Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -772 |
| | | Upstream | -773 |
Matrix_109 | GBF3 | Not available | Upstream | -772 |
Matrix_113 | ABI5 | Not available | Upstream | -774 |
Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -770 |
| | | Upstream | -771 |
Matrix_120 | BEE2 | Not available | Upstream | -773 |
| | | Upstream | -774 |
Matrix_122 | ABF1;AREB2 | Not available | Upstream | -772 |
| | | Upstream | -773 |
Matrix_129 | ABF1 | Not available | Upstream | -773 |
| | | Upstream | -774 |
Matrix_133 | DYT1 | Not available | Upstream | -774 |
| | | Upstream | -775 |
Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -769 |
| | | Upstream | -770 |
Matrix_153 | AP2 | Not available | Upstream | -772 |
| | | Upstream | -773 |
Matrix_156 | POC1 | Not available | Upstream | -772 |
| | | Upstream | -773 |
| | | Upstream | -774 |
| | | Upstream | -775 |
Matrix_158 | AT1G03040;LRL1;UNE12;LRL2;LRL3 | Not available | Upstream | -773 |
Matrix_176 | MYB98 | Not available | Upstream | -218 |
Matrix_179 | AtMYB84;MYB36;MYB68;O49746_ARATH | Not available | Upstream | -225 |
| | | Upstream | -229 |
| | | Upstream | -232 |
| | | Upstream | -233 |
Matrix_181 | Dof5.7 | Not available | Upstream | -290 |
Matrix_19 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -770 |
| | | Upstream | -771 |
Matrix_200 | PIL5;AT4G28790;AT4G28800;AT4G28811;AT4G28815 | Not available | Upstream | -773 |
| | | Upstream | -774 |
Matrix_24 | POC1 | Not available | Upstream | -769 |
Matrix_247 | PIF3 | Not available | Upstream | -773 |
| | | Upstream | -774 |
Matrix_25 | AP3 | Not available | Downstream | 1203 |
| | | Downstream | 1109 |
Matrix_264 | ATAREB1 | Not available | Upstream | -773 |
Matrix_278 | AtbZIP44 | Not available | Upstream | -772 |
Matrix_283 | GATA15;GATA17;AT4G16141;GATA22;GATA23;GATA16;GNC | Not available | Upstream | -816 |
| | | Upstream | -817 |
Matrix_301 | PIL5 | Not available | Upstream | -774 |
| | | Upstream | -775 |
Matrix_307 | RGL2;RGL3 | Not available | Upstream | -267 |
Matrix_327 | ARR11 | Not available | Upstream | -851 |
| | | Upstream | -852 |
Matrix_330 | MYC2;TT8 | Not available | Upstream | -773 |
Matrix_331 | GBF1 | Not available | Upstream | -772 |
Matrix_332 | SPT;ALC | Not available | Upstream | -773 |
| | | Upstream | -774 |
Matrix_345 | POC1 | Not available | Upstream | -355 |
| | | Upstream | -769 |
| | | Upstream | -770 |
Matrix_37 | GATA27 | Not available | Upstream | -816 |
| | | Upstream | -817 |
Matrix_389 | ILR3 | Not available | Upstream | -773 |
Matrix_39 | AP1 | Not available | Downstream | 1144 |
Matrix_401 | MYB55 | Not available | Upstream | -224 |
| | | Upstream | -882 |
Matrix_403 | BZR1 | Not available | Upstream | -771 |
| | | Upstream | -772 |
Matrix_414 | AGL15 | Not available | Downstream | 1117 |
Matrix_42 | AT2G45680 | Not available | Upstream | -471 |
Matrix_438 | AtbZIP63 | Not available | Upstream | -773 |
Matrix_443 | AGL15 | Not available | Upstream | -771 |
Matrix_449 | BIM2 | Not available | Upstream | -773 |
| | | Upstream | -774 |
Matrix_470 | WRKY18 | Not available | Downstream | 962 |
Matrix_48 | PI | Not available | Upstream | -224 |
| | | Upstream | -228 |
| | | Upstream | -232 |
| | | Upstream | -465 |
Matrix_480 | BES1 | Not available | Upstream | -773 |
Matrix_488 | ABF1 | Not available | Upstream | -772 |
| | | Upstream | -773 |
Matrix_499 | ARR18 | Not available | Upstream | -850 |
| | | Upstream | -851 |
Matrix_504 | WRKY40 | Not available | Downstream | 961 |
Matrix_53 | MYC3 | Not available | Upstream | -771 |
Matrix_55 | PIF3 | Not available | Upstream | -772 |
| | | Upstream | -773 |
Matrix_56 | BZIP17;BZIP28;BZIP49 | Not available | Upstream | -774 |
Matrix_64 | PIF5 | Not available | Upstream | -774 |
| | | Upstream | -775 |
Matrix_65 | POC1;PIL1 | Not available | Upstream | -774 |
Matrix_7 | PIF4 | Not available | Upstream | -773 |
| | | Upstream | -774 |
Matrix_77 | PRR5 | Not available | Upstream | -772 |
| | | Upstream | -773 |
Matrix_80 | BIM1 | Not available | Upstream | -774 |
| | | Upstream | -775 |
Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -273 |
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 | -122 |
| | | Upstream | -285 |
| | | Upstream | -543 |
Motif_136 | SEF4MOTIFGM7S | SEF4 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) | Downstream | 1017 |
Motif_139 | RHERPATEXPA7 | Right part of RHEs (Root Hair-specific cis-Elements) conserved among the Arabidopsis thaliana A7 (AtEXPA7) orthologous (and paralogous) genes from diverse angiosperm species with different hair distribution patterns | Upstream | -776 |
| | | Upstream | -820 |
Motif_141 | BP5OSWX | OsBP-5 (a MYC protein) binding site in Wx promoter | Upstream | -361 |
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 | -775 |
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 | Downstream | 1208 |
| | | Upstream | -221 |
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 | Upstream | -350 |
| | | Upstream | -377 |
| | | Upstream | -775 |
Motif_210 | REBETALGLHCB21 | REbeta 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 regulation | Upstream | -848 |
| | | Upstream | -1383 |
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 | -360 |
| | | Upstream | -774 |
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 | Downstream | 1208 |
| | | Upstream | -221 |
Motif_261 | S1FBOXSORPS1L21 | S1F 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 activity | Downstream | 1133 |
| | | Upstream | -265 |
Motif_270 | ELRECOREPCRP1 | ElRE (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 Arabidopsis | Downstream | 960 |
Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Upstream | -196 |
| | | Upstream | -1527 |
| | | Upstream | -1531 |
Motif_285 | HDZIP2ATATHB2 | Binding site of the Arabidopsis homeobox gene (ATHB-2) found in its own promoter; Located between -72 and -80; Similar to the HD-ZIP-2 binding consensus sequence; ATHB-2 is regulated by light signals which function as a negative autoregulator of its own gene | Upstream | -1529 |
Motif_286 | SEBFCONSSTPR10A | 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 auxin response element | Upstream | -1435 |
Motif_321 | TATABOX5 | TATA box; TATA box found in the 5'upstream region of pea (Pisum sativum) glutamine synthetase gene; a functional TATA element by in vivo analysis | Upstream | -1494 |
Motif_323 | MYB1LEPR | Tomato Pti4(ERF) regulates defence-related gene expression via GCC box and non-GCC box cis elements (Myb1(GTTAGTT), G box (CACGTG)) | Upstream | -397 |
Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Downstream | 1208 |
| | | Upstream | -221 |
Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -775 |
Motif_342 | POLASIG1 | PolyA 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 Arabidopsis | Upstream | -199 |
| | | Upstream | -1495 |
Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Upstream | -203 |
Motif_348 | WBBOXPCWRKY1 | WB 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 Arabidopsis | Upstream | -762 |
| | | Upstream | -1334 |
Motif_365 | ARF1 binding site motif | ARF (auxin response factor) binding site found in the promoters of primary/early auxin response genes of Arabidopsis thaliana; AuxRE;Binding site of Arabidopsis ARF1 (Auxin response factor1); Sequence found in NDE element in Soybean SAUR (Small Auxin-Up RNA) 15A gene promoter;Found in D1 or D4 element in Soybean GH3 promoter; This element was enriched in the 5'-flanking region of genes up-regulated by both IAA and BL;Dimerization and DNA binding of auxin response factors | Upstream | -834 |
Motif_410 | ANAERO1CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1); Arbitrary named ANAERO1CONSENSUS by the PLACEdb curator | Downstream | 1094 |
Motif_411 | PRECONSCRHSP70A | Consensus sequence of PRE (plastid response element) in the promoters of HSP70A in Chlamydomonas; Involved in induction of HSP70A gene by both MgProto and light | Downstream | 1044 |
Motif_419 | MYB4 binding site motif | Not available | Upstream | -397 |
