Matrix_104 | PI | Not available | Intron | 1489 |
| | | Intron | 1304 |
Matrix_113 | ABI5 | Not available | Intron | 1489 |
| | | Intron | 1487 |
| | | Intron | 1304 |
| | | Intron | 1302 |
Matrix_117 | ANT | Not available | Intron | 1192 |
Matrix_122 | ABF1;AREB2 | Not available | Intron | 1488 |
| | | Intron | 1339 |
| | | Intron | 1303 |
Matrix_129 | ABF1 | Not available | Intron | 1488 |
| | | Intron | 1303 |
Matrix_145 | GBF4;AT5G44080 | Not available | Intron | 1487 |
| | | Intron | 1302 |
Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Intron | 1492 |
Matrix_162 | AtPHR1 | Not available | Downstream | 4162 |
Matrix_172 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -382 |
| | | Upstream | -383 |
Matrix_192 | FHY3/FAR1 | Not available | Intron | 1491 |
| | | Intron | 1306 |
Matrix_194 | HYH;HY5 | Not available | Intron | 1491 |
| | | Intron | 1306 |
Matrix_214 | AP1 | Not available | Intron | 1490 |
| | | Intron | 1305 |
Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Intron | 1491 |
| | | Intron | 1306 |
Matrix_264 | ATAREB1 | Not available | Intron | 1488 |
| | | Intron | 1303 |
Matrix_270 | ANT | DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA | Intron | 1193 |
Matrix_300 | bZIP68;bZIP16 | Not available | Intron | 1488 |
| | | Intron | 1303 |
Matrix_301 | PIL5 | Not available | Intron | 1487 |
Matrix_338 | AP2 | Not available | Intron | 1491 |
| | | Intron | 1306 |
Matrix_356 | PRR5 | Not available | Intron | 1491 |
| | | Intron | 1306 |
Matrix_359 | FLC | Not available | Intron | 1490 |
Matrix_381 | ATHB9 | Not available | Downstream | 3714 |
Matrix_403 | BZR1 | Not available | Intron | 1490 |
| | | Intron | 1305 |
Matrix_439 | AP3 | Not available | Upstream | -99 |
Matrix_443 | AGL15 | Not available | Intron | 1490 |
| | | Intron | 1305 |
Matrix_459 | ATHB9;CNA;PHB;ATHB-8;REV | Not available | Downstream | 3714 |
Matrix_468 | ATHB9 | The Arabidopsis Athb-8, -9 and -14 genes are members of a small gene family coding for highly related HD-ZIP proteins | Downstream | 3714 |
Matrix_48 | PI | Not available | Upstream | -391 |
| | | Upstream | -392 |
Matrix_53 | MYC3 | Not available | Intron | 1336 |
| | | Intron | 1305 |
Matrix_55 | PIF3 | Not available | Intron | 1489 |
| | | Intron | 1304 |
Matrix_7 | PIF4 | Not available | Intron | 1488 |
| | | Intron | 1303 |
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 | -486 |
| | | Upstream | -550 |
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 | -395 |
| | | Upstream | -397 |
| | | Upstream | -399 |
| | | Upstream | -401 |
| | | Upstream | -403 |
| | | Upstream | -405 |
| | | Upstream | -407 |
| | | Upstream | -409 |
| | | Upstream | -411 |
| | | Upstream | -413 |
| | | Upstream | -415 |
| | | Upstream | -417 |
| | | Upstream | -419 |
| | | Upstream | -421 |
| | | Upstream | -1003 |
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 | Intron | 1193 |
| | | Intron | 1160 |
Motif_153 | MARABOX1 | A-box found in SAR(scaffold attachment region; or matrix attachment region, MAR) | Upstream | -753 |
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 | -382 |
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 | -385 |
Motif_181 | IBOXCORENT | I-box core motif in the CAMs (conserved DNA modular arrays) associated with light-responsive promoter regions | Upstream | -385 |
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 | 1167 |
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 | Intron | 1489 |
| | | Intron | 1304 |
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 | Intron | 1160 |
Motif_22 | RYREPEATLEGUMINBOX | RY repeat (CATGCAY) or legumin box found in seed-storage protein genes in legume such as soybean | Intron | 2687 |
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 | -299 |
Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Downstream | 3708 |
| | | Intron | 2691 |
| | | Upstream | -441 |
| | | Upstream | -444 |
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 | Downstream | 3709 |
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 | Intron | 1489 |
| | | Intron | 1304 |
Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -384 |
Motif_317 | GAREAT | GARE (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%, respectively | Downstream | 3691 |
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 | Intron | 2692 |
Motif_371 | DRE-like promoter motif | The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses | Intron | 1185 |
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 | Intron | 2717 |
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 | Intron | 2688 |
Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -395 |
| | | Upstream | -397 |
| | | Upstream | -399 |
| | | Upstream | -401 |
| | | Upstream | -403 |
| | | Upstream | -405 |
| | | Upstream | -407 |
| | | Upstream | -409 |
| | | Upstream | -411 |
| | | Upstream | -413 |
| | | Upstream | -415 |
| | | Upstream | -417 |
| | | Upstream | -419 |
| | | Upstream | -421 |
| | | Upstream | -423 |
| | | Upstream | -1003 |
| | | Upstream | -1005 |
Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Intron | 1488 |
| | | Intron | 1303 |
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) | Intron | 1185 |
Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Intron | 1194 |
| | | Intron | 1161 |
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 | Intron | 1167 |
Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Upstream | -299 |
Motif_511 | RYREPEATGMGY2 | RY repeat motif (CATGCAT); Present in the 5' region of the soybean glycinin gene (Gy2) | Intron | 2687 |
Motif_520 | AMYBOX1 | amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barley | Downstream | 3691 |
Motif_552 | MRE1 | MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1 | Intron | 1196 |
| | | Intron | 1163 |
Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Intron | 1489 |
| | | Intron | 1304 |
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 | Intron | 1159 |
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 | Intron | 1162 |
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) | Intron | 1185 |
Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 3691 |
Motif_614 | MYBGAHV | Central 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 repression | Downstream | 3691 |
Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Intron | 2716 |
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 | Intron | 2686 |
Motif_643 | DRE2COREZMRAB17 | DRE2 core found in maize rab17 gene promoter; DBF1 and DBF2 bound to DRE2; rab17 is expressed during late embryogenesis, and is induced by ABA | Intron | 1185 |
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 | Intron | 1188 |
| | | Upstream | -547 |
Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 3691 |
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 | -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 | -395 |
| | | Upstream | -397 |
| | | Upstream | -399 |
| | | Upstream | -401 |
| | | Upstream | -403 |
| | | Upstream | -405 |
| | | Upstream | -407 |
| | | Upstream | -409 |
| | | Upstream | -411 |
| | | Upstream | -413 |
| | | Upstream | -415 |
| | | Upstream | -417 |
| | | Upstream | -419 |
| | | Upstream | -421 |
| | | Upstream | -423 |
| | | Upstream | -425 |
| | | Upstream | -427 |
| | | Upstream | -429 |
| | | Upstream | -1003 |
| | | Upstream | -1005 |
| | | Upstream | -1007 |
| | | Upstream | -1009 |
| | | Upstream | -1011 |
| | | Upstream | -1013 |
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 | -304 |