Matrix_101 | ERF5 | Not available | Upstream | -18 |
| | | Upstream | -19 |
Matrix_110 | ATABI4;AT3G57600 | Not available | Upstream | -19 |
| | | Upstream | -20 |
| | | Upstream | -64 |
| | | Upstream | -65 |
| | | Upstream | -69 |
| | | Upstream | -70 |
Matrix_115 | AGL15 | Not available | Upstream | -605 |
Matrix_119 | RRTF1 | Not available | Upstream | -17 |
| | | Upstream | -18 |
| | | Upstream | -71 |
| | | Upstream | -72 |
Matrix_126 | RBE | Not available | Upstream | -1149 |
Matrix_128 | TGA2 | Not available | Downstream | 2171 |
Matrix_138 | RRTF1 | Not available | Upstream | -71 |
| | | Upstream | -72 |
Matrix_179 | AtMYB84;MYB36;MYB68;O49746_ARATH | Not available | Upstream | -3 |
| | | Upstream | -4 |
Matrix_183 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -1171 |
| | | Upstream | -1273 |
Matrix_186 | FHY3 | Not available | Upstream | -1170 |
| | | Upstream | -1272 |
Matrix_190 | ATERF1 | Not available | Upstream | -19 |
| | | Upstream | -20 |
Matrix_196 | TCP20;AT5G41030 | Not available | Upstream | -6 |
| | | Upstream | -7 |
Matrix_224 | ERF1 | Not available | Upstream | -3 |
| | | Upstream | -17 |
| | | Upstream | -18 |
| | | Upstream | -20 |
| | | Upstream | -21 |
Matrix_231 | HDG2;HDG3;ATML1;HB-7 | Not available | Upstream | -34 |
Matrix_232 | TCP23 | Not available | Upstream | -28 |
Matrix_234 | RAP2.3 | Not available | Upstream | -18 |
| | | Upstream | -19 |
Matrix_24 | POC1 | Not available | Upstream | -8 |
| | | Upstream | -64 |
Matrix_243 | RAP2.12;RAP2.2 | Not available | Upstream | -19 |
Matrix_25 | AP3 | Not available | Upstream | -465 |
| | | Upstream | -806 |
Matrix_252 | RAP2.6 | Not available | Upstream | -3 |
| | | Upstream | -4 |
| | | Upstream | -18 |
| | | Upstream | -19 |
| | | Upstream | -21 |
| | | Upstream | -22 |
Matrix_256 | IXR11;KNAT5;KNAT4;KNAT3 | Not available | Upstream | -64 |
Matrix_269 | FHY3/FAR1 | Not available | Upstream | -605 |
| | | Upstream | -608 |
| | | Upstream | -1068 |
Matrix_277 | RAP2.6 | Not available | Upstream | -17 |
| | | Upstream | -18 |
Matrix_280 | TCP24;TCP1;BRC2;ATTCP18 | Not available | Upstream | -26 |
| | | Upstream | -27 |
Matrix_282 | bZIP60 | Not available | Upstream | -1144 |
Matrix_287 | ERF2 | Not available | Upstream | -18 |
| | | Upstream | -19 |
Matrix_288 | RAP2.3 | Not available | Upstream | -71 |
| | | Upstream | -72 |
Matrix_295 | ERF1 | Not available | Upstream | -18 |
| | | Upstream | -19 |
Matrix_297 | TCP15 | Not available | Upstream | -7 |
| | | Upstream | -8 |
| | | Upstream | -28 |
| | | Upstream | -29 |
Matrix_298 | RAV1 | Not available | Upstream | -12 |
Matrix_305 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -57 |
Matrix_306 | TGA1 | TGA1 and G-box binding factors: two distinct classes of Arabidopsis leucine zipper proteins compete for the G-box-like element TGACGTGG | Downstream | 2173 |
Matrix_311 | TGA1 | Not available | Downstream | 2171 |
Matrix_321 | HRD | Not available | Upstream | -18 |
Matrix_326 | AT5G07310;Rap2.6L;AT5G61890 | Not available | Upstream | -17 |
| | | Upstream | -18 |
Matrix_334 | AT3G23230 | Not available | Upstream | -19 |
| | | Upstream | -20 |
Matrix_343 | AT2G33710 | Not available | Upstream | -3 |
| | | Upstream | -4 |
| | | Upstream | -18 |
| | | Upstream | -19 |
| | | Upstream | -21 |
| | | Upstream | -22 |
Matrix_348 | AT5G51910 | Not available | Upstream | -8 |
| | | Upstream | -26 |
| | | Upstream | -27 |
Matrix_355 | ERF10;ERF11 | Not available | Upstream | -17 |
Matrix_360 | ORA59 | Not available | Upstream | -21 |
Matrix_363 | RAP2.3 | Not available | Upstream | -17 |
| | | Upstream | -18 |
| | | Upstream | -71 |
| | | Upstream | -72 |
Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -1062 |
Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Upstream | -3 |
| | | Upstream | -4 |
Matrix_378 | ATERF1 | Not available | Upstream | -18 |
| | | Upstream | -19 |
| | | Upstream | -70 |
| | | Upstream | -71 |
