| Matrix_119 | RRTF1 | Not available | Upstream | -1123 |
| Matrix_138 | RRTF1 | Not available | Upstream | -1123 |
| Matrix_146 | ORA47 | Not available | Upstream | -1122 |
| Matrix_155 | RAP2.6;ERF110;ABR1 | Not available | Upstream | -1121 |
| Matrix_174 | ZAT2 | Not available | Downstream | 2904 |
| Matrix_179 | AtMYB84;MYB36;MYB68;O49746_ARATH | Not available | Upstream | -1167 |
| Matrix_184 | AGL15 | Not available | Upstream | -1276 |
| Matrix_23 | ANAC46 | Not available | Upstream | -1549 |
| Matrix_234 | RAP2.3 | Not available | Upstream | -1122 |
| Matrix_242 | AT2G25820;AT3G16280;AT4G32800;TINY2;tny | Not available | Upstream | -1122 |
| Matrix_244 | DREB2C | Not available | Upstream | -1123 |
| Matrix_25 | AP3 | Not available | Intron | 1597 |
| Matrix_261 | ATERF-1 | Not available | Upstream | -1122 |
| Matrix_288 | RAP2.3 | Not available | Upstream | -1123 |
| Matrix_312 | ARF11;MP;ARF6;IAA21;ARF8;ARF4 | Not available | Upstream | -1124 |
| | | Upstream | -1103 |
| Matrix_317 | AT1G06070;AT2G31370;AT2G40620 | Not available | Downstream | 2903 |
| Matrix_321 | HRD | Not available | Upstream | -1122 |
| Matrix_326 | AT5G07310;Rap2.6L;AT5G61890 | Not available | Upstream | -1123 |
| Matrix_334 | AT3G23230 | Not available | Upstream | -1121 |
| Matrix_343 | AT2G33710 | Not available | Upstream | -1122 |
| Matrix_355 | ERF10;ERF11 | Not available | Upstream | -1123 |
| Matrix_363 | RAP2.3 | Not available | Upstream | -1123 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -1477 |
| Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Upstream | -1122 |
| Matrix_378 | ATERF1 | Not available | Upstream | -1122 |
| Matrix_385 | DEAR4 | Not available | Upstream | -1123 |
| Matrix_394 | DREB_U | Not available | Upstream | -1123 |
| Matrix_409 | DEAR3 | Not available | Upstream | -1123 |
| Matrix_448 | ATERF6 | Not available | Upstream | -1123 |
| Matrix_454 | AT1G77200;ATERF38;AT4G16750;AT5G52020 | Not available | Upstream | -1123 |
| Matrix_473 | RRTF1 | Not available | Upstream | -1122 |
| Matrix_478 | AT1G01250 | Not available | Upstream | -1122 |
| Matrix_50 | ATERF14;AT5G43410 | Not available | Upstream | -1123 |
| Matrix_510 | AtMYB84 | More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -1167 |
| Matrix_515 | ddf2;ATCBF3;CBF1;CBF4 | Not available | Upstream | -1124 |
| | | Upstream | -1103 |
| Matrix_518 | AT2G21230 | Not available | Downstream | 2903 |
| Matrix_61 | ATCBF3 | Not available | Upstream | -1123 |
| Matrix_73 | DEAR3;RAP2.9;RAP2.10 | Not available | Upstream | -1122 |
| Matrix_74 | LFY | Not available | Intron | 1646 |
| Matrix_86 | CRF5;CRF6;CRF4 | Not available | Upstream | -1121 |
| Matrix_91 | CRF3 | Not available | Upstream | -1122 |
| Matrix_92 | AT1G33760 | Not available | Upstream | -1123 |
| Motif_127 | SBOXATRBCS | S-box conserved in several rbcS promoters in Arabidopsis; ABI4 binding site; Important for the sugar and ABA responsiveness of CMA5 | Upstream | -1157 |
| 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 | -1436 |
| | | Upstream | -1434 |
| 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) | Intron | 1611 |
| | | Intron | 1648 |
| 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 | -587 |
| 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 | -1456 |
| 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 | -1490 |
| | | Intron | 1551 |
| | | Intron | 1555 |
| 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 | 2932 |
| Motif_184 | PROXBBNNAPA | prox B (proximal portion of B-box) found in napA gene of Brassica napus; CA-rich sequence; Found between -130 and -124; Required for seed specific expression and ABA responsiveness; 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 | -1166 |
| Motif_190 | WUSATAg | Target sequence of WUS in the intron of AGAMOUS gene in Arabidopsis | Intron | 1629 |
| 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 | Intron | 1570 |
| | | Downstream | 2906 |
| | | Downstream | 2932 |
| Motif_22 | RYREPEATLEGUMINBOX | RY repeat (CATGCAY) or legumin box found in seed-storage protein genes in legume such as soybean | Upstream | -417 |
| 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 | -1571 |
| | | Downstream | 2932 |
| 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 | -1163 |
| 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 light | Upstream | -1292 |
| | | Downstream | 2896 |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Upstream | -597 |
| | | Downstream | 3057 |
| 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 | -1417 |
| | | Upstream | -592 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -998 |
| | | Intron | 1608 |
| Motif_310 | ANAERO3CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1); Arbitrary named ANAERO3CONSENSUS by the PLACEdb curator | Upstream | -1184 |
| 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 | -1535 |
| | | Upstream | -1469 |
| | | Upstream | -596 |
| | | Downstream | 3058 |
