| Matrix_101 | ERF5 | Not available | Intron | 1293 |
| Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -1558 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -1561 |
| Matrix_120 | BEE2 | Not available | Upstream | -1557 |
| Matrix_127 | AtMYB15 | More than 80R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -573 |
| Matrix_14 | ZCW32;AT5G62610 | Not available | Upstream | -1557 |
| | | Upstream | -1556 |
| Matrix_153 | AP2 | Not available | Upstream | -1558 |
| Matrix_158 | AT1G03040;LRL1;UNE12;LRL2;LRL3 | Not available | Upstream | -1557 |
| Matrix_184 | AGL15 | Not available | Intron | 2037 |
| Matrix_200 | PIL5;AT4G28790;AT4G28800;AT4G28811;AT4G28815 | Not available | Upstream | -1557 |
| Matrix_233 | MYC3 | Not available | Upstream | -1556 |
| Matrix_25 | AP3 | Not available | Upstream | -710 |
| | | Intron | 4099 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -714 |
| Matrix_27 | ATAIB;ATNIG1 | Not available | Upstream | -1556 |
| | | Upstream | -1555 |
| Matrix_287 | ERF2 | Not available | Intron | 1293 |
| Matrix_301 | PIL5 | Not available | Upstream | -1556 |
| Matrix_320 | MYC4 | Not available | Upstream | -1556 |
| Matrix_323 | BIM3 | Not available | Upstream | -1557 |
| Matrix_330 | MYC2;TT8 | Not available | Upstream | -1557 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -1557 |
| | | Upstream | -1556 |
| Matrix_339 | bHLH104 | Not available | Upstream | -1557 |
| Matrix_344 | ATERF15;AT4G18450 | Not available | Intron | 1293 |
| Matrix_356 | PRR5 | Not available | Upstream | -1564 |
| Matrix_365 | AT1G10120;AT1G25330;CIB5;AT1G68920;AT3G23690;CIB1 | Not available | Upstream | -1556 |
| Matrix_369 | AT2G18300 | Not available | Upstream | -1559 |
| | | Upstream | -1557 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -728 |
| | | Upstream | -562 |
| Matrix_374 | AT5G07580;AT5G61590 | Not available | Intron | 1293 |
| Matrix_389 | ILR3 | Not available | Upstream | -1557 |
| Matrix_39 | AP1 | Not available | Upstream | -721 |
| Matrix_397 | GT2L | Not available | Upstream | -571 |
| Matrix_414 | AGL15 | Not available | Upstream | -732 |
| | | Upstream | -727 |
| Matrix_437 | MYC2 | Not available | Upstream | -1556 |
| Matrix_439 | AP3 | Not available | Upstream | -118 |
| Matrix_448 | ATERF6 | Not available | Intron | 1292 |
| Matrix_449 | BIM2 | Not available | Upstream | -1557 |
| Matrix_465 | MYC4 | Not available | Upstream | -1557 |
| Matrix_476 | bHLH115;bHLH34 | Not available | Upstream | -1556 |
| Matrix_48 | PI | Not available | Upstream | -721 |
| Matrix_480 | BES1 | Not available | Upstream | -1558 |
| | | Upstream | -1557 |
| Matrix_496 | ATMYB15 | Not available | Upstream | -573 |
| Matrix_53 | MYC3 | Not available | Upstream | -1559 |
| Matrix_7 | PIF4 | Not available | Upstream | -1555 |
| Matrix_77 | PRR5 | Not available | Upstream | -1558 |
| Matrix_80 | BIM1 | Not available | Upstream | -1558 |
| | | Upstream | -1556 |
| Matrix_90 | BEE1;BEE3;AT3G07340;AT5G48560;AT5G50915 | Not available | Upstream | -1556 |
| Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -386 |
| 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 | -1542 |
| | | Upstream | -500 |
| 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 | -1556 |
| | | Upstream | -1554 |
| Motif_155 | NODCON1GM | One 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 nodules | Upstream | -1367 |
| | | Upstream | -1320 |
| | | Upstream | -636 |
| Motif_16 | -300ELEMENT | Present 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 -300MOTIF | Upstream | -1615 |
| Motif_163 | BOXCPSAS1 | Box C in pea (P.s.) asparagine synthetase (AS1) gene; Found at -45; AS1 is negatively regulated by light; Box C binds with nuclear proteins, which was competed by a putative repressor element RE1 | Intron | 1594 |
| Motif_166 | RAP2.2 | Transcription factor RAP2.2 and its interacting partner SINAT2: stable elements in the carotenogenesis of Arabidopsis leaves | Upstream | -1375 |
| Motif_168 | IBOX | I box; I-box; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis; I box; Binding site of LeMYB1, that is a member of a novel class of myb-like proteins; LeMYBI act as a transcriptional activator; An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene | Upstream | -1323 |
| 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 | -1555 |
| Motif_181 | IBOXCORENT | I-box core motif in the CAMs (conserved DNA modular arrays) associated with light-responsive promoter regions | Upstream | -1324 |
| 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 | -1626 |
| | | Intron | 1659 |
| | | Downstream | 6533 |
| Motif_183 | TRANSINITDICOTS | Context sequence of translational initiation codon in dicots | Upstream | -1654 |
| | | Intron | 1641 |
| Motif_193 | GLK1 | GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis | Intron | 1397 |
| 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 | -1555 |
| | | Upstream | -1488 |
| | | Intron | 1659 |
| Motif_207 | MAMMALENHAN | Core sequence in enhancers from polyoma virus and from the IgM heavy chain gene | Upstream | -440 |
| 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 | -1556 |
| | | Upstream | -1555 |
| 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 | -1626 |
| | | Intron | 1659 |
| | | Downstream | 6533 |
