View conserved binding sites


Gene
PPE_001G37970
Description
SHI RELATED SEQUENCE
Alias
ppa019307m.g;ppa019307m;PAC:17653900;ppa019307m
Binding siteNameDescriptionLocationPosition
Matrix_104PINot availableUpstream-714
Upstream-715
Upstream-922
Matrix_113ABI5Not availableUpstream-716
Upstream-717
Upstream-922
Matrix_119RRTF1Not availableUpstream-359
Upstream-360
Matrix_122ABF1;AREB2Not availableUpstream-715
Upstream-716
Upstream-923
Matrix_129ABF1Not availableUpstream-715
Upstream-716
Upstream-923
Matrix_134ABF1Not availableUpstream-715
Upstream-716
Upstream-923
Matrix_138RRTF1Not availableUpstream-359
Upstream-360
Matrix_145GBF4;AT5G44080Not availableUpstream-716
Upstream-717
Upstream-924
Matrix_147ERF3;AT1G80580Not availableUpstream-360
Upstream-361
Matrix_19PIF5Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signalingUpstream-923
Matrix_192FHY3/FAR1Not availableUpstream-716
Upstream-717
Upstream-920
Matrix_194HYH;HY5Not availableUpstream-712
Upstream-713
Matrix_214AP1Not availableUpstream-713
Upstream-714
Matrix_217BES1A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thalianaUpstream-920
Matrix_224ERF1Not availableUpstream-359
Upstream-360
Matrix_227AT1G64620Not availableDownstream2135
Matrix_234RAP2.3Not availableUpstream-358
Upstream-359
Matrix_251PIF5Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signalingUpstream-712
Upstream-713
Matrix_261ATERF-1Not availableUpstream-359
Upstream-360
Matrix_264ATAREB1Not availableUpstream-715
Upstream-716
Upstream-920
Matrix_288RAP2.3Not availableUpstream-359
Upstream-360
Matrix_295ERF1Not availableUpstream-360
Upstream-361
Matrix_296GBF2Not availableUpstream-716
Upstream-717
Matrix_300bZIP68;bZIP16Not availableUpstream-716
Upstream-717
Upstream-923
Matrix_301PIL5Not availableUpstream-716
Upstream-717
Upstream-918
Matrix_326AT5G07310;Rap2.6L;AT5G61890Not availableUpstream-359
Upstream-360
Matrix_332SPT;ALCNot availableUpstream-923
Matrix_338AP2Not availableUpstream-712
Upstream-713
Upstream-920
Matrix_355ERF10;ERF11Not availableUpstream-359
Upstream-360
Matrix_356PRR5Not availableUpstream-708
Upstream-709
Upstream-916
Matrix_360ORA59Not availableUpstream-360
Upstream-361
Matrix_363RAP2.3Not availableUpstream-359
Upstream-360
Matrix_372ANAC81DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virusIntron1045
Intron1037
Matrix_378ATERF1Not availableUpstream-358
Upstream-359
Matrix_401MYB55Not availableUpstream-694
Matrix_403BZR1Not availableUpstream-713
Upstream-714
Upstream-921
Matrix_406ATERF-7Not availableUpstream-360
Upstream-361
Matrix_420ANAC58Not availableIntron967
Intron966
Matrix_426CRF1;CRF2Not availableUpstream-359
Upstream-360
Matrix_443AGL15Not availableUpstream-713
Upstream-714
Upstream-921
Matrix_45DRNNot availableUpstream-360
Upstream-361
Matrix_453EIL3Not availableUpstream-660
Matrix_462ATERF-8Not availableUpstream-360
Upstream-361
Matrix_463HAT3.1Not availableUpstream-374
Upstream-375
Matrix_473RRTF1Not availableUpstream-358
Upstream-359
Matrix_480BES1Not availableUpstream-922
Matrix_484ATERF13Not availableUpstream-360
Upstream-361
Matrix_493AT1G22985;AT1G71130Not availableUpstream-359
Upstream-360
Matrix_50ATERF14;AT5G43410Not availableUpstream-359
Upstream-360
Matrix_501DAG2Not availableUpstream-773
Matrix_506DRNL;ATERF-4Not availableUpstream-359
Upstream-360
Matrix_517ERF12Not availableUpstream-360
Upstream-361
Matrix_55PIF3Not availableUpstream-922
Matrix_7PIF4Not availableUpstream-923
Matrix_77PRR5Not availableUpstream-714
Upstream-715
Matrix_86CRF5;CRF6;CRF4Not availableUpstream-359
Upstream-360
Matrix_91CRF3Not availableUpstream-359
Upstream-360
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 complexDownstream2197
Downstream2195
Upstream-410
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 boxDownstream1828
