, Pfitzner UM.��An as-1-like motif controls the level of expression of the genefor the pathogenesis-related protein 1a from tobaccoA xenobiotic-stress-activated transcription factor and itscognate target genes are preferentially expressed in root tipmeristemsSalicylic acid and the hypersensitive response initiate distinctsignal transduction pathways in tobacco that converge on theas-1-like element of the PR-1a promoter.fPlant Mol Biol 37:871-883 (1998)Plant Mol Biol 42: 679-688 (2000)Eur J Biochem. 270: 4876-4886 (2003)1PubMed: 9678582;PubMed: 10809441;PubMed: 14653814 CGTCATCGAGATGACG TGACGTVMAMYS000377 23-Aug-2001 (last modified) uchi�"TGACGT motif" found in the Vigna mungo (V.m.) alpha-Amylase(Amy) gene promoter; Located between -128 and -123; Required forhigh level expression of alpha-Amylase in the cotyledons of thegerminated seeds; See S000234;
alpha-Amylase cotyledonseed germinationseed Vigna mungo
Yamauchi D�A TGACGT Motif in the 5'-Upstream Region of alpha-Amylase Genefrom Vigna mungo is a cis-Element for Expression in Cotyledons ofGerminated Seeds%Plant Cell Physiol 42: 635-641 (2001)PubMed: 11427683; TGACGTTGTCACACMCUCUMISINS000422 29-Sep-2003 (last modified) kehi�"TGTCACA motif" found in the region (from -254 to -215) ofcucumisin (a subtilisin-like serine protease) in the fruit ofmelon (Cucumis melo L.); A novel enhancer element necessary forfruit-specific expression of the cucumisin gene; cucumisinfruitCucumis melo L. (melon))Yamagata H, Yonesu K, Hirata A, Aizono Y.tTGTCACA motif is a novel cis-regulatory enhancer element involvedin fruit-specific expression of the cucumisin gene.#J Biol Chem. 277:11582-11590 (2002)PubMed: 11782472; TGTCACATL1ATSARS000473#13-August-2005 (last modified) kehi�"TL1", a consensus sequence overrepresented in the promoterregions of all 13 NPR1-responsive ER-resident genes surveyed;NPR1 is "Nonexpressor of pathogenesis-related genes 1", alsoknown as NIM1;SARERPRNIM1Arabidopsis thaliana'Wang D, Weaver ND, Kesarwani M, Dong X.SInduction of protein secretory pathway is required for systemicacquired resistance. Science 308: 1036-1040 (2005)PubMed: 15890886 in silico CTGAAGAAGAATOPOISOMS000112 13-Feb-2001 (last modified) kehi�Topoisomerase cleavage site consensus sequence; Motif found inSAR (scaffold attachment region; or matrix attachment region,MAR); W=T/A,MARSAR topoisomerasscaffoldmatrix(fruit fly; Drosophila melanogaster; fly;>Sander M, Hsieh TGasser SM, Amati BB, Cardenas ME, Hofmann JFX�Drosophila topoisomerase II double-strand DNA cleavage: analysisof DNA sequence homology at the cleavage site.Studies on scaffold attachment sites and their relation to genomefunction.ENucleic Acid Res 13:1057-1072 (1985)Intnatl Rev Cyto 119:57-96 (1989)9PubMed: 2987816; GenBank: M30907, M30908;PubMed: 2695485;ReviewGTNWAYATTNATNNGTRANSINITDICOTSS000201 3-May-1998 (last modified) kehiCContext sequence of translational initiation codon in dicots;M=A/C; Translation
Initiationdicots;$Joshi CP, Zhou H, Huang X, Chiang VL;Context sequences of translation initiation codon in plants!Plant Mol Biol 35:993-1001 (1997)PubMed: 9426620; AMNAUGGCTRANSINITMONOCOTSS000202 3-May-1998 (last modified) kehiLContext sequence of translational initiation codon in monocots;R=A/G; M=A/C; Translation
