View conserved binding sites

Binding siteNameDescriptionLocationPosition
Matrix_101ERF5Not availableUpstream-516
Matrix_104PINot availableUpstream-817
Matrix_109GBF3Not availableUpstream-817
Matrix_113ABI5Not availableUpstream-817
Matrix_117ANTNot availableDownstream2165
Matrix_118PIF3_2Direct targeting of light signals to a promoter element-bound transcription factorUpstream-819
Matrix_119RRTF1Not availableUpstream-517
Matrix_122ABF1;AREB2Not availableUpstream-817
Matrix_124AtHB23;ATHB13;ATHB20;ATHB5Not availableUpstream-486
Matrix_129ABF1Not availableUpstream-816
Matrix_134ABF1Not availableUpstream-815
Matrix_138RRTF1Not availableUpstream-517
Matrix_145GBF4;AT5G44080Not availableUpstream-815
Matrix_146ORA47Not availableUpstream-516
Matrix_147ERF3;AT1G80580Not availableUpstream-516
Matrix_154AT1G22190;AT1G36060;AT1G64380;RAP2.4;AT2G20880;AT2G22200;AT4G13620;AT4G28140;AT4G39780;AT5G65130Not availableUpstream-518
Matrix_192FHY3/FAR1Not availableUpstream-819
Matrix_194HYH;HY5Not availableUpstream-819
Matrix_209RAP2.6Not availableUpstream-518
Matrix_214AP1Not availableUpstream-818
Matrix_217BES1A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thalianaUpstream-819
Matrix_224ERF1Not availableUpstream-517
Matrix_227AT1G64620Not availableDownstream2321
Matrix_234RAP2.3Not availableUpstream-516
Matrix_250ADAP;AT1G79700;WRI1;ANTNot availableDownstream2161
Matrix_251PIF5Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signalingUpstream-817
Matrix_252RAP2.6Not availableUpstream-516
Matrix_261ATERF-1Not availableUpstream-516
Matrix_264ATAREB1Not availableUpstream-819
Matrix_269FHY3/FAR1Not availableUpstream-69
Matrix_270ANTDNA binding properties of the Arabidopsis floral development protein AINTEGUMENTADownstream2164
Matrix_277RAP2.6Not availableUpstream-517
Matrix_285DDF1Not availableUpstream-518
Matrix_287ERF2Not availableUpstream-516
Matrix_288RAP2.3Not availableUpstream-517
Matrix_295ERF1Not availableUpstream-516
Matrix_296GBF2Not availableUpstream-816
Matrix_300bZIP68;bZIP16Not availableUpstream-816
Matrix_301PIL5Not availableUpstream-821
Matrix_326AT5G07310;Rap2.6L;AT5G61890Not availableUpstream-517
Matrix_331GBF1Not availableUpstream-817
Matrix_334AT3G23230Not availableUpstream-515
Matrix_338AP2Not availableUpstream-819
Matrix_343AT2G33710Not availableUpstream-516
Matrix_345POC1Not availableUpstream-819
Matrix_355ERF10;ERF11Not availableUpstream-517
Matrix_356PRR5Not availableUpstream-819
Matrix_360ORA59Not availableUpstream-516
Matrix_363RAP2.3Not availableUpstream-517
Matrix_372ANAC81DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virusDownstream2049
Matrix_374AT5G07580;AT5G61590Not availableUpstream-516
Matrix_377AT1G75490;DREB2C;AT2G40350;AT5G18450Not availableUpstream-516
Matrix_378ATERF1Not availableUpstream-516
Matrix_381ATHB9Not availableUpstream-491
Matrix_403BZR1Not availableUpstream-818
Matrix_406ATERF-7Not availableUpstream-518
Matrix_409DEAR3Not availableUpstream-517
Matrix_426CRF1;CRF2Not availableUpstream-515
Matrix_443AGL15Not availableUpstream-818
Matrix_45DRNNot availableUpstream-516
Matrix_459ATHB9;CNA;PHB;ATHB-8;REVNot availableUpstream-491
Matrix_462ATERF-8Not availableUpstream-518
Matrix_468ATHB9The Arabidopsis Athb-8, -9 and -14 genes are members of a small gene family coding for highly related HD-ZIP proteinsUpstream-491
Matrix_473RRTF1Not availableUpstream-516
Matrix_484ATERF13Not availableUpstream-516
Matrix_488ABF1Not availableUpstream-817
Matrix_493AT1G22985;AT1G71130Not availableUpstream-516
Matrix_50ATERF14;AT5G43410Not availableUpstream-517
Matrix_506DRNL;ATERF-4Not availableUpstream-515
Matrix_517ERF12Not availableUpstream-516
Matrix_53MYC3Not availableUpstream-818
Matrix_55PIF3Not availableUpstream-817
Matrix_57WIN1;SHN3;SHN2Not availableUpstream-517
Matrix_60AT1G01260;AT5G57150Not availableUpstream-815
Matrix_65POC1;PIL1Not availableUpstream-814
Matrix_7PIF4Not availableUpstream-816
Matrix_77PRR5Not availableUpstream-818
Matrix_80BIM1Not availableUpstream-817
Matrix_86CRF5;CRF6;CRF4Not availableUpstream-515
Matrix_91CRF3Not availableUpstream-516
