| 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 | | 88.89% |
| Motif_625 | AtERF-4; AtERF-3 | Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression | | 77.78% |
| Motif_37 | AtERF-4 | Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression | | 77.78% |
| Motif_402 | AtTINY2 | Molecular cloning, phylogenetic analysis, expressional profiling and in vitro studies of TINY2 from Arabidopsis thaliana | | 77.78% |
| Motif_191 | AtERF-4; AtERF-3 | Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression | | 77.78% |
| Motif_60 | AtERF-4; AtERF-3 | Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression | | 77.78% |
| 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 | | 77.78% |
| Matrix_295 | ERF1 | Not Available | | 76.54% |
| Matrix_360 | ORA59 | Not Available | | 72.98% |
| Matrix_484 | ATERF13 | Not Available | | 71.73% |
| Matrix_147 | ERF3; AT1G80580 | Not Available | | 69.35% |
| Matrix_517 | ERF12 | Not Available | | 68.12% |
| Matrix_224 | ERF1 | Not Available | | 68.07% |
| Matrix_426 | CRF1; CRF2 | Not Available | | 67.90% |
| Matrix_45 | DRN | Not Available | | 67.54% |
| Motif_685 | PALINDROMICCBOXGM | Palindromic C-box in soybean;bZIP factors, STGA1 and STFs (STF1 and STF2) found in soybean apical hypocotyl, bind to this sequence | | 66.67% |
| Motif_99 | DREB1A; DREB1C; DREB1B | Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems;Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression;Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit | | 66.67% |
| 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 | | 66.67% |
| Motif_368 | CBF1 BS in cor15a | Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs | | 66.67% |
| Motif_577 | GRAZMRAB28 | GRA; GC-rich rab activator; Found in the promoter of ABA responsive rab28 gene from maize; Similar (seven of 12 bases) to the GRA element from the maize rab17 promoter (GRAZMRAB17); Found at -138 to -130 | | 66.67% |
| Motif_127 | SBOXATRBCS | S-box conserved in several rbcS promoters in Arabidopsis; ABI4 binding site; Important for the sugar and ABA responsiveness of CMA5 | | 66.67% |
| Motif_54 | LTREATLTI78 | Putative low temperature responsive element (LTRE); Found in Arabidopsis thaliana low-temperature-induced (lti) genes, lti78 and lti65; Repeated four times in lti78 which is also known as cor78 and rd29A; Found also in barley low temperature responsive genes, blt4.2, blt4.6, blt4.9 (lipid transfer genes); cold inducible; See LTRECORE; Also present in rab18, kin1, and kin2; Differential expression of two related, low-temperature-induced genes in Arabidopsis thaliana | | 66.67% |
| Motif_144 | DREB2A; DREB1A | Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems;Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses | | 66.67% |
| Motif_620 | DREB1&2 BS in rd29a | Related to responsiveness to drought, low-temperature or high-salt stress; Binding site of DREB1 and DREB2: Binding site of Arabidopsis CBF1(C-repeat/DRE binding factor); Overexpression of DREB1A activated the expression of stress tolerance genes; CBF1 overexpression induces COR genes and enhances freezing tolerance; Heterologous CBF1 expression enhances oxidative stresses tolerance; DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A in Arabidopsis;Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor | | 66.67% |
| Matrix_378 | ATERF1 | Not Available | | 66.56% |
| Matrix_86 | CRF5; CRF6; CRF4 | Not Available | | 66.20% |
| Matrix_242 | AT2G25820; AT3G16280; AT4G32800; TINY2; tny | Not Available | | 66.14% |
| Matrix_506 | DRNL; ATERF-4 | Not Available | | 64.16% |
| Matrix_277 | RAP2.6 | Not Available | | 63.94% |
| Matrix_363 | RAP2.3 | Not Available | | 63.84% |