Motif_420 | SORLREP2AT | one of Sequences Over-Represented in Light-Repressed Promoters (SORLREPs) in Arabidopsis; Computationally identified phyA-repressed motifs; See also all SORLREPs and all SORLIPs; Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | Upstream | -200 |
Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -405 |
Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -774 |
Motif_484 | RAV1-B binding site motif | Binding consensus sequence of an Arabidopsis transcription factor, RAV1; RAV1 specifically binds to DNA with bipartite sequence motifs of RAV1-A (CAACA) and RAV1-B (CACCTG); RAV1 protein contain AP2-like and B3-like domains; The AP2-like and B3-like domains recognize the CAACA and CACCTG motifs, respectively; The expression level of RAV1 were relatively high in rosette leaves and roots; RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants | Upstream | -350 |
Motif_530 | CPBCSPOR | The sequence critical for Cytokinin-enhanced Protein Binding in vitro, found in -490 to -340 of the promoter of the cucumber POR (NADPH-protochlorophyllide reductase) gene | Upstream | -323 |
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 | Upstream | -810 |
Motif_567 | T/GBOXATPIN2 | T/G-box found in tomato proteinase inhibitor II (pin2) and leucine aminopeptidase (LAP) genes; Involved in jasmonate (JA) induction of these genes; bHLH-Leu zipper JAMYC2 and JAMYC10 proteins specifically recognize this motif | Upstream | -361 |
| | | Upstream | -1847 |
| | | Upstream | -1961 |
Motif_57 | ABREOSRAB21 | ABA responsive element (ABRE) of wheat Em and rice rab21 genes; Proposed consensus sequence for the repeated motif (Em1a and Em1b) of wheat Em gene | Upstream | -772 |
Motif_575 | TATABOX3 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene | Upstream | -1533 |
| | | Upstream | -1538 |
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) | Downstream | 1051 |
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 | Upstream | -771 |
Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 1093 |
Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Downstream | 1067 |
| | | Upstream | -196 |
| | | Upstream | -1490 |
| | | Upstream | -1492 |
Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Downstream | 1030 |
Motif_626 | ACGTTBOX | T-box according to the nomenclature of ACGT elements; One of ACGT elements; See also ACGTABOX,ACGTCBOX, and CACGTGMOTIF | Upstream | -204 |
Motif_630 | WBOXNTCHN48 | W 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 tobacco | Upstream | -344 |
| | | Upstream | -537 |
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 | Upstream | -532 |
Motif_65 | BS1EGCCR | BS1 (binding site 1) found in E. gunnii Cinnamoyl-CoA reductase (CCR) gene promoter; nuclear protein binding site; Required for vascular expression | Upstream | -784 |
Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -352 |
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 | 1173 |
| | | Upstream | -211 |
| | | Upstream | -812 |
| | | Upstream | -894 |
| | | Upstream | -895 |
| | | Upstream | -1488 |
Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 1093 |
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 | 1173 |
| | | Upstream | -211 |
| | | Upstream | -1488 |
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 | -406 |
| | | Upstream | -408 |
| | | Upstream | -410 |
| | | Upstream | -412 |
| | | Upstream | -464 |
Motif_70 | CANBNNAPA | Core 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 repressor | Upstream | -115 |
Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Downstream | 1017 |
Motif_85 | SORLIP5AT | one 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 data | Upstream | -123 |
| | | Upstream | -544 |
Motif_88 | MYB2AT | Binding site for ATMYB2, an Arabidopsis MYB homolog; ATMYB2 binds oligonucleotides that contained a consensus MYB recognition sequence (TAACTG), such as is in the SV40 enhancer and the maize bronze-1 promoter; ATMYB2 is involved in regulation of genes that are responsive to water stress in Arabidopsis | Downstream | 1208 |
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 | Upstream | -147 |
| | | Upstream | -586 |
| | | Upstream | -841 |