Initiation monocots;$Joshi CP, Zhou H, Huang X, Chiang VL;Context sequences of translation initiation codon in plants!Plant Mol Biol 35:993-1001 (1997)PubMed: 9426620; RMNAUGGC TRANSTARTS000113 17-May-1998 (last modified) kehi4plant consensus sequence for translation start site; translationrice (Oryza sativa);1Joshi CPde Pater S, Hensgens LAM, Schilperoort RA�An inspection of the domain between putative TATA box andtranslation start site in 79 plant genes.Structure and expression of a light-inducible shoot-specific ricegene.ENucleic Acids Res 15:6643-6653 (1987)Plant Mol Biol 15:399-406 (1990)1PubMed: 3628002;PubMed: 2103460; GenBank: X51911; TAAACAATGGCTUP1ATMSDS000471#13-August-2005 (last modified) kehi�"Up1" motif found in 162 of the 1184 up-regulated genes aftermain stem decapitation in Arabidopsis; W=A/T; See also S000470,S000472;Axillary bud outgrowthArabidopsis thaliana3Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E.wIdentification of cis-elements that regulate gene expressionduring initiation of axillary bud outgrowth in Arabidopsis.$Plant Physiology 138: 757-766 (2005)PubMed: 15908603 GGCCCAWWWUP2ATMSDS000472#13-August-2005 (last modified) kehi�"Up2" motif found in 193 of the 1184 up-regulated genes aftermain stem decapitation in Arabidopsis; W=A/T; See also S000470,S000471;Axillary bud outgrowthArabidopsis thaliana3Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E.wIdentification of cis-elements that regulate gene expressionduring initiation of axillary bud outgrowth in Arabidopsis.$Plant Physiology 138: 757-766 (2005)PubMed: 15908603 AAACCCTAUPRE1ATS000428$04-January-2007 (last modified) kehi�"ERSEII-like sequence" found in the plant UPRE (unfolded proteinresponse element) in A.t.; See S000429; Either of ERSEII or XBP1binding sites is essential and sufficient for the UPR; SeeS000425, S000426;UPRUPREunfolded protein responseERSEIIERSEArabidopsis thaliananOh DH, Kwon CS, Sano H, Chung WI, Koizumi N.Martinez IM, Chrispeels MJ.Iwata Y, Koizumi N.Tajima H, Koizumi N.��Conservation between animals and plants of the cis-acting elementinvolved in the unfolded protein response.Genomic analysis of the unfolded protein response in Arabidopsisshows its connection to important cellular processes.An Arabidopsis transcription factor, AtbZIP60, regulates theendoplasmic reticulum stress response in a manner unique toplants.Induction of BiP by sugar independent of a cis-element for theunfolded protein response in Arabidopsis thaliana.�Biochem Biophys Res Commun. 301:225-230 (2003)Plant Cell. 15:561-576 (2003)Proc Natl Acad Sci U S A. 102: 5280-5285. (2005)Biochem Biophys Res Commun. 346:926-930 (2006)BPubMed: 12535667;PubMed: 12566592;PubMed: 15781873PubMed: 16781668 ATTGGTCCACGUPRE2ATS000429$04-January-2007 (last modified) kehi�"XBP1 binding site-like sequence" found in the plant UPRE(unfolded protein response element) in A.t.; See S000428; Eitherof ERSEII or XBP1 binding sites is essential and sufficient forthe UPR; See S000425 (CCACGTCA), S000426;UPRUPREunfolded protein responseERSEIIERSEArabidopsis thaliananOh DH, Kwon CS, Sano H, Chung WI, Koizumi N.Martinez IM, Chrispeels MJ.Iwata Y, Koizumi N.Tajima H, Koizumi N.��Conservation between animals and plants of the cis-acting elementinvolved in the unfolded protein response.Genomic analysis of the unfolded protein response in Arabidopsisshows its connection to important cellular processes.An Arabidopsis transcription factor, AtbZIP60, regulates theendoplasmic reticulum stress response in a manner unique toplants.Induction of BiP by sugar independent of a cis-element for theunfolded protein response in Arabidopsis thaliana.�Biochem Biophys Res Commun. 301:225-230 (2003)Plant Cell. 15:561-576 (2003)Proc Natl Acad Sci U S A. 102: 5280-5285. (2005)Biochem Biophys Res Commun. 346:926-930 (2006)@PubMed: 12535667PubMed: 12566592PubMed: 15781873PubMed: 16781668
