Matrix_101 | ERF5 | Not available | Upstream | -65 |
| | | Upstream | -66 |
| | | Upstream | -218 |
| | | Upstream | -219 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_138 | RRTF1 | Not available | Upstream | -66 |
| | | Upstream | -67 |
Matrix_146 | ORA47 | Not available | Upstream | -65 |
| | | Upstream | -66 |
| | | Upstream | -218 |
| | | Upstream | -219 |
Matrix_147 | ERF3;AT1G80580 | Not available | Upstream | -67 |
| | | Upstream | -68 |
| | | Upstream | -162 |
| | | Upstream | -163 |
Matrix_151 | ASIL1 | Not available | Upstream | -161 |
| | | Upstream | -162 |
Matrix_154 | AT1G22190;AT1G36060;AT1G64380;RAP2.4;AT2G20880;AT2G22200;AT4G13620;AT4G28140;AT4G39780;AT5G65130 | Not available | Upstream | -216 |
| | | Upstream | -217 |
Matrix_155 | RAP2.6;ERF110;ABR1 | Not available | Upstream | -163 |
| | | Upstream | -164 |
| | | Upstream | -219 |
| | | Upstream | -220 |
Matrix_174 | ZAT2 | Not available | Upstream | -222 |
| | | Upstream | -223 |
Matrix_179 | AtMYB84;MYB36;MYB68;O49746_ARATH | Not available | Upstream | -32 |
Matrix_190 | ATERF1 | Not available | Upstream | -218 |
| | | Upstream | -219 |
| | | Upstream | -220 |
Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -174 |
Matrix_224 | ERF1 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -220 |
| | | Upstream | -221 |
Matrix_234 | RAP2.3 | Not available | Upstream | -65 |
| | | Upstream | -66 |
| | | Upstream | -218 |
| | | Upstream | -219 |
Matrix_25 | AP3 | Not available | Upstream | -196 |
Matrix_252 | RAP2.6 | Not available | Upstream | -65 |
| | | Upstream | -66 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_255 | cdf3 | Not available | Upstream | -184 |
| | | Upstream | -185 |
Matrix_261 | ATERF-1 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -218 |
| | | Upstream | -219 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_272 | DEAR4 | Not available | Upstream | -65 |
| | | Upstream | -66 |
| | | Upstream | -218 |
| | | Upstream | -219 |
Matrix_277 | RAP2.6 | Not available | Upstream | -220 |
Matrix_287 | ERF2 | Not available | Upstream | -65 |
| | | Upstream | -66 |
| | | Upstream | -218 |
| | | Upstream | -219 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_288 | RAP2.3 | Not available | Upstream | -66 |
| | | Upstream | -67 |
Matrix_295 | ERF1 | Not available | Upstream | -67 |
| | | Upstream | -68 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_321 | HRD | Not available | Upstream | -221 |
Matrix_326 | AT5G07310;Rap2.6L;AT5G61890 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -217 |
| | | Upstream | -218 |
| | | Upstream | -220 |
| | | Upstream | -221 |
Matrix_334 | AT3G23230 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -219 |
| | | Upstream | -220 |
| | | Upstream | -222 |
| | | Upstream | -223 |
Matrix_343 | AT2G33710 | Not available | Upstream | -65 |
| | | Upstream | -66 |
| | | Upstream | -218 |
| | | Upstream | -219 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_344 | ATERF15;AT4G18450 | Not available | Upstream | -67 |
| | | Upstream | -68 |
| | | Upstream | -162 |
| | | Upstream | -163 |
Matrix_355 | ERF10;ERF11 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -217 |
| | | Upstream | -218 |
| | | Upstream | -220 |
| | | Upstream | -221 |
Matrix_360 | ORA59 | Not available | Upstream | -67 |
| | | Upstream | -68 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_363 | RAP2.3 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -220 |
| | | Upstream | -221 |
Matrix_374 | AT5G07580;AT5G61590 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -217 |
| | | Upstream | -218 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -218 |
| | | Upstream | -219 |
Matrix_378 | ATERF1 | Not available | Upstream | -65 |
| | | Upstream | -66 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_39 | AP1 | Not available | Upstream | -196 |
Matrix_395 | AT1G19210;ORA47;AT4G31060;AT5G21960 | Not available | Upstream | -217 |
| | | Upstream | -218 |
Matrix_401 | MYB55 | Not available | Upstream | -221 |
Matrix_406 | ATERF-7 | Not available | Upstream | -67 |
| | | Upstream | -68 |
| | | Upstream | -160 |
| | | Upstream | -161 |
| | | Upstream | -216 |
| | | Upstream | -217 |
| | | Upstream | -219 |
| | | Upstream | -220 |
Matrix_409 | DEAR3 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -217 |
| | | Upstream | -218 |
Matrix_414 | AGL15 | Not available | Upstream | -199 |
Matrix_426 | CRF1;CRF2 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -219 |
| | | Upstream | -220 |
| | | Upstream | -222 |
| | | Upstream | -223 |
Matrix_433 | ATERF1 | Not available | Upstream | -161 |
| | | Upstream | -162 |
Matrix_448 | ATERF6 | Not available | Upstream | -161 |
| | | Upstream | -162 |
Matrix_45 | DRN | Not available | Upstream | -67 |
| | | Upstream | -68 |
| | | Upstream | -162 |
| | | Upstream | -163 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_450 | SPL7 | Not available | Upstream | -118 |
| | | Upstream | -120 |
Matrix_454 | AT1G77200;ATERF38;AT4G16750;AT5G52020 | Not available | Upstream | -217 |
Matrix_462 | ATERF-8 | Not available | Upstream | -67 |
| | | Upstream | -68 |
| | | Upstream | -160 |
| | | Upstream | -161 |
| | | Upstream | -216 |
| | | Upstream | -217 |
Matrix_473 | RRTF1 | Not available | Upstream | -65 |
| | | Upstream | -66 |
Matrix_48 | PI | Not available | Upstream | -198 |
| | | Upstream | -209 |
Matrix_482 | AT2G25650;AT4G00270 | Not available | Upstream | -223 |