| Motif_254 | MYB46;MYB83 | MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes | Upstream | -1586 |
| | | Upstream | -1437 |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Intron | 1151 |
| 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 | -1648 |
| | | Upstream | -670 |
| | | Intron | 3548 |
| | | Intron | 4192 |
| Motif_297 | Bellringer/replumless/pennywise BS1 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | Upstream | -633 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -1322 |
| | | Upstream | -445 |
| | | Intron | 1582 |
| | | Intron | 1616 |
| | | Intron | 1648 |
| Motif_318 | CGCGBOXAT | CGCG box recognized by AtSR1-6 (Arabidopsis thaliana signal-responsive genes); Multiple CGCG elements are found in promoters of many genes; Ca2+/calmodulin binds to all AtSRs | Upstream | -566 |
| 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 | -1316 |
| | | Intron | 1152 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -1626 |
| | | Intron | 1659 |
| | | Downstream | 6533 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -1555 |
| | | Intron | 1475 |
| 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 | -1317 |
| | | Upstream | -1312 |
| | | Upstream | -677 |
| 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 | Intron | 3549 |
| | | Intron | 4193 |
| Motif_391 | REALPHALGLHCB21 | 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 much lower in green plants; Required for phytochrome regulation | Upstream | -40 |
| 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 | Upstream | -520 |
| Motif_419 | MYB4 binding site motif | Not available | Upstream | -1586 |
| | | Upstream | -1358 |
| Motif_43 | CCA1 binding site motif | CCA1 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 gene | Downstream | 6545 |
| Motif_469 | QELEMENTZMZM13 | Q(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 gene | Upstream | -1453 |
| Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -1557 |
| Motif_495 | TRANSINITMONOCOTS | Context sequence of translational initiation codon in monocots | Upstream | -1654 |
| | | Intron | 1641 |
| Motif_497 | ARE1 | ARE (antioxidant response element); antioxidant response element of rat glutathione S-transferase Ya subunit, and rat NAD(P)H:quinone reductase genes | Upstream | -1649 |
| Motif_503 | EECCRCAH1 | EEC; 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 LCR1 | Upstream | -387 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Upstream | -1438 |
| Motif_527 | LFY | Structural basis for LEAFY floral switch function and similarity with helix-turn-helix proteins | Intron | 1637 |
| 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 | Upstream | -1336 |
| Motif_562 | -300CORE | TGTAAAG 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 factors | Upstream | -408 |
| 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 | -543 |
| | | Intron | 1283 |
| | | Intron | 1289 |
| | | Intron | 3562 |
| Motif_570 | POLASIG2 | PolyA signal; poly A signal found in rice alpha-amylase; -10 to -30 in the case of animal genes | Upstream | -633 |
| Motif_575 | TATABOX3 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene | Upstream | -1479 |
| Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -555 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -1316 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Upstream | -439 |
| Motif_645 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -1488 |
| Motif_648 | ARE2 | ARE (antioxidant response element); antioxidant response element of mouse metallothionein-I (MT-I) gene; Consensus sequence of mouse MT-I and MT-II genes, and MT genes isolated from rat, hamster, human, sheep, chicken, Drosophila melanogaster, C. elegans; See ARE1 | Upstream | -1648 |
| Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -390 |
| 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 | Upstream | -1571 |
| | | Upstream | -1505 |
| | | Upstream | -578 |
| | | Upstream | -427 |
| | | Intron | 1287 |
| | | Intron | 1623 |
| | | Intron | 3569 |
| | | Intron | 3570 |
| | | Intron | 3896 |
| Motif_662 | MYB26PS | Myb26 binding site; Myb26 recognizes the c-Myb and P-box-like binding sites representing cis-elements in the promoter regions of several phenylpropanoid biosynthetic genes; Identical to P-box in maize, and to Myb305 binding site in snapdragon | Upstream | -1587 |
| Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Upstream | -1587 |
| Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -555 |
| 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 | Upstream | -578 |
| | | Intron | 3570 |
| 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 | -691 |
| | | Upstream | -689 |
| | | Upstream | -687 |
| | | Upstream | -508 |
| | | Upstream | -474 |
| | | Upstream | -472 |
| | | Upstream | -470 |
| | | Upstream | -468 |
| | | Intron | 1069 |
| | | Intron | 1071 |
| | | Intron | 3245 |
| | | Intron | 3247 |
| | | Intron | 3249 |
| | | Intron | 4195 |
| | | Intron | 4197 |
| | | Intron | 4199 |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Upstream | -1340 |
| 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 | -495 |
| 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 | Upstream | -1626 |
| | | Downstream | 6533 |
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