Motif_1GT1CORECritical for GT-1 binding to box II of rbcS; Transcriptional activation by Arabidopsis GT-1 may be through interaction with TFIIA-TBP-TATA complexDownstream2386
Motif_104CAREOSREP1CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in riceDownstream2311
Motif_116INRNTPSADBInr (initiator) elements found in the tobacco psaDb gene promoter without TATA boxes; Light-responsive transcription of psaDb depends on Inr, but not TATA boxDownstream2686
Motif_125BOXIINTPATPBBox II found in the tobacco plastid atpB gene promoter; Conserved in several NCII (nonconsensus type II) promoters of plastid genes; Important for the activity of this NCII promoterDownstream2394
Motif_136SEF4MOTIFGM7SSEF4 binding site; Soybean consensus sequence found in 5'upstream region (-199) of beta-conglycinin (7S globulin) gene (Gmg17.1); Binding with SEF4 (soybean embryo factor 4)Downstream2399
Motif_15AMYBOX2amylase box; amylase element; Conserved sequence found in 5'upstream region of alpha-amylase gene of rice, wheat, barleyUpstream-56
Motif_155NODCON1GMOne of two putative nodulin consensus sequences; See also NODCON2GM; One of the consensus sequence motifs of organ-specific elements (OSE) characteristic of the promoters activated in infected cells of root nodulesUpstream-898
Motif_179CACGTGMOTIF;BES1;PIF4;PIF5Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling;A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana; CACGTG motif; G-box; Binding site of Arabidopsis GBF4; C. roseus G-box binding factor 1 (CrGBF1) and 1 (CrGBF2) can act as transcriptional repressors of the Str promoter via direct interaction with the G-box; Essential for expression of beta-phaseolin gene during embryogenesis in bean, tobacco, Arabidopsis; Tomato Pti4 (ERF) regulates defense-related gene expression via GCC box and non-GCC box cis-element (Myb1 (GTTAGTT) and G-box (CACGTG)); Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein; Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responsesUpstream-814
Motif_182MYB2CONSENSUSATMYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; see MYB2 and MYBATRD22Upstream-525
Motif_192BOXLCOREDCPALConsensus of the putative core sequences of box-L-like sequences in carrot; PAL1 promoter region; DCMYB1 bound to these sequences in vitroDownstream2301
Motif_194EBOXBNNAPAE-box of napA storage-protein gene of Brassica napus;This sequence is also known as RRE (R response element); MYC recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; Binding site of ATMYC2 (previously known as rd22BP1); see E-box and MYCATRD22; MYC recognition sequence in CBF3 promoter; Binding site of ICE1 (inducer of CBF expression 1) that regulates the transcription of CBF/DREB1 genes in the cold in Arabidopsis; ICE1Upstream-814
Motif_218ABRERATCALABRE-related sequence or Repeated sequence motifs identified in the upstream regions of 162 Ca(2+)-responsive upregulated genes; see also ABREUpstream-815
Motif_22RYREPEATLEGUMINBOXRY repeat (CATGCAY) or legumin box found in seed-storage protein genes in legume such as soybeanDownstream2647
Motif_221MYBCOREBinding site for all animal MYB and at least two plant MYB proteins ATMYB1 and ATMYB2, both isolated from Arabidopsis; ATMYB2 is involved in regulation of genes that are responsive to water stress in Arabidopsis; A petunia MYB protein (MYB.Ph3) is involved in regulation of flavonoid biosynthesisUpstream-525
Motif_244ABRE-like binding site motifNot availableUpstream-816
Motif_249DPBF1&2 binding site motifA novel class of bZIP transcription factors, DPBF-1 and 2 (Dc3 promoter-binding factor-1 and 2) binding core sequence; Found in the carrot Dc3 gene promoter; Dc3 expression is normally embryo-specific, and also can be induced by ABA; The Arabidopsis abscisic acid response gene ABI5 encodes a bZIP transcription factor; 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; Isolation of a novel class of bZIP transcription factors that interact with ABA-responsive and embryo-specification elements in the Dc3 promoter using a modified yeast one-hybrid systemUpstream-815
