| Matrix_104 | PI | Not available | Upstream | -534 |
| Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -534 |
| Matrix_109 | GBF3 | Not available | Upstream | -534 |
| | | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_113 | ABI5 | Not available | Upstream | -534 |
| | | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Downstream | 1791 |
| | | Upstream | -531 |
| Matrix_122 | ABF1;AREB2 | Not available | Upstream | -534 |
| | | Upstream | -535 |
| Matrix_129 | ABF1 | Not available | Upstream | -535 |
| Matrix_134 | ABF1 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_14 | ZCW32;AT5G62610 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_141 | AT3G25990 | Not available | Upstream | -547 |
| Matrix_145 | GBF4;AT5G44080 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -531 |
| Matrix_156 | POC1 | Not available | Upstream | -534 |
| | | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_181 | Dof5.7 | Not available | Upstream | -288 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_194 | HYH;HY5 | Not available | Upstream | -532 |
| Matrix_196 | TCP20;AT5G41030 | Not available | Downstream | 1778 |
| | | Upstream | -570 |
| | | Upstream | -575 |
| Matrix_200 | PIL5;AT4G28790;AT4G28800;AT4G28811;AT4G28815 | Not available | Upstream | -535 |
| Matrix_214 | AP1 | Not available | Upstream | -533 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_232 | TCP23 | Not available | Upstream | -571 |
| | | Upstream | -574 |
| Matrix_233 | MYC3 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_24 | POC1 | Not available | Upstream | -531 |
| Matrix_247 | PIF3 | Not available | Upstream | -535 |
| Matrix_264 | ATAREB1 | Not available | Upstream | -535 |
| Matrix_296 | GBF2 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_301 | PIL5 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_305 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -533 |
| Matrix_331 | GBF1 | Not available | Upstream | -534 |
| | | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_338 | AP2 | Not available | Upstream | -532 |
| Matrix_345 | POC1 | Not available | Downstream | 1792 |
| | | Downstream | 1791 |
| | | Upstream | -531 |
| Matrix_348 | AT5G51910 | Not available | Upstream | -572 |
| | | Upstream | -573 |
| Matrix_356 | PRR5 | Not available | Upstream | -528 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -193 |
| Matrix_389 | ILR3 | Not available | Upstream | -535 |
| Matrix_403 | BZR1 | Not available | Upstream | -533 |
| Matrix_42 | AT2G45680 | Not available | Upstream | -572 |
| | | Upstream | -573 |
| Matrix_443 | AGL15 | Not available | Upstream | -533 |
| Matrix_480 | BES1 | Not available | Upstream | -535 |
| Matrix_488 | ABF1 | Not available | Upstream | -534 |
| Matrix_53 | MYC3 | Not available | Upstream | -536 |
| | | Upstream | -537 |
| Matrix_55 | PIF3 | Not available | Upstream | -534 |
| Matrix_56 | BZIP17;BZIP28;BZIP49 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_60 | AT1G01260;AT5G57150 | Not available | Upstream | -535 |
| Matrix_64 | PIF5 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_65 | POC1;PIL1 | Not available | Upstream | -535 |
| | | Upstream | -536 |
| Matrix_7 | PIF4 | Not available | Upstream | -536 |
| | | Upstream | -537 |
| Matrix_77 | PRR5 | Not available | Upstream | -533 |
| | | Upstream | -534 |
| Matrix_80 | BIM1 | Not available | Upstream | -535 |
| Motif_116 | INRNTPSADB | Inr (initiator) elements found in the tobacco psaDb gene promoter without TATA boxes; Light-responsive transcription of psaDb depends on Inr, but not TATA box | Upstream | -332 |
| | | Upstream | -375 |
| Motif_125 | BOXIINTPATPB | Box 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 promoter | Downstream | 1769 |
| Motif_129 | GAGAGMGSA1 | GAGA 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 DNA | Upstream | -199 |
| | | Upstream | -201 |
| | | Upstream | -203 |
| | | Upstream | -205 |
| | | Upstream | -207 |
| | | Upstream | -209 |
| | | Upstream | -211 |
| | | Upstream | -213 |
| | | Upstream | -215 |
| Motif_145 | MYCATERD1 | MYC recognition sequence (from -466 to -461) necessary for expression of erd1 (early responsive to dehydration) in dehydrated Arabidopsis; NAC protein bound specifically to the CATGTG motif; NAC protein bound specifically to the CATGTG motif | Downstream | 1786 |
| Motif_174 | SREATMSD | sugar-repressive element (SRE) found in 272 of the 1592 down-regulated genes after main stem decapitation in Arabidopsis | Downstream | 1649 |