CCACGTCATC UPRMOTIFIATS000425 29-Sep-2003 (last modified) kehi�"Motif I" in the conserved UPR (unfolded protein response)cis-acting element in Arabidopsis genes coding for SAR1B, HSP-90,SBR-like, Ca-ATPase 4, CNX1, PDI, etc.; See S000429 (CCACGTCATC);See also S000426, S000428, S000429;UPRunfolded protein responseArabidopsis thalianaGMartinez IM, Chrispeels MJ.Oh DH, Kwon CS, Sano H, Chung WI, Koizumi N.�Genomic analysis of the unfolded protein response in Arabidopsisshows its connection to important cellular processes.Conservation between animals and plants of the cis-acting elementinvolved in the unfolded protein response.KPlant Cell. 15:561-576 (2003)Biochem Biophys Res Commun. 301:225-230 (2003)"PubMed: 12566592;PubMed: 12535667; CCACGTCA UPRMOTIFIIATS000426 29-Sep-2003 (last modified) kehi�"Motif II" in the conserved UPR (unfolded protein response)cis-acting element in Arabidopsis genes coding for SAR1B, HSP-90,SBR-like, Ca-ATPase 4, CNX1, PDI, etc.; See S000425, S000428,S000429;UPRunfolded protein responseArabidopsis thalianaGMartinez IM, Chrispeels MJ.Oh DH, Kwon CS, Sano H, Chung WI, Koizumi N.�Genomic analysis of the unfolded protein response in Arabidopsisshows its connection to important cellular processes.Conservation between animals and plants of the cis-acting elementinvolved in the unfolded protein response.KPlant Cell. 15:561-576 (2003)Biochem Biophys Res Commun. 301:225-230 (2003)"PubMed: 12566592;PubMed: 12535667; CCNNNNNNNNNNNNCCACGVOZATVPPS000456%29-November-2004 (last modified) kehi�"VOZ-binding sequence" found in the promoter of A. thalianaV-PPase (vacuolar H+-pyrophosphatase) gene; Involved in itsexpression during pollen development; one-zinc finger;(Mitsuda etal., 2004);VOZV-PPasepollenArabidopsis thaliana+Mitsuda N, Hisabori T, Takeyasu K, Sato MH.�VOZ; isolation and characterization of novel vascular planttranscription factors with a one-zinc finger from Arabidopsisthaliana.'Plant Cell Physiol. 45: 845-854 (2004).PubMed: 15295067 GCGTNNNNNNNACGC VSF1PVGRP18S000249#19-August-2004 (last modified) kehi�jVSF-1 binding site in French bean (P.v.) grp1.8 gene promoter;VSF-1 is a tomato bZIP transcription factor; VSF-1 binding siteis found in 28 bp vs-1 element; This sequence controls vasculargene expression in transgenic tobacco; "VS-1" found in beangrp1.8 gene promoter; Located between -203 and -176; Partiallyoverlaps with NRE; Confers xylem-specific expression;VSF-1vasculargrp1.8VS-1bZIPXylem_French bean (Phaseolus vulgaris); tomato (Lycopersiconesculentum); tobacco (Nicotiana tabacum);NRingli C, Keller BTorres-Schumann S, Ringli C, Heierli D, Amrhein N, Keller B.�Specific interaction of the tomato bZIP transcription factorVSF-1 with a non-palindromic DNA sequence that controls vasculargene expressionIn vitro binding of the tomato bZIP transcriptional activatorVSF-1 to a regulatory element that controls xylem-specific geneexpression9Plant Mol Biol 37:977-988 (1998)Plant J 9:283-296 (1996) PubMed: 9700070;PubMed: 8919907; GCTCCGTTG WARBNEXTAS000241 11-0ct-1999 (last modified) kehiN"WAR (wounding activating region)" in Brassica napus (B.n.) extAextensin gene;woundingextextensinBrassica napusElliott KA , Shirsat AH{Promoter regions of the extA extensin gene from Brassica napuscontrol activation in response to wounding and tensile stress!Plant Mol Biol 37:675-687 (1998)PubMed: 9687071; GTACGTGTTATAAAACGTGT WBBOXPCWRKY1S000310!22-June-2006 (last modified) kehi�v"WB