Matrix_484 | ATERF13 | Not available | Upstream | -67 |
| | | Upstream | -68 |
| | | Upstream | -162 |
| | | Upstream | -163 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_493 | AT1G22985;AT1G71130 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -218 |
| | | Upstream | -219 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Matrix_5 | AT5G51190;ERF104 | Not available | Upstream | -67 |
| | | Upstream | -68 |
| | | Upstream | -162 |
| | | Upstream | -163 |
Matrix_50 | ATERF14;AT5G43410 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -217 |
| | | Upstream | -218 |
| | | Upstream | -220 |
| | | Upstream | -221 |
Matrix_506 | DRNL;ATERF-4 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -219 |
| | | Upstream | -220 |
| | | Upstream | -222 |
| | | Upstream | -223 |
Matrix_517 | ERF12 | Not available | Upstream | -67 |
| | | Upstream | -68 |
Matrix_57 | WIN1;SHN3;SHN2 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -220 |
| | | Upstream | -221 |
Matrix_78 | AT3G45610 | Not available | Upstream | -120 |
Matrix_86 | CRF5;CRF6;CRF4 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -219 |
| | | Upstream | -220 |
| | | Upstream | -222 |
| | | Upstream | -223 |
Matrix_91 | CRF3 | Not available | Upstream | -66 |
| | | Upstream | -67 |
| | | Upstream | -218 |
| | | Upstream | -219 |
| | | Upstream | -221 |
| | | Upstream | -222 |
Motif_1 | GT1CORE | Critical for GT-1 binding to box II of rbcS; Transcriptional activation by Arabidopsis GT-1 may be through interaction with TFIIA-TBP-TATA complex | Upstream | -398 |
Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -158 |
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 | -176 |
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 | -369 |
Motif_192 | BOXLCOREDCPAL | Consensus of the putative core sequences of box-L-like sequences in carrot; PAL1 promoter region; DCMYB1 bound to these sequences in vitro | Downstream | 4602 |
| | | Upstream | -329 |
Motif_193 | GLK1 | GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis | Upstream | -14 |
Motif_195 | TATABOX4 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation | Downstream | 4517 |
| | | Downstream | 4496 |
| | | Downstream | 4477 |
Motif_207 | MAMMALENHAN | Core sequence in enhancers from polyoma virus and from the IgM heavy chain gene | Upstream | -238 |
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 | -324 |
Motif_223 | LTRE1HVBLT49 | LTRE-1 (low-temperature-responsive element) in barley (H.v.) blt4.9 gene promoter; A new LTRE; A previously known LTRE is CCGAC | Upstream | -340 |
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 | -61 |
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 | Downstream | 4614 |
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 | -348 |
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 | -26 |
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 | -68 |
| | | Upstream | -222 |
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 | -222 |
Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -175 |
Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Downstream | 4599 |
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 | -411 |
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 | Downstream | 4494 |
| | | Downstream | 4479 |
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 | -12 |
| | | Upstream | -60 |
Motif_392 | PALBOXAPC | Box A; 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 (P.c.); 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; See also Box P, Box L | Upstream | -218 |
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 | -6 |
Motif_419 | MYB4 binding site motif | Not available | Upstream | -61 |
Motif_489 | SORLREP3AT | one of Sequences Over-Represented in Light-Repressed Promoters (SORLREPs) in Arabidopsis; Computationally identified phyA-repressed motifs; See also all SORLREPs and also 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 | Downstream | 4513 |
Motif_49 | TATAPVTRNALEU | TATA-like motif; A TATA-like sequence found in Phaseolus vulgaris tRNALeu gene promoter; Frequently observed upstream of plant tRNA genes; Found in maize glycolytic glyceraldehyde-3-phospate dehydrogenase 4 (GapC4) gene promoter; Binding site of TATA binding protein (TBP) | Downstream | 4496 |
| | | Downstream | 4478 |
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 | 4559 |
| | | Upstream | -158 |
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 | -409 |
Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Downstream | 5286 |
| | | Downstream | 5285 |
| | | Downstream | 5284 |
| | | Downstream | 5283 |
Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Upstream | -59 |
| | | Upstream | -239 |
Motif_642 | SEF1MOTIF | SEF1 (soybean embryo factor 1) binding motif; sequence found in 5'-upstream region (-640; -765) of soybean beta-conglicinin (7S globulin) gene | Downstream | 4582 |
| | | Downstream | 4494 |
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 | -183 |
| | | Upstream | -304 |
| | | Upstream | -374 |
Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Upstream | -60 |
Motif_667 | TATABOXOSPAL | Binding site for OsTBP2, found in the promoter of rice pal gene encoding phenylalanine ammonia-lyase; OsTFIIB stimulated the DNA binding and bending activities of OsTBP2 and synergistically enhanced OsTBP2-mediated transcription from the pal promoter | Downstream | 4581 |
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 | -208 |