Intron1044
Upstream-13
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 promoterDownstream2585
Motif_129GAGAGMGSA1GAGA element found in the promoter of the heme and chlorophyll synthesis gene Gsa1 in soybean; GAGA binding protein (GBP) binds to (GA)n/(CT)n DNADownstream2417
Downstream2415
Upstream-479
Upstream-481
Upstream-483
Upstream-485
Upstream-487
Upstream-489
Upstream-491
Upstream-493
Upstream-495
Upstream-497
Upstream-499
Upstream-501
Upstream-503
Upstream-505
Upstream-507
Motif_15AMYBOX2amylase box; amylase element; Conserved sequence found in 5'upstream region of alpha-amylase gene of rice, wheat, barleyDownstream2499
Motif_16-300ELEMENTPresent upstream of the promoter from the B-hordein gene of barley and the alpha-gliadin, gamma-gliadin, and low molecular weight glutenin genes of wheat; See S000001 -300CORE; See S000002 -300MOTIFDownstream2546
Downstream2509
Motif_174SREATMSDsugar-repressive element (SRE) found in 272 of the 1592 down-regulated genes after main stem decapitation in ArabidopsisDownstream2500
Downstream2145
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-717
Upstream-924
Motif_182MYB2CONSENSUSATMYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; see MYB2 and MYBATRD22Upstream-699
Motif_193GLK1GLK transcription factors coordinate expression of the photosynthetic apparatus in ArabidopsisUpstream-786
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-524
Upstream-717
Motif_200GBOXLERBCSG box; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis; Binding with GBFUpstream-922
Motif_210REBETALGLHCB21REbeta found in Lemna gibba Lhcb21 gene promoter; Located at -114 to -109; A GATA sequence created at a position six nucleotides upstream could replace the function of REbeta; Required for phytochrome regulationDownstream2146
Motif_218ABRERATCALABRE-related sequence or Repeated sequence motifs identified in the upstream regions of 162 Ca(2+)-responsive upregulated genes; see also ABREUpstream-716
Upstream-717
Upstream-923
Upstream-924
Motif_22RYREPEATLEGUMINBOXRY repeat (CATGCAY) or legumin box found in seed-storage protein genes in legume such as soybeanDownstream2345
Downstream1709
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-699
Motif_235C8GCARGATBinding site of plant MADS-domain protein AGL15; CArG motif with a longer A/T-rich core;A variant of CArG motif, with a longer A/T-rich core; Binding site for AGL15 (AGAMOUS-like 15)Downstream2550
Motif_244ABRE-like binding site motifNot availableUpstream-715
Upstream-717
Upstream-922
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-717
Motif_254MYB46;MYB83MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genesDownstream2192
Downstream1809
Motif_258-10PEHVPSBD-10 promoter element found in the barley (H.v.) chloroplast psbD gene promoter; Involved in the expression of the plastid gene psbD which encodes a photosystem II reaction center chlorophyll-binding protein that is activated by blue, white or UV-A lightIntron1050
Motif_261S1FBOXSORPS1L21S1F box conserved both in spinach RPS1 and RPL21 genes encoding the plastid ribosomal protein S1 and L21, respectively; Negative element; Might play a role in downregulating RPS1 and RPL21 promoter activityDownstream2589
Motif_291ABFs binding site motifBinding site of trans-acting factor EMBP-1; wheat Em gene;Binding site of ABFs; ABFs (ABRE binding factors) were isolated from Arabidopsis by a yeast one-hybrid screening system; Expression ABFs is induced by ABA and various stress treatment; ABFs belongs to a distinct subfamily of bZIP proteins; Involved in ABA-mediated stress-signaling pathway;A plant leucine zipper protein that recognizes an abscisic acid response elementUpstream-922
