Matrix_119 | RRTF1 | Not available | Upstream | -477 |
| | | Upstream | -478 |
Matrix_127 | AtMYB15 | More than 80R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -503 |
Matrix_138 | RRTF1 | Not available | Upstream | -477 |
| | | Upstream | -478 |
Matrix_141 | AT3G25990 | Not available | Upstream | -1393 |
Matrix_171 | LBD3;LBD4 | Not available | Upstream | -564 |
Matrix_179 | AtMYB84;MYB36;MYB68;O49746_ARATH | Not available | Upstream | -503 |
| | | Upstream | -504 |
| | | Upstream | -507 |
| | | Upstream | -508 |
| | | Upstream | -555 |
| | | Upstream | -556 |
| | | Upstream | -557 |
| | | Upstream | -559 |
| | | Upstream | -560 |
| | | Upstream | -1200 |
| | | Upstream | -1201 |
Matrix_187 | CDC5 | Not available | Upstream | -471 |
Matrix_215 | ARF1 | ARF1, a transcription factor that binds to auxin response elements | Upstream | -283 |
| | | Upstream | -284 |
Matrix_224 | ERF1 | Not available | Upstream | -477 |
Matrix_234 | RAP2.3 | Not available | Upstream | -476 |
Matrix_25 | AP3 | Not available | Upstream | -1247 |
Matrix_269 | FHY3/FAR1 | Not available | Upstream | -110 |
Matrix_277 | RAP2.6 | Not available | Upstream | -477 |
| | | Upstream | -478 |
Matrix_287 | ERF2 | Not available | Upstream | -476 |
| | | Upstream | -477 |
Matrix_288 | RAP2.3 | Not available | Upstream | -477 |
| | | Upstream | -478 |
Matrix_291 | EDF3 | Not available | Upstream | -197 |
Matrix_295 | ERF1 | Not available | Upstream | -478 |
| | | Upstream | -479 |
Matrix_334 | AT3G23230 | Not available | Upstream | -477 |
Matrix_349 | CDC5 | Not available | Upstream | -471 |
Matrix_360 | ORA59 | Not available | Upstream | -478 |
Matrix_363 | RAP2.3 | Not available | Upstream | -477 |
| | | Upstream | -478 |
Matrix_369 | AT2G18300 | Not available | Upstream | -497 |
Matrix_374 | AT5G07580;AT5G61590 | Not available | Upstream | -477 |
| | | Upstream | -478 |
Matrix_378 | ATERF1 | Not available | Upstream | -476 |
Matrix_401 | MYB55 | Not available | Upstream | -559 |
Matrix_407 | AP1 | Not available | Upstream | -273 |
| | | Upstream | -274 |
Matrix_414 | AGL15 | Not available | Upstream | -374 |
| | | Upstream | -390 |
| | | Upstream | -1582 |
Matrix_48 | PI | Not available | Upstream | -315 |
| | | Upstream | -316 |
| | | Upstream | -373 |
| | | Upstream | -389 |
| | | Upstream | -463 |
| | | Upstream | -464 |
Matrix_480 | BES1 | Not available | Upstream | -499 |
| | | Upstream | -500 |
Matrix_484 | ATERF13 | Not available | Upstream | -478 |
Matrix_489 | RAV1 | Not available | Upstream | -195 |
Matrix_496 | ATMYB15 | Not available | Upstream | -503 |
| | | Upstream | -504 |
Matrix_497 | AP3 | Not available | Upstream | -274 |
| | | Upstream | -275 |
Matrix_498 | AT2G28710;AT3G46070;AT3G46080;ZAT7 | Not available | Upstream | -213 |
Matrix_50 | ATERF14;AT5G43410 | Not available | Upstream | -477 |
Matrix_510 | AtMYB84 | More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -503 |
| | | Upstream | -507 |
| | | Upstream | -556 |
| | | Upstream | -559 |
Matrix_74 | LFY | Not available | Upstream | -274 |
Matrix_84 | AtGRF6 | Not available | Upstream | -1203 |
Matrix_86 | CRF5;CRF6;CRF4 | Not available | Upstream | -477 |
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 | Downstream | 2601 |
| | | Upstream | -187 |
Motif_131 | P1BS | PHR1-binding sequence found in the upstream regions of phosphate starvation responsive genes from several plant species; phr1 (phosphate starvation response 1) gene codes for PHR1 protein related to PSR1 gene in C. reinhardtii | Intron | 401 |
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) | Upstream | -276 |
| | | Upstream | -774 |
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 | -500 |
| | | Upstream | -1527 |
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 | -980 |
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 | Upstream | -288 |
| | | Upstream | -1134 |
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 | -253 |
Motif_190 | WUSATAg | Target sequence of WUS in the intron of AGAMOUS gene in Arabidopsis | Upstream | -442 |
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 | 2659 |
| | | Upstream | -178 |
| | | Upstream | -253 |
| | | Upstream | -1215 |
| | | Upstream | -1308 |
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 | -198 |
| | | Upstream | -253 |
| | | Upstream | -256 |
| | | Upstream | -417 |
| | | Upstream | -1413 |
Motif_249 | DPBF1&2 binding site motif | A novel class of bZIP transcription factors, DPBF-1 and 2 (Dc3 promoter-binding factor-1 and 2) binding core sequence; Found in the carrot Dc3 gene promoter; Dc3 expression is normally embryo-specific, and also can be induced by ABA; The Arabidopsis abscisic acid response gene ABI5 encodes a bZIP transcription factor; abi5 mutant have a pleiotropic defects in ABA response; ABI5 regulates a subset of late embryogenesis-abundant genes; GIA1 (growth-insensitivity to ABA) is identical to ABI5; Isolation of a novel class of bZIP transcription factors that interact with ABA-responsive and embryo-specification elements in the Dc3 promoter using a modified yeast one-hybrid system | Downstream | 2507 |
