Matrix_101 | ERF5 | Not available | Upstream | -480 |
| | | Upstream | -481 |
Matrix_104 | PI | Not available | Upstream | -812 |
| | | Upstream | -813 |
Matrix_113 | ABI5 | Not available | Upstream | -814 |
| | | Upstream | -815 |
Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -809 |
| | | Upstream | -810 |
| | | Upstream | -811 |
Matrix_119 | RRTF1 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_120 | BEE2 | Not available | Upstream | -813 |
Matrix_122 | ABF1;AREB2 | Not available | Upstream | -813 |
| | | Upstream | -814 |
Matrix_129 | ABF1 | Not available | Upstream | -813 |
| | | Upstream | -814 |
Matrix_138 | RRTF1 | Not available | Upstream | -75 |
| | | Upstream | -481 |
| | | Upstream | -482 |
Matrix_145 | GBF4;AT5G44080 | Not available | Upstream | -814 |
| | | Upstream | -815 |
Matrix_146 | ORA47 | Not available | Upstream | -76 |
Matrix_147 | ERF3;AT1G80580 | Not available | Upstream | -482 |
| | | Upstream | -483 |
Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -809 |
| | | Upstream | -810 |
Matrix_156 | POC1 | Not available | Upstream | -812 |
| | | Upstream | -813 |
Matrix_158 | AT1G03040;LRL1;UNE12;LRL2;LRL3 | Not available | Upstream | -813 |
Matrix_181 | Dof5.7 | Not available | Upstream | -905 |
Matrix_19 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -810 |
Matrix_192 | FHY3/FAR1 | Not available | Upstream | -814 |
| | | Upstream | -815 |
Matrix_194 | HYH;HY5 | Not available | Upstream | -810 |
| | | Upstream | -811 |
Matrix_200 | PIL5;AT4G28790;AT4G28800;AT4G28811;AT4G28815 | Not available | Upstream | -813 |
| | | Upstream | -814 |
Matrix_224 | ERF1 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_234 | RAP2.3 | Not available | Upstream | -76 |
| | | Upstream | -77 |
| | | Upstream | -480 |
| | | Upstream | -481 |
Matrix_24 | POC1 | Not available | Upstream | -809 |
| | | Upstream | -810 |
Matrix_247 | PIF3 | Not available | Upstream | -813 |
| | | Upstream | -814 |
Matrix_252 | RAP2.6 | Not available | Upstream | -76 |
Matrix_261 | ATERF-1 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_264 | ATAREB1 | Not available | Upstream | -813 |
| | | Upstream | -814 |
Matrix_277 | RAP2.6 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_285 | DDF1 | Not available | Upstream | -482 |
| | | Upstream | -483 |
Matrix_287 | ERF2 | Not available | Upstream | -480 |
| | | Upstream | -481 |
Matrix_288 | RAP2.3 | Not available | Upstream | -75 |
| | | Upstream | -481 |
| | | Upstream | -482 |
Matrix_295 | ERF1 | Not available | Upstream | -482 |
| | | Upstream | -483 |
Matrix_296 | GBF2 | Not available | Upstream | -814 |
| | | Upstream | -815 |
Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -814 |
| | | Upstream | -815 |
Matrix_301 | PIL5 | Not available | Upstream | -814 |
| | | Upstream | -815 |
Matrix_326 | AT5G07310;Rap2.6L;AT5G61890 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_330 | MYC2;TT8 | Not available | Upstream | -813 |
Matrix_331 | GBF1 | Not available | Upstream | -814 |
| | | Upstream | -815 |
Matrix_332 | SPT;ALC | Not available | Upstream | -813 |
| | | Upstream | -814 |
Matrix_334 | AT3G23230 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_338 | AP2 | Not available | Upstream | -810 |
| | | Upstream | -811 |
Matrix_343 | AT2G33710 | Not available | Upstream | -76 |
| | | Upstream | -480 |
| | | Upstream | -481 |
Matrix_345 | POC1 | Not available | Upstream | -809 |
| | | Upstream | -810 |
Matrix_355 | ERF10;ERF11 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_356 | PRR5 | Not available | Upstream | -806 |
| | | Upstream | -807 |
Matrix_360 | ORA59 | Not available | Upstream | -482 |
| | | Upstream | -483 |
Matrix_363 | RAP2.3 | Not available | Upstream | -75 |
| | | Upstream | -481 |
| | | Upstream | -482 |
Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -199 |
| | | Upstream | -200 |
Matrix_378 | ATERF1 | Not available | Upstream | -76 |
| | | Upstream | -480 |
| | | Upstream | -481 |
Matrix_389 | ILR3 | Not available | Upstream | -813 |
| | | Upstream | -814 |
Matrix_406 | ATERF-7 | Not available | Upstream | -482 |
| | | Upstream | -483 |
Matrix_41 | anac058 | Not available | Intron | 662 |
Matrix_414 | AGL15 | Not available | Upstream | -405 |
| | | Upstream | -509 |
| | | Upstream | -514 |
| | | Upstream | -536 |
Matrix_426 | CRF1;CRF2 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_439 | AP3 | Not available | Upstream | -756 |
Matrix_443 | AGL15 | Not available | Upstream | -811 |
| | | Upstream | -812 |
Matrix_45 | DRN | Not available | Upstream | -482 |
| | | Upstream | -483 |
Matrix_462 | ATERF-8 | Not available | Upstream | -482 |
| | | Upstream | -483 |
Matrix_465 | MYC4 | Not available | Upstream | -813 |
Matrix_473 | RRTF1 | Not available | Upstream | -76 |
| | | Upstream | -480 |
| | | Upstream | -481 |
Matrix_48 | PI | Not available | Upstream | -467 |
| | | Upstream | -468 |
| | | Upstream | -1645 |
Matrix_480 | BES1 | Not available | Upstream | -812 |
| | | Upstream | -813 |
| | | Upstream | -814 |
Matrix_484 | ATERF13 | Not available | Upstream | -482 |
| | | Upstream | -483 |
Matrix_488 | ABF1 | Not available | Upstream | -470 |
| | | Upstream | -471 |
| | | Upstream | -805 |
| | | Upstream | -806 |
Matrix_493 | AT1G22985;AT1G71130 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_50 | ATERF14;AT5G43410 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_506 | DRNL;ATERF-4 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_517 | ERF12 | Not available | Upstream | -482 |