| Motif_179 | CACGTGMOTIF;BES1;PIF4;PIF5 | Phytochrome 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 responses | Upstream | -536 |
| Motif_182 | MYB2CONSENSUSAT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; see MYB2 and MYBATRD22 | Upstream | -365 |
| Motif_192 | BOXLCOREDCPAL | Consensus of the putative core sequences of box-L-like sequences in carrot; PAL1 promoter region; DCMYB1 bound to these sequences in vitro | Downstream | 1781 |
| Motif_194 | EBOXBNNAPA | E-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; ICE1 | Downstream | 1786 |
| | | Upstream | -536 |
| Motif_200 | GBOXLERBCS | G box; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis; Binding with GBF | Upstream | -535 |
| Motif_218 | ABRERATCAL | ABRE-related sequence or Repeated sequence motifs identified in the upstream regions of 162 Ca(2+)-responsive upregulated genes; see also ABRE | Upstream | -535 |
| | | Upstream | -536 |
| | | Upstream | -1298 |
| Motif_22 | RYREPEATLEGUMINBOX | RY repeat (CATGCAY) or legumin box found in seed-storage protein genes in legume such as soybean | Downstream | 1673 |
| Motif_221 | MYBCORE | Binding 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 biosynthesis | Upstream | -365 |
| Motif_222 | AGMOTIFNTMYB2 | AG-motif found at -114 of the promoter of NtMyb2 gene; NtMyb2 is a regulator of the tobacco retrotransposon Tto1 and the defence-related gene phenylalanine ammonia lyase (PAL), which are induced by various stress such as wounding or elicitor treatment; AGP1 (GATA-type zinc finger protein) binding site | Upstream | -409 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -534 |
| | | Upstream | -536 |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Downstream | 1668 |
| Motif_288 | NONAMERMOTIFTAH3H4 | Nonamer motif found in promoter of wheat histone genes H3 and H4 | Upstream | -366 |
| Motif_291 | ABFs binding site motif | Binding 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 element | Upstream | -536 |
| Motif_292 | MYBPZM | Core 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 genes | Downstream | 1530 |
| Motif_297 | Bellringer/replumless/pennywise BS1 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | Downstream | 1723 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -184 |
| Motif_332 | SV40COREENHAN | SV40 core enhancer; Similar sequences found in rbcS genes | Upstream | -547 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -365 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -536 |
| Motif_370 | TATABOX2 | TATA box; TATA box found in the 5'upstream region of pea legA gene; sporamin A of sweet potato; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation | Upstream | -1025 |
| Motif_371 | DRE-like promoter motif | The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses | Upstream | -453 |
| Motif_414 | ABI3 | Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene product | Downstream | 1673 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -199 |
| | | Upstream | -201 |
| | | Upstream | -203 |
| | | Upstream | -205 |
| | | Upstream | -207 |
| | | Upstream | -209 |
| | | Upstream | -211 |
| | | Upstream | -213 |
| | | Upstream | -215 |
| | | Upstream | -217 |
| Motif_447 | AtMYC2 BS in RD22;PIF4 | Binding site for MYC (rd22BP1) in Arabidopsis dehydration-resposive gene, rd22; MYC binding site in rd22 gene of Arabidopsis thaliana; ABA-induction; Located at ca. -200 of rd22 gene; Also MYB at ca. -141 of rd22 gene; See also MYBATRD22; Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Downstream | 1786 |
| Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -535 |
| | | Upstream | -536 |
| Motif_450 | E2FCONSENSUS | E2F consensus sequence of all different E2F-DP-binding motifs that were experimentally verified in plants | Upstream | -520 |
| Motif_454 | DRECRTCOREAT | Core motif of DRE/CRT (dehydration-responsive element/C-repeat) cis-acting element found in many genes in Arabidopsis and in rice; Os DREB1A bound to GCCGAC more preferentially than to ACCGAC whereas At DREB1A bound to both GCCGAC and ACCGAC efficiently; Maize ZmDREB1A bound to DRE; HaDREB2 in Helianthus annuus (sunflower) | Upstream | -454 |
| | | Upstream | -1710 |
| Motif_459 | SORLIP1 | Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | Upstream | -344 |