Matrix_399 | TGA1 | Not available | Downstream | 2172 |
Matrix_405 | DREB2C | Not available | Upstream | -19 |
| | | Upstream | -20 |
| | | Upstream | -72 |
| | | Upstream | -73 |
Matrix_409 | DEAR3 | Not available | Upstream | -3 |
Matrix_413 | RAV1 | Not available | Upstream | -12 |
Matrix_414 | AGL15 | Not available | Upstream | -441 |
| | | Upstream | -442 |
Matrix_42 | AT2G45680 | Not available | Upstream | -8 |
| | | Upstream | -9 |
| | | Upstream | -26 |
| | | Upstream | -27 |
| | | Upstream | -28 |
| | | Upstream | -1164 |
Matrix_426 | CRF1;CRF2 | Not available | Upstream | -19 |
| | | Upstream | -20 |
Matrix_433 | ATERF1 | Not available | Upstream | -17 |
Matrix_454 | AT1G77200;ATERF38;AT4G16750;AT5G52020 | Not available | Upstream | -3 |
Matrix_473 | RRTF1 | Not available | Upstream | -18 |
| | | Upstream | -19 |
| | | Upstream | -70 |
| | | Upstream | -71 |
Matrix_48 | PI | Not available | Upstream | -1019 |
| | | Upstream | -1020 |
| | | Upstream | -1068 |
| | | Upstream | -1069 |
Matrix_488 | ABF1 | Not available | Upstream | -11 |
| | | Upstream | -58 |
Matrix_489 | RAV1 | Not available | Upstream | -14 |
Matrix_50 | ATERF14;AT5G43410 | Not available | Upstream | -17 |
| | | Upstream | -18 |
| | | Upstream | -20 |
| | | Upstream | -21 |
Matrix_506 | DRNL;ATERF-4 | Not available | Upstream | -19 |
| | | Upstream | -20 |
Matrix_510 | AtMYB84 | More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -3 |
| | | Upstream | -4 |
Matrix_514 | DYT1 | Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development | Upstream | -1137 |
Matrix_57 | WIN1;SHN3;SHN2 | Not available | Upstream | -3 |
| | | Upstream | -14 |
| | | Upstream | -15 |
| | | Upstream | -20 |
| | | Upstream | -21 |
Matrix_90 | BEE1;BEE3;AT3G07340;AT5G48560;AT5G50915 | Not available | Upstream | -1275 |
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 | -959 |
| | | Upstream | -966 |
| | | Upstream | -1182 |
Motif_12 | CEREGLUBOX2PSLEGA | cereal glutenin box in pea legumin gene (legA); sequence homologous to the cereal glutenin gene control element (-300 element) | Downstream | 2245 |
| | | Upstream | -963 |
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 | -252 |
| | | Upstream | -258 |
| | | Upstream | -1108 |
Motif_145 | MYCATERD1 | MYC recognition sequence (from -466 to -461) necessary for expression of erd1 (early responsive to dehydration) in dehydrated Arabidopsis; NAC protein bound specifically to the CATGTG motif; NAC protein bound specifically to the CATGTG motif | Upstream | -1141 |
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 | -1004 |
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 | -165 |
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 | -165 |
| | | Upstream | -1141 |
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 | -165 |
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 | -654 |
Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Downstream | 1878 |
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 | -19 |
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 | -71 |
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 | -255 |
| | | Upstream | -261 |
| | | Upstream | -924 |
Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -165 |
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 | -250 |
| | | Upstream | -256 |
| | | Upstream | -262 |
| | | Upstream | -923 |
Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Downstream | 2156 |
Motif_353 | HEXAMERATH4 | hexamer motif of Arabidopsis thaliana histone H4 promoter;Identification of cis-elements regulating the expression of an Arabidopsis histone H4 gene | Upstream | -60 |
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 | 1870 |
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 | -632 |
Motif_447 | AtMYC2 BS in RD22;PIF4 | Binding site for MYC (rd22BP1) in Arabidopsis dehydration-resposive gene, rd22; MYC binding site in rd22 gene of Arabidopsis thaliana; ABA-induction; Located at ca. -200 of rd22 gene; Also MYB at ca. -141 of rd22 gene; See also MYBATRD22; Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -1141 |