| | | Upstream | -483 |
Matrix_55 | PIF3 | Not available | Upstream | -812 |
| | | Upstream | -813 |
Matrix_57 | WIN1;SHN3;SHN2 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_7 | PIF4 | Not available | Upstream | -813 |
| | | Upstream | -814 |
Matrix_77 | PRR5 | Not available | Upstream | -812 |
| | | Upstream | -813 |
Matrix_86 | CRF5;CRF6;CRF4 | Not available | Upstream | -481 |
| | | Upstream | -482 |
Matrix_91 | CRF3 | Not available | Upstream | -481 |
| | | Upstream | -482 |
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 | -373 |
| | | Upstream | -586 |
Motif_12 | CEREGLUBOX2PSLEGA | cereal glutenin box in pea legumin gene (legA); sequence homologous to the cereal glutenin gene control element (-300 element) | Upstream | -580 |
Motif_125 | BOXIINTPATPB | Box II found in the tobacco plastid atpB gene promoter; Conserved in several NCII (nonconsensus type II) promoters of plastid genes; Important for the activity of this NCII promoter | Upstream | -940 |
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 | -916 |
| | | Upstream | -922 |
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 | -382 |
Motif_179 | CACGTGMOTIF;BES1;PIF4;PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling;A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana; CACGTG motif; G-box; Binding site of Arabidopsis GBF4; C. roseus G-box binding factor 1 (CrGBF1) and 1 (CrGBF2) can act as transcriptional repressors of the Str promoter via direct interaction with the G-box; Essential for expression of beta-phaseolin gene during embryogenesis in bean, tobacco, Arabidopsis; Tomato Pti4 (ERF) regulates defense-related gene expression via GCC box and non-GCC box cis-element (Myb1 (GTTAGTT) and G-box (CACGTG)); Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein; Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -815 |
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 | -815 |
Motif_197 | HY5 | Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression | Upstream | -813 |
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 | Upstream | -357 |
| | | Upstream | -814 |
| | | Upstream | -815 |
Motif_244 | ABRE-like binding site motif | Not available | Upstream | -815 |
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 | Upstream | -815 |
Motif_261 | S1FBOXSORPS1L21 | S1F box conserved both in spinach RPS1 and RPL21 genes encoding the plastid ribosomal protein S1 and L21, respectively; Negative element; Might play a role in downregulating RPS1 and RPL21 promoter activity | Downstream | 2071 |
Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Upstream | -928 |
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 | -873 |
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 | Downstream | 2069 |
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 | -483 |
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 | -914 |
| | | Upstream | -920 |
| | | Upstream | -929 |
Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -815 |
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 | -913 |
| | | Upstream | -919 |
| | | Upstream | -925 |
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 | -874 |
Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -814 |
Motif_450 | E2FCONSENSUS | E2F consensus sequence of all different E2F-DP-binding motifs that were experimentally verified in plants | Upstream | -835 |
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 | -336 |
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 | -30 |
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 | Upstream | -461 |
Motif_563 | PYRIMIDINEBOXOSRAMY1A | Pyrimidine box found in rice alpha-amylase (RAmy1A) gene; Gibberellin-respons cis-element of GARE and pyrimidine box are partially involved in sugar repression; Found in the promoter of barley alpha-amylase (Amy2/32b) gene which is induced in the aleurone layers in response to GA; BPBF protein binds specifically to this site | Upstream | -908 |
Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Downstream | 1630 |
| | | Downstream | 1629 |
| | | Downstream | 1191 |
| | | Downstream | 1190 |
| | | Upstream | -206 |
| | | Upstream | -912 |
| | | Upstream | -918 |
| | | Upstream | -924 |
| | | Upstream | -1663 |
| | | Upstream | -1664 |
| | | Upstream | -1665 |
Motif_627 | ACGTABREMOTIFA2OSEM | Experimentally determined sequence requirement of ACGT-core of motif A in ABRE of the rice gene, OSEM; DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A in Arabidopsis | Upstream | -816 |
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 | Downstream | 2074 |
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 | -864 |
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 | 1185 |
| | | Upstream | -205 |
| | | Upstream | -414 |
| | | Upstream | -858 |
| | | Upstream | -1657 |
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 | 1185 |
| | | Upstream | -205 |
| | | Upstream | -414 |
| | | Upstream | -858 |
| | | Upstream | -1657 |
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 | -973 |
| | | Upstream | -975 |
| | | Upstream | -977 |
Motif_72 | GADOWNAT | Sequence present in 24 genes in the GA-down regulated d1 cluster (106 genes) found in Arabidopsis seed germination; This motif is similar to ABRE | Upstream | -816 |
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 | -823 |