Motif_305SP1SV40SP-1 binding site (GC box) in enhancer regions of SV40 and human metallothionein IIA (hMT IIA)Downstream2305
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 repressionDownstream2499
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-361
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%, respectivelyIntron1064
Motif_332SV40COREENHANSV40 core enhancer; Similar sequences found in rbcS genesUpstream-673
Upstream-769
Motif_336MYBMOUSEBinding site for mouse c-myb proteinUpstream-699
Motif_339ABRE-like binding site motifMolecular responses to dehydration and low temperatureUpstream-717
Upstream-924
Motif_342POLASIG1PolyA signal; poly A signal found in legA gene of pea, rice alpha-amylase; -10 to -30 in the case of animal genes. Near upstream elements (NUE) in ArabidopsisDownstream1846
Motif_346SND1;VND6;VND7;NST1;NST2Global analysis of direct targets of secondary wall NAC master switches in ArabidopsisIntron705
Motif_347OPAQUE2ZMB32opaque-2 binding site of maize b-32 (type I ribosome-inactivating protein gene); O2; O2S; O2S and GARE form a gibberellin response complex (GARC)Upstream-32
Motif_382CATATGGMSAURSequence found in NDE element in soybean SAUR (Small Auxin-Up RNA) 15A gene promoter; Involved in auxin responsivenessUpstream-524
Motif_383UPRE-III(bZIP60)The plant-specific transcription factor NAC103 is induced by bZIP60 through a new cis-regulatory element to modulate the unfolded protein response in ArabidopsisDownstream1872
Upstream-669
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 regulationDownstream2199
Downstream2193
Downstream1810
Motif_392PALBOXAPCBox A; Consensus; One of three putative cis-acting elements (boxes P, A, and L) of phenylalanine ammonia-lyase (PAL; EC 4.3.1.5) genes in parsley (P.c.); None of these elements (boxes P, A, and L) alone, or the promoter region containing all of them together, conferred elicitor or light responsiveness. These elements appear to be necessary but not sufficient for elicitor- or light-mediated PAL gene activation; See also Box P, Box LUpstream-430
Motif_404AACACOREOSGLUB1Core of AACA motifs found in rice glutelin genes, involved in controlling the endosperm-specific expression; AACA is also closely associated with the GCN4 motif in all rice glutelin genes and together have been shown to confer endosperm-specific enhancement to the truncated -90 CaMV 35S promoterIntron1063
Motif_414ABI3Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene productDownstream2346
Motif_419MYB4 binding site motifNot availableDownstream2192
Downstream1809
Intron1063
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-802
Motif_441GAGA8HVBKN3GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBRDownstream2417
Downstream2415
Downstream2413
Upstream-479
Upstream-481
Upstream-483
Upstream-485
Upstream-487
Upstream-489
Upstream-491
Upstream-493
Upstream-495
Upstream-497
Upstream-499
Upstream-501
Upstream-503
Upstream-505
Upstream-507
Upstream-509
Motif_448IRO2OSOsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiencyUpstream-716
Upstream-923
Motif_469QELEMENTZMZM13Q(quantitative)-element in maize ZM13 gene promoter; Found at -107 to -102; Involved in expression enhancing activity; ZM13 is a maize homolog of tomato LAT52 gene; ZM13 is a pollen-specific maize geneUpstream-9
Motif_48BES1A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thalianaIntron967
Motif_498SGBFGMGMAUX28bZIP proteins SGBF-1 and SGBF-2 binding site in soybean GmAux28 gene promoterUpstream-715
Motif_503EECCRCAH1EEC; Consensus motif of the two enhancer elements, EE-1 and EE-2, both found in the promoter region of the Chlamydomonas Cah1 (encoding a periplasmic carbonic anhydrase); Binding site of Myb transcription factor LCR1Downstream1823