| | | Downstream | 3360 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Downstream | 2932 |
| 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 | -1534 |
| | | Upstream | -1147 |
| | | Downstream | 3361 |
| Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Intron | 1595 |
| Motif_351 | GARE1OSREP1 | Gibberellin-responsive element (GARE) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -1572 |
| Motif_357 | NTBBF1ARROLB | NtBBF1(Dof protein from tobacco) binding site in Agrobacterium rhizogenes rolB gene; Found in regulatory domain B (-341 to -306); Required for tissue-specific expression and auxin induction | Upstream | -1490 |
| 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 | -591 |
| 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 | -1122 |
| | | Upstream | -1101 |
| Motif_375 | ERELEE4 | ERE (ethylene responsive element) of tomato E4 and carnation GST1 genes; GST1 is related to senescence; Found in the 5'-LTR region of TLC1.1 retrotransposon family in Lycopersicon chilense; ERE motifs mediate ethylene-induced activation of the U3 promoter region | Upstream | -1176 |
| Motif_383 | UPRE-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 Arabidopsis | Upstream | -1072 |
| 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 | -1119 |
| Motif_419 | MYB4 binding site motif | Not available | Upstream | -1163 |
| Motif_437 | ANAERO2CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1) | Upstream | -377 |
| | | Downstream | 2908 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -1436 |
| | | Upstream | -1434 |
| | | Upstream | -1432 |
| 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 | -1121 |
| | | Upstream | -1100 |
| 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 | Intron | 1575 |
| 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 | -1112 |
| Motif_490 | PROLAMINBOXOSGLUB1 | Prolamine box found in the rice GluB-1 gene promoter; Involved in quantitative regulation of the GluB-1 gene | Intron | 1552 |
| 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 | -1115 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Upstream | -1163 |
| Motif_520 | AMYBOX1 | amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barley | Upstream | -1572 |
| 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 | -645 |
| 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 | -1489 |
| Motif_580 | L1BOXATPDF1 | L1 box found in promoter of Arabidopsis thaliana PROTODERMAL FACTOR1 (PDF1) gene; Located between -134 and -127; Involved in L1 layer-specific expression; L1-specific homeodomain protein ATML can bind to the L1 box; Y=C/T; A cotton fiber gene, RD22-like 1 (RDL1), contains a homeodomain binding L1 box and a MYB binding motif ; HDZip IV; Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein | Downstream | 3031 |
| Motif_584 | UPRE-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 Arabidopsis | Upstream | -1072 |
| 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 | -1121 |
| | | Upstream | -1100 |
| 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 | -1483 |
| Motif_604 | EMHVCHORD | Endosperm motif (EM) found in the promoter of barley c-hordein gene; Involved in the nitrogen response of c-hordein promoter | Upstream | -1490 |
| Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 3061 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -1476 |
| | | Upstream | -1473 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Downstream | 3052 |
| Motif_628 | TATCCAOSAMY | TATCCA 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 AMYBOX2 | Intron | 1617 |
| 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 | -1115 |
| Motif_649 | 2SSEEDPROTBANAPA | Conserved in many storage-protein gene promoters; May be important for high activity of the napA promoter | Upstream | -1165 |
| Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -426 |
| 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 | -1538 |
| | | Upstream | -1463 |
| | | Upstream | -1150 |
| | | Upstream | -1039 |
| | | Upstream | -633 |
| | | Intron | 1609 |
| | | Downstream | 3021 |
| Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Upstream | -1163 |
| Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 3061 |
| 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 | -1538 |
| | | Upstream | -1463 |
| | | Upstream | -1039 |
| 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 | -1436 |
| | | Upstream | -1434 |
| | | Upstream | -1432 |
| | | Upstream | -1430 |
| | | Upstream | -1428 |
| | | Upstream | -1426 |
| | | Upstream | -1424 |
| | | Upstream | -1410 |
| | | Upstream | -1046 |
| 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 | -1165 |
| Motif_8 | PALBOXPPC | Box P; 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; 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 | Upstream | -1166 |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Upstream | -1182 |
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