| Motif_473 | ABREOSRGA1 | ABRE (ABA responsive element) in rice RGA1 encoding a G protein alpha subunit;ABRE; ABA and water-stress responses; Found in maize rab28; maize rab28 is ABA-inducible in embryos and vegetative tissues; Found in the Arabidopsis (A.t.) alcohol dehydrogenase (Adh) gene promoter; ABRE2; Found in the maize (Z.m.) Cat1 gene promoter; Responsible for the induction by ABA; Binding site of CBF2; Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance; The CBF genes do not appear to be autoregulated through the CRT/DRE sequence;The cis-regulatory element CCACGTGG is involved in ABA and water-stress responses of the maize gene rab28. Characterization of a maize G-box binding factor that is induced by hypoxia | Upstream | -535 |
| Motif_511 | RYREPEATGMGY2 | RY repeat motif (CATGCAT); Present in the 5' region of the soybean glycinin gene (Gy2) | Downstream | 1673 |
| Motif_536 | TBOXATGAPB | Tbox found in the Arabidopsis thaliana GAPB gene promoter; Located between -94 and -89 (T1) and also between -84 and -79 (T2); Mutations in the Tbox resulted in reductions of light-activated gene transcription; GAPB encodes the B subunit of chloroplast glyceraldehyde-3-phosphate dehydrogenase(GADPH) of A.T.; Promoter analysis of the nuclear gene encoding the chloroplast glyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsis thaliana | Downstream | 1736 |
| | | Upstream | -406 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -537 |
| Motif_563 | PYRIMIDINEBOXOSRAMY1A | Pyrimidine box found in rice alpha-amylase (RAmy1A) gene; Gibberellin-respons cis-element of GARE and pyrimidine box are partially involved in sugar repression; Found in the promoter of barley alpha-amylase (Amy2/32b) gene which is induced in the aleurone layers in response to GA; BPBF protein binds specifically to this site | Downstream | 1594 |
| Motif_570 | POLASIG2 | PolyA signal; poly A signal found in rice alpha-amylase; -10 to -30 in the case of animal genes | Downstream | 1723 |
| Motif_591 | CBFHV | Binding site of barley CBF1, and also of barley CBF2; CBF = C-repeat (CRT) binding factors; CBFs are also known as dehydration-responsive element (DRE) binding proteins (DREBs) | Upstream | -454 |
| Motif_599 | LREBOXIIPCCHS1;HY5 | BoxII; Light responsive element (LRE) found in the parsley CHS-1 (chalcone synthase-1) gene promoter; Required for light responsiveness; nuclear protein binding site; Highly conserved in various light inducible gene promoters; Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression | Upstream | -534 |
| Motif_603 | SITEIIATCYTC | Site II element found in the promoter regions of cytochrome genes (Cytc-1, Cytc-2) in Arabidopsis; Located between -147 and -156 from the translational starts sites;Overrepresented in the promoters of nuclear genes encoding components of the oxidative phosphorylation (OxPhos) machinery from both Arabidopsis and rice | Downstream | 1790 |
| Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 1643 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Upstream | -548 |
| Motif_627 | ACGTABREMOTIFA2OSEM | Experimentally 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 Arabidopsis | Upstream | -537 |
| Motif_638 | ABRE binding site motif | Not available | Upstream | -536 |
| Motif_640 | RYREPEATBNNAPA | RY 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 ABRE | Downstream | 1673 |
| Motif_658 | GT1CONSENSUS | Consensus 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 expression | Downstream | 1648 |
| | | Downstream | 1368 |
| Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 1643 |
| Motif_682 | GT1GMSCAM4 | GT-1 motif found in the promoter of soybean CaM isoform, SCaM-4; Plays a role in pathogen- and salt-induced SCaM-4 gene expression | Downstream | 1368 |
| Motif_683 | AtMYB2 BS in RD22 | 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; Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression | Upstream | -547 |
| Motif_69 | CTRMCAMV35S | CT-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 GAGA | Upstream | -178 |
| | | Upstream | -188 |
| | | Upstream | -200 |
| | | Upstream | -202 |
| | | Upstream | -204 |
| | | Upstream | -206 |
| | | Upstream | -208 |
| | | Upstream | -210 |
| | | Upstream | -212 |
| | | Upstream | -214 |
| | | Upstream | -216 |
| | | Upstream | -218 |
| | | Upstream | -220 |
| | | Upstream | -222 |
| | | Upstream | -224 |
| Motif_79 | UPRMOTIFIIAT | 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 | Upstream | -538 |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Upstream | -504 |
| Motif_98 | SEF3MOTIFGM | SEF3 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; SEF4 | Downstream | 2155 |
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