Motif_453 | HEXMOTIFTAH3H4 | hexamer motif found in promoter of wheat histone genes H3 and H4; CaMV35S; NOS; Binding with HBP-1A and HBP-1B; Binding site of wheat nuclear protein HBP-1 (histone DNA binding protein-1); HBP-1 has a leucine zipper motif; hexamer motif in type 1 element may play important roles in regulation of replication- dependent but not of replication-independent expression of the wheat histone H3 gene;Rice OBF1-homodimer-binding site | Downstream | 2169 |
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 | Upstream | -160 |
| | | Upstream | -641 |
Motif_502 | MYB98 | The MYB98 subcircuit of the synergid gene regulatory network includes genes directly and indirectly regulated by MYB98 | Downstream | 2167 |
| | | Upstream | -144 |
Motif_525 | CRTDREHVCBF2 | Preferred sequence for AP2 transcriptional activator HvCBF2 of barley; Core CRT/DRE motif; HvCBF2 bound to a (G/a)(T/c)CGAC core motif; DNA binding is regulated by temperature | Upstream | -58 |
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 | -659 |
Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -607 |
Motif_576 | TGACGTVMAMY | TGACGT motif found in the Vigna mungo alpha-Amylase (Amy) gene promoter; Located between -128 and -123; Required for high level expression of alpha-Amylase in the cotyledons of the germinated seeds | Downstream | 2169 |
Motif_585 | ATB2/AtbZIP53/AtbZIP44/GBF5 BS in ProDH | PRE (Pro- or hypoosmolarity-responsive element) found in the promoter region of proline dehydrogenase (ProDH) gene in Arabidopsis; Core of 9-bp sequence ACTCATCCT which is necessary for the efficient expression of ProDH in response to L-Pro and hypoosmolarity; ATB2-binding site; Similar to GCN4 motif (ATGA(C/G)TCAT); ATB2 subgroup of bZIP transcription factors function as transcriptional activator for hypoosmolarity-inducible ProDH; A Novel Subgroup of bZIP Proteins Functions as Transctiptional Activators in Hypsosmolarity-Responsive Expression of the ProDH gene in Arabidopsis | Upstream | -1152 |
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 | -58 |
Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -1097 |
Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -253 |
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 | 1813 |
Motif_65 | BS1EGCCR | BS1 (binding site 1) found in E. gunnii Cinnamoyl-CoA reductase (CCR) gene promoter; nuclear protein binding site; Required for vascular expression | Upstream | -25 |
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 | 1879 |
| | | Upstream | -442 |
| | | Upstream | -927 |
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 | 1812 |
Motif_668 | TCA1MOTIF | TCA-1 (tobacco nuclear protein 1) binding site; Related to salicylic acid-inducible expression of many genes; Found in barley beta-1,3-glucanase and over 30 different plant genes which are known to be induced by one or more forms of stress; A similar sequence (TCATTTCTT) was found in tobacco Tnt1 retrotransposon promoter | Upstream | -864 |
Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -1097 |
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 | -927 |
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 | -566 |
| | | Upstream | -703 |
| | | Upstream | -705 |
| | | Upstream | -813 |
| | | Upstream | -845 |
| | | Upstream | -847 |
| | | Upstream | -1023 |
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 | Downstream | 2139 |
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 | -698 |
| | | Upstream | -1182 |
| | | Upstream | -1502 |
| | | Upstream | -1506 |
| | | Upstream | -1510 |
Motif_98 | SEF3MOTIFGM | SEF3 binding site; Soybean consensus sequence found in the 5' upstream region of beta-conglycinin (7S globulin) gene; AACCCA(-27bp-)AACCCA; SEF=soybean embryo factor; SEF2; SEF3; SEF4 | Upstream | -975 |