box"; WRKY proteins bind specifically to the DNA sequencemotif (T)(T)TGAC(C/T), which is known as the W box; Found inamylase gene in sweet potato, alpha-Amy2 genes in wheat, barley,and wild oat, PR1 gene in parsley, and a transcription factorgene in Arabidopsis; The motif was initially registered inPLACEdb as TTGACT, and was corrected to TTGACY on 22 June, 2006;Y=C/T;W boxWRKY�Ipomoea batatas (sweet potato); Triticum aestivum (wheat);Hordeum vulgare (barley); Avena fatua (wild oat); Petroseliumcrispum (parsley); Arabidopsis thaliana;�Ishiguro S, Nakamura K.Rushton PJ, Macdonald H, Huttly AK, Lazarus CM, Hooley R.Rushton PJ, Torres JT, Parniske M, Wernert P, Hahlbrock K,Somssich IE.de Pater S, Greco V, Pham K, Memelink J, Kijne J.Eulgem T, Rushton PJ, Robatzek S, Somssich IE�-Characterization of a cDNA encoding a novel DNA-binding protein,SPF1, that recognizes SP8 sequences in the 5' upstream regions ofgenes coding for sporamin and beta-amylase from sweet potato.Members of a new family of DNA-binding proteins bind to aconserved cis-element in the promoters of alpha-Amy2 genes.Interaction of elicitor-induced DNA-binding proteins withelicitor response elements in the promoters of parsley PR1genes.Characterization of a zinc-dependent transcriptional activatorfrom Arabidopsis.The WRKY superfamily of plant transcription factors�Mol Gen Genet. 244:563-571.(1994)Plant Mol Biol. 29:691-702 (1995)EMBO J. 15:5690-5700 (1996)Nucleic Acids Res. 24:4624-4631 (1996)Trends Plant Sci 5: 199-206 (2000)MPubMed: 7969025PubMed: 8541496PubMed: 8896462PubMed: 8972846PubMed: 10785665;ReviewTTTGACY
WBOXATNPR1S000390!23-June-2006 (last modified) kehi��"W-box" found in promoter of Arabidopsis thaliana (A.t.) NPR1gene; Located between +70 and +79 in tandem; They were recognizedspecifically by salicylic acid (SA)-induced WRKY DNA bindingproteins; See S000142 (SQ=TTGACC); See S000310 (SQ=TTTGACY); Acluster of WRKY binding sites act as negative regulatory elementsfor the inducible expression of AtWRKY18 (Chena and Chen, 2002);See also S000142;NPR1WRKYWRKY18disease resistanceSAW boxArabidopsis thaliana�:Yu D, Chen C, Chen ZChen W, Provart NJ, Glazebrook J, Katagiri F, Chang HS, Eulgem T,Mauch F, Luan S, Zou G, Whitham SA, Budworth PR, Tao Y, XieEulgem T, Rushton PJ, Robatzek S, Somssich IE.Chen C, Chen Z.Maleck K, Levine A, Eulgem T, Morgan A, Schmid J, Lawton KA,Dangl JL, Dietrich RA.Xu X, Chen C, Fan B, Chen Z�hEvidence for an important role of WRKY DNA binding proteins inthe regulation of NPR1 gene expressionExpression profile matrix of Arabidopsis transcription factorgenes suggests their putative functions in response toenvironmental stressesThe WRKY superfamily of plant transcription factors.Potentiation of developmentally regulated plant defense responseby AtWRKY18, a pathogen-induced Arabidopsis transcriptionfactor.The transcriptome of Arabidopsis thaliana during systemicacquired resistance.Physical and Functional Interactions between Pathogen-InducedArabidopsis WRKY18, WRKY40, and WRKY60 Transcription Factors.�Plant Cell 13: 1527-1540 (2001)Plant Cell 14: 559-574 (2002)Trends Plant Sci. 5:199-206. (2000)Plant Physiol. 129:706-716 (2002)Nat Genet. 26:403-410 (2000)Plant Cell 18:1310-1326 (2006)RPubMed: 11449049;PubMed: 11910004;PubMed: 10785665PubMed: 12068113PubMed: 11101835Review.TTGAC WBOXGACAD1AS000448#19-August-2004 (last modified) kehi�W-box found in the promoter region of the CAD1-A (cotton (+)delta-cadinene synthase-A) gene (located in the region -340 to-327) of cotton (G.a); Binding site of GaWRKY1; GaWRKY1 regulatessesquiterpene biosynthesis in cotton; See S000390 (TTGAC),S000142 (TTGACC);W-boxTGACCADWRKYGossypium arboreum (cotton))Xu YH, Wang JW, Wang S, Wang JY, Chen XY.�Characterization of GaWRKY1, a cotton transcription factor thatregulates the sesquiterpene synthase gene (+)-delta-cadinenesynthase-A. Plant Physiol. 135:507-515(2004)PubMed: 15133151 AGTCAAAATTGACC