Intron975
Motif_511RYREPEATGMGY2RY repeat motif (CATGCAT); Present in the 5' region of the soybean glycinin gene (Gy2)Downstream2345
Motif_520AMYBOX1amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barleyIntron1064
Motif_552MRE1MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1Downstream1711
Upstream-375
Upstream-917
Motif_556INTRONUPPER5' exon-intron splice junctions of plant introns; Plant intron upper sequence; Consensus sequence for plant intronsDownstream2532
Motif_558BOXIIPCCHSCore of Box II/G box found in the parsley chs genes; Essential for light regulationUpstream-922
Motif_562-300CORETGTAAAG core motif in -300 elements of alpha-zein genes of maize; -300 element core; prolamin box; P-box; Binds with P-box binding factor (PBF); Binds with BPBF (Barley PBF); PBF is a DNA-binding protein of the DOF class of transcription factorsDownstream2508
Motif_584UPRE-III(bZIP60)The plant-specific transcription factor NAC103 is induced by bZIP60 through a new cis-regulatory element to modulate the unfolded protein response in ArabidopsisDownstream1872
Upstream-669
Motif_609AP2The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence elementDownstream1815
Intron1063
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 repressionIntron1064
Motif_615MARTBOXT-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR)Upstream-1964
Upstream-1965
Upstream-1966
Upstream-1967
Upstream-1968
Motif_618MYB1ATMYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in ArabidopsisDownstream2198
Downstream2194
Downstream1811
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-718
Upstream-922
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 AMYBOX2Downstream2499
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-560
Upstream-782
Motif_638ABRE binding site motifNot availableUpstream-922
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 ABREDownstream2344
Downstream1708
Motif_6492SSEEDPROTBANAPAConserved in many storage-protein gene promoters; May be important for high activity of the napA promoterDownstream2190
Motif_65BS1EGCCRBS1 (binding site 1) found in E. gunnii Cinnamoyl-CoA reductase (CCR) gene promoter; nuclear protein binding site; Required for vascular expressionUpstream-765
Motif_653INTRONLOWER3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant intronsDownstream2534
Upstream-353
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 expressionDownstream2501
Downstream2494
Downstream2349
Downstream2166
Downstream2144
Downstream2136
Downstream2135
Upstream-759
Upstream-777
Motif_666MYB binding site promoterA flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genesDownstream2193
Downstream1810
Motif_672AP2The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence elementDownstream1815
Intron1063
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 expressionDownstream2135
Upstream-777
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 GAGADownstream2418
Downstream2416
Downstream2414
Downstream2412
Downstream2410
Downstream2408
Downstream2406
Upstream-479
Upstream-481
Upstream-483
Upstream-485
Upstream-487
Upstream-489
Upstream-491
Upstream-493
Upstream-495
Upstream-497
Upstream-499
Upstream-501
Upstream-503
Upstream-505
Upstream-507
Upstream-509
Upstream-511
Upstream-513
Upstream-515
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 repressorDownstream2190
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-718
Motif_85SORLIP5ATone of Sequences Over-Represented in Light-Induced Promoters (SORLIPs) in Arabidopsis; Computationally identified phyA-induced motifs; Over-represented in both light-induced cotyledon-specific and root-specific genes; Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray dataUpstream-269
Upstream-546
Upstream-591