Motif_254MYB46;MYB83MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genesDownstream2301
Motif_270ELRECOREPCRP1ElRE (Elicitor Responsive Element) core of parsley PR1 genes; consensus sequence of elements W1 and W2 of parsley PR1-1 and PR1-2 promoters; Box W1 and W2 are the binding site of WRKY1 and WRKY2, respectively; ERE; WA box; One of the W boxes found in the Parsley WRKY1 gene promoter; Required for elicitor responsiveness; WC box WB box and WC box constitute a palindrome; WRKY1 protein binding site; W-box found in thioredoxin h5 gene in ArabidopsisUpstream-787
Motif_292MYBPZMCore of consensus maize P (myb homolog) binding site; 6 bp core; Maize P gene specifies red pigmentation of kernel pericarp, cob, and other floral organs; P binds to A1 gene, but not Bz1 gene; Maize C1 (myb homolog) activates both A1 and Bz1 genesDownstream2301
Motif_307TATCCAYMOTIFOSRAMY3DTATCCAY motif found in rice RAmy3D alpha-amylase gene promoter; a GATA motif as its antisense sequence; TATCCAY motif and G motif are responsible for sugar repressionUpstream-56
Motif_309GATA promoter motifArabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristicsUpstream-49
Motif_313ERF1 BS in AtCHI-BCore of GCC-box found in many pathogen-responsive genes such as PDF1.2, Thi2.1, and PR4; Has been shown to function as ethylene-responsive element; Appears to play important roles in regulating jasmonate-responsive gene expression; Tomato Pti4 (ERF) regulates defence-related gene expression via GCC box and non-GCC box cis elements (Myb1 (GTTAGTT) and G-box(CACGTG)); Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1;Molecular responses to dehydration and low temperatureUpstream-515
Motif_317GAREATGARE (GA-responsive element); Occurrence of GARE in GA-inducible, GA-responsible, and GA-nonresponsive genes found in Arabidopsis seed germination was 20, 18, and 12%, respectivelyDownstream2215
Motif_336MYBMOUSEBinding site for mouse c-myb proteinUpstream-525
Motif_339ABRE-like binding site motifMolecular responses to dehydration and low temperatureUpstream-814
Motif_348WBBOXPCWRKY1WB box; WRKY proteins bind specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box; Found in amylase gene in sweet potato, alpha-Amy2 genes in wheat, barley, and wild oat, PR1 gene in parsley, and a transcription factor gene in ArabidopsisUpstream-787
Motif_391REALPHALGLHCB21REalpha 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 much lower in green plants; Required for phytochrome regulationDownstream2342
Motif_419MYB4 binding site motifNot availableDownstream2301
Motif_426MYB58;MYB63MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in ArabidopsisDownstream2301
Motif_43CCA1 binding site motifCCA1 binding site; CCA1 protein (myb-related transcription factor) interact with two imperfect repeats of AAMAATCT in Lhcb1*3 gene of Arabidopsis thaliana; Related to regulation by phytochrome;A myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb geneUpstream-902
Motif_448IRO2OSOsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiencyUpstream-814
Motif_450E2FCONSENSUSE2F consensus sequence of all different E2F-DP-binding motifs that were experimentally verified in plantsDownstream2326
Motif_498SGBFGMGMAUX28bZIP proteins SGBF-1 and SGBF-2 binding site in soybean GmAux28 gene promoterUpstream-816
Motif_51MYB46Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesisDownstream2301
Motif_511RYREPEATGMGY2RY repeat motif (CATGCAT); Present in the 5' region of the soybean glycinin gene (Gy2)Downstream2647
Motif_517LEAFYATAGTarget sequence of LEAFY in the intron of AGAMOUS gene in ArabidopsisUpstream-826
Motif_520AMYBOX1amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barleyDownstream2215
Motif_527LFYStructural basis for LEAFY floral switch function and similarity with helix-turn-helix proteinsUpstream-831
Motif_549TBF1The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transitionUpstream-69
Motif_552MRE1MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1Upstream-530
Motif_609AP2The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence elementDownstream2215