WBOXHVISO1S000442 28-Jan-2004 (last modified) kehiLSUSIBA2 bind to W-box element in barley iso1 (encodingisoamylase1) promoter;sugarSUREpatatinWRKY
isoamylaseSUSIBA2Hordeum vulgare (barley)@Sun C, Palmqvist S, Olsson H, Boren M, Ahlandsberg S, Jansson C.�A novel WRKY transcription factor, SUSIBA2, participates in sugarsignaling in barley by binding to the sugar-responsive elementsof the iso1 promoter. Plant Cell 15: 2076-2092 (2003)PubMed: 12953112; TGACT WBOXNTCHN48S000508$04-January-2007 (last modified) kehi� "W box" identified in the region between -125 and -69 of atobacco class I basic chitinase gene CHN48; NtWRKY1, NtWRKY2 andNtWRKY4 bound to W box; NtWRKYs possibly involved inelicitor-respsonsive transcription of defense genes in tobacco;Y=C/T; see also S000442 (TGACT) and S000447 (TGAC);W-boxW boxWRKYelicitorNicotiana tabacum (tobacco)*Yamamoto S, Nakano T, Suzuki K, Shinshi H.�Elicitor-induced activation of transcription via W box-relatedcis-acting elements from a basic chitinase gene by WRKYtranscription factors in tobacco.)Biochim Biophys Acta. 1679:279-287(2004).PubMed: 15358520 CTGACY
WBOXNTERF3S000457%29-November-2004 (last modified) kehi�"W box" found in the promoter region of a transcriptionalrepressor ERF3 gene in tobacco; May be involved in activation ofERF3 gene by wounding;(Nishiuchi et al., 2004) Y=C/T; SeeS000142, S000390, S000442, S000447;W boxERF3woundingNicotiana tabacum (tobacco)!Nishiuchi T, Shinshi H, Suzuki K.�Rapid and transient activation of transcription of the ERF3 geneby wounding in tobacco leaves: Possible involvement of NtWRKYsand autorepression.$J Biol Chem. 279: 55355-55361 (2004)PubMed: 15509567 TGACY WINPSTPIIIKS000495 10-May-2006 (last modified) kehi�Binding site of wound-inducible nuclear protein from woundedtomato leaves; Found in the promoter region of a proteaseinhibitor IIK gene from potato (S.t.);woundwoundingSolanum tuberosum (potato)!Palm CJ, Costa MA, An G, Ryan CA.lWound-inducible nuclear protein binds DNA fragments that regulatea proteinase inhibitor II gene from potato.,Proc Natl Acad Sci U S A. 87: 603-607 (1990)PubMed: 2405385
AAGCGTAAGT WRECSAA01S000496 10-May-2006 (last modified) kehi�"Wound-responsive element (WRE)" found in the promoter region ofcucumber (C.s.) ascorbate oxidase gene, CsAAO1; Binding site ofproteins in tobacco nuclear extracts; W=A/T; S=C/G;woundAAOwoundingCucumis sativas (cucumber)!Palm CJ, Costa MA, An G, Ryan CA.lWound-inducible nuclear protein binds DNA fragments that regulatea proteinase inhibitor II gene from potato.,Proc Natl Acad Sci U S A. 87: 603-607 (1990)PubMed: 2405385