| | | Upstream | -1488 |
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 | -1109 |
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 | -1511 |
Motif_26 | GRF7 | Arabidopsis GROWTH-REGULATING FACTOR7 Functions as a Transcriptional Repressor of Abscisic Acid- and Osmotic Stress-Responsive Genes, Including DREB2A | Upstream | -1501 |
Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Upstream | -632 |
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 | -446 |
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 | -284 |
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 | Upstream | -1414 |
Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Downstream | 2615 |
| | | Upstream | -487 |
| | | Upstream | -491 |
Motif_313 | ERF1 BS in AtCHI-B | Core of GCC-box found in many pathogen-responsive genes such as PDF1.2, Thi2.1, and PR4; Has been shown to function as ethylene-responsive element; Appears to play important roles in regulating jasmonate-responsive gene expression; Tomato Pti4 (ERF) regulates defence-related gene expression via GCC box and non-GCC box cis elements (Myb1 (GTTAGTT) and G-box(CACGTG)); Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1;Molecular responses to dehydration and low temperature | Upstream | -479 |
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 | -496 |
Motif_320 | AGCBOXNPGLB | AGC box repeated twice in a 61 bp enhancer element in tobacco class I beta-1,3-glucanase (GLB) gene;GCC-box; Binding sequence of Arabidopsis AtERFs; AtERF1,2 and 5 functioned as activators of GCC box-dependent transcription; AtERF3 and 4 acted as repressors; AtERF proteins are stress signal-response factors; EREBP2 binding site; Conserved in most PR-protein genes; Rice MAPK (BWMK1) phosphorylates OS EREBP1, which enhance DNA-binding activity of the factor to the GCC box | Upstream | -478 |
Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -253 |
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 | -412 |
| | | Upstream | -629 |
Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Upstream | -1117 |
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 | Downstream | 2450 |
Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | Downstream | 2438 |
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 | -285 |
| | | Upstream | -1196 |
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 | -170 |
Motif_382 | CATATGGMSAUR | Sequence found in NDE element in soybean SAUR (Small Auxin-Up RNA) 15A gene promoter; Involved in auxin responsiveness | Downstream | 2659 |
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 | -124 |
| | | Upstream | -531 |
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 | -280 |
Motif_419 | MYB4 binding site motif | Not available | Upstream | -549 |
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 | -959 |
Motif_443 | KN1;BP | The knotted1-like homeobox gene BREVIPEDICELLUS regulates cell differentiation by modulating metabolic pathways. Selective interaction of plant homeodomain proteins mediates high DNA-binding affinity | Upstream | -1503 |
Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -499 |
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 | -178 |
Motif_50 | AtERF-7;AtERF-4;AtERF-3;AtERF-1;AtERF-2;AtERF-5 | Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses | Upstream | -477 |
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 | Downstream | 2689 |
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 | -1144 |
Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -112 |
Motif_552 | MRE1 | MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1 | Upstream | -496 |
| | | Upstream | -1523 |
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 | -124 |
| | | Upstream | -531 |
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 | 2643 |
Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Downstream | 2682 |
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 | -1393 |
| | | Upstream | -1428 |
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 | -1404 |
Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -1402 |
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 | 2689 |
| | | Downstream | 2563 |
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 | 2563 |
Motif_689 | ANAC092 | NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis | Upstream | -216 |
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 | -383 |