Motif_614MYBGAHVCentral element of gibberellin (GA) response complex (GARC) in high-pI alpha-amylase gene in barley; Similar to c-myb and v-myb consensus binding site; GAmyb binds specifically to the TAACAAA box in vitro; GAmyb is the sole GA-regulated transcriptional factor required for transcriptional activation of the high-pI alpha-amylase; GARC consist of the pyrimidine, TAACAAA and TATCCAC boxes; GARE in RAmy1A gene; GARE and pyrimidine box in RAmy1A are partially involved in sugar repressionDownstream2215
Motif_615MARTBOXT-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR)Upstream-910
Motif_618MYB1ATMYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in ArabidopsisDownstream2343
Motif_627ACGTABREMOTIFA2OSEMExperimentally determined sequence requirement of ACGT-core of motif A in ABRE of the rice gene, OSEM; DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A in ArabidopsisUpstream-816
Motif_628TATCCAOSAMYTATCCA element found in alpha-amylase promoters of rice at positions ca.90 to 150bp upstream of the transcription start sites; Binding sites of OsMYBS1, OsMYBS2 and OsMYBS3 which mediate sugar and hormone regulation of alpha-amylase gene expression; See also AMYBOX2Upstream-55
Motif_630WBOXNTCHN48W box identified in the region between -125 and -69 of a tobacco class I basic chitinase gene CHN48; NtWRKY1, NtWRKY2 and NtWRKY4 bound to W box; NtWRKYs possibly involved in elicitor-respsonsive transcription of defense genes in tobaccoUpstream-196
Motif_640RYREPEATBNNAPARY repeat found in RY/G box (the complex containing the two RY repeats and the G-box) of napA gene in Brassica napus; Found between -78 and -50; Required for seed specific expression;dist B ABRE mediated transactivation by ABI3 adn ABI3-dependent response to ABA; a tetramer of the composite RY/G complex mediated only ABA-independent transactivation by ABI3; B2 domain of ABI3 is necessary for ABA-independent and ABA-dependent activation through the dist B ABREDownstream2647
Motif_6492SSEEDPROTBANAPAConserved in many storage-protein gene promoters; May be important for high activity of the napA promoterDownstream2380
Motif_65BS1EGCCRBS1 (binding site 1) found in E. gunnii Cinnamoyl-CoA reductase (CCR) gene promoter; nuclear protein binding site; Required for vascular expressionUpstream-862
Motif_653INTRONLOWER3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant intronsUpstream-802
Motif_658GT1CONSENSUSConsensus GT-1 binding site in many light-regulated genes, e.g., RBCS from many species, PHYA from oat and rice, spinach RCA and PETA, and bean CHS15; GT-1 can stabilize the TFIIA-TBP-DNA (TATA box) complex; The activation mechanism of GT-1 may be achieved through direct interaction between TFIIA and GT-1; Binding of GT-1-like factors to the PR-1a promoter influences the level of SA-inducible gene expressionUpstream-856
Motif_666MYB binding site promoterA flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genesDownstream2301
Motif_672AP2The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence elementDownstream2215
Motif_682GT1GMSCAM4GT-1 motif found in the promoter of soybean CaM isoform, SCaM-4; Plays a role in pathogen- and salt-induced SCaM-4 gene expressionUpstream-367
Motif_69CTRMCAMV35SCT-rich motif (inverted GAGA) found in a 60-nucleotide region (S1) downstream of the transcription start site of the CaMV 35S RNA; Can enhance gene expression; Inverted GAGAUpstream-773
Motif_70CANBNNAPACore of (CA)n element in storage protein genes in Brasica napus; embryo- and endosperm-specific transcription of napin (storage protein) gene, napA; seed specificity; activator and repressorDownstream2380
Motif_72GADOWNATSequence present in 24 genes in the GA-down regulated d1 cluster (106 genes) found in Arabidopsis seed germination; This motif is similar to ABREUpstream-816
Motif_98SEF3MOTIFGMSEF3 binding site; Soybean consensus sequence found in the 5' upstream region of beta-conglycinin (7S globulin) gene; AACCCA(-27bp-)AACCCA; SEF=soybean embryo factor; SEF2; SEF3; SEF4Upstream-360