AAWGTATCSAWRKY71OSS000447!22-June-2006 (last modified) kehi�S"A core of TGAC-containing W-box" of, e.g., Amy32b promoter;Binding site of rice WRKY71, a transcriptional repressor of thegibberellin signaling pathway; Parsley WRKY proteins bindspecifically to TGAC-containing W box elements within thePathogenesis-Related Class10 (PR-10) genes (Eulgem et al., 1999);See S000390 (TTGAC), S000442 (TGACT);WRKYGAMYBW boxTGAC PR proteins4Oryza sativa (rice); Petroselinum crispum (parsley);�Zhang ZL, Xie Z, Zou X, Casaretto J, Ho TH, Shen QJ.Xie Z, Zhang ZL, Zou X, Huang J, Ruas P, Thompson D, Shen QJ.Eulgem T, Rushton PJ, Schmelzer E, Hahlbrock K, Somssich IE.Eulgem T, Rushton PJ, Robatzek S, Somssich IE.��A rice WRKY gene encodes a transcriptional repressor of thegibberellin signaling pathway in aleurone cells.Annotations and functional analyses of the rice WRKY genesuperfamily reveal positive and negative regulators of abscisicacid signaling in aleurone cells.Early nuclear events in plant defence signalling: rapid geneactivation by WRKY transcription factors.The WRKY superfamily of plant transcription factors.�Plant Physiol. 134:1500-1513(2004)Plant Physiol. 137:176-189 (2005)EMBO J. 18:4689-4699 (1999)Trends Plant Sci. 5:199-206. (2000)@PubMed: 15047897PubMed: 15618416PubMed: 10469648PubMed: 10785665Review.TGACWUSATAgS000433 27-Jan-2004 (last modified) kehioTarget sequence of WUS in the intron of AGAMOUS gene inArabidopsis; See Lohmann et al. Cell 105:793-803 (2003); Oryza sativa (rice)5Kamiya N, Nagasaki H, Morikami A, Sato Y, Matsuoka M.�Isolation and characterization of arice WUSCHEL-tyope homoeboxgene that is specifically expressed in the central cells of aquiescent center in the root apical meristem.Plant J. 35: 429-441 (2003)PubMed: 12904206; TTAATGGXYLATS000510$04-January-2007 (last modified) kehiGcis-element identified among the promoters of the "core xylemgene set";secondary xylemwood formationArabidopsis thalianaKo JH, Beers EP, Han KH.�Global comparative transcriptome analysis identifies gene networkregulating secondary xylem development in Arabidopsis thaliana.&Mol Genet Genomics. 276:517-531 (2006)PubMed: 16969662in silico; consensus;ACAAAGAAYREGIONNTPRB1BS000365 16-Feb-2001 (last modified) seki�"Y region" found in tobacco (N.t.) PRB-1b gene promoter; Locatedat -179 to -154; Binding site of nuclear protein; Required forethylene induction; See S000364;PR-1PRB-1bethyleneYTobacco (Nicotiana tabacum)"Meller Y, Sessa G, Eyal Y, Fluhr RNDNA-protein interactions on a cis-DNA element essential forethylene regulation!Plant Mol Biol 23: 453-463 (1993)PubMed: 8219081; TGTGACATTGAAATTCTTTGACTTTAZDNAFORMINGATCAB1S000321#13-August-2005 (last modified) kehi�~"Z-DNA-forming sequence" found in the Arabidopsis (A.t.)chlorophyll a/b binding protein gene (cab1) promoter; Involved inlight-dependent developmental expression of the gene; "Z-box";Activation of Z-box containing promoters is regulated bydownstream regulatory components, COP1 and HY5; phyB and CRY1photoreceptors act redundantly to induce Z-box containingpromoters in white light; cab1lightZ-DNAleafshootHY5COP1LREZ-boxZBF1Z-box binding factorArabidopsis thaliana�Ha SB, An GYadav V, Kundu S, Chattopadhyay D, Negi P, Wei N, Deng XW,Chattopadhyay SYadav V, Mallappa C, Gangappa SN, Bhatia S, Chattopadhyay S.��Identification of upstream regulatory elements involved in thedevelopmental expression of the Arabidopsis thaliana cab1 gene.Light regulated modulation of Z-box containing promoters byphotoreceptors and downstream regulatory components, COP1 andHY5, in ArabidopsisA Basic Helix-Loop-Helix Transcription Factor in Arabidopsis,MYC2, Acts as a Repressor of Blue Light-Mediated PhotomorphogenicGrowth.eProc Natl Acad Sci USA 85: 8017-8021 (1988)Plant J. 31: 741-753 (2002)Plant Cell 17: 1953-1966 (2005)0PubMed: 3054877PubMed: 12220265;PubMed: 15923349 ATACGTGT��ABREATCONSENSUS CEREGLUBOX2PSLEGA� CGACGOSAMY3�GBOXPC� SORLIP4AT��ANAERO1CONSENSUSLRYREPEATBNNAPA�w AACAOSGLUB1 GTGANTG10�POLASIG3�T
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