| Matrix_478 | AT1G01250 | Not Available | | 63.57% |
| Matrix_321 | HRD | Not Available | | 63.16% |
| Matrix_261 | ATERF-1 | Not Available | | 62.97% |
| Matrix_5 | AT5G51190; ERF104 | Not Available | | 62.63% |
| Matrix_138 | RRTF1 | Not Available | | 62.56% |
| Matrix_119 | RRTF1 | Not Available | | 62.56% |
| Matrix_473 | RRTF1 | Not Available | | 62.44% |
| Matrix_73 | DEAR3; RAP2.9; RAP2.10 | Not Available | | 62.21% |
| Matrix_91 | CRF3 | Not Available | | 61.95% |
| Matrix_493 | AT1G22985; AT1G71130 | Not Available | | 61.82% |
| Matrix_252 | RAP2.6 | Not Available | | 61.79% |
| Matrix_146 | ORA47 | Not Available | | 61.51% |
| Matrix_50 | ATERF14; AT5G43410 | Not Available | | 61.27% |
| Matrix_288 | RAP2.3 | Not Available | | 61.08% |
| Matrix_234 | RAP2.3 | Not Available | | 59.05% |
| Matrix_343 | AT2G33710 | Not Available | | 58.74% |
| Matrix_377 | AT1G75490; DREB2C; AT2G40350; AT5G18450 | Not Available | | 58.17% |
| Matrix_334 | AT3G23230 | Not Available | | 57.81% |
| Motif_372 | E2FAT | E2F-binding site found in many potential E2F target genes; most potential E2F targets identified in silico show a cell cycle-regulated expression | | 57.04% |
| Matrix_433 | ATERF1 | Not Available | | 56.98% |
| Matrix_448 | ATERF6 | Not Available | | 56.95% |
| Matrix_344 | ATERF15; AT4G18450 | Not Available | | 56.22% |
| Matrix_374 | AT5G07580; AT5G61590 | Not Available | | 56.19% |
| Matrix_272 | DEAR4 | Not Available | | 56.19% |
| 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 | | 55.56% |
| Motif_239 | MYB2 | Evidence for a role for AtMYB2 in the induction of the Arabidopsis alcohol dehydrogenase gene (ADH1) by low oxygen | | 55.56% |
| 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 | | 55.56% |
| Motif_100 | DREB2A; DREB1A | Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems;Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses | | 55.56% |
| Motif_478 | DREB2A; DREB1A | Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems;Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses | | 55.56% |
| Motif_219 | E2Fa | The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants | | 55.56% |
| Motif_379 | ABRECE1HVA22 | CE1(coupling element 1) of barley HVA22 gene; possible binding site for nuclear bZIP protein; ABA responsive complex consists of a G-box, namely ABRE3 (GCCACGTACA), and CE1 | | 55.56% |
| Motif_89 | AtTINY2 | Molecular cloning, phylogenetic analysis, expressional profiling and in vitro studies of TINY2 from Arabidopsis thaliana | | 55.56% |
| 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 | | 55.56% |
| Motif_461 | MYB80 | The MYB80 transcription factor is required for pollen development and the regulation of tapetal programmed cell death in Arabidopsis thaliana | | 55.56% |
| Motif_209 | AtSR1 | A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants | | 55.56% |
| Motif_255 | B2GMAUX28 | B2; DNase I protected sequence found in the soybean auxin responsive gene, Aux28, promoter; Located between -310 and -301; Contains a TGACGACA sequence which is similar to TGACGT/C sequence found in Ocs, CaMV35S and histone H3 promoter; Contains as-1 motif | | 55.56% |
| Motif_86 | ACGTABOX | A-box according to the nomenclature of ACGT elements; One of ACGT elements; Found in ocs gene; RITA-1 binding site; G motif; G motif and TATCCAY motif (a GATA motif as its antisense sequence) are responsible for sugar repression | | 55.56% |
| Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | | 55.56% |
| Motif_199 | GCN4OSGLUB1 | GCN4 motif found in GluB-1 gene in rice; Required for endosperm-specific expression; AACA and ACGT motifs was found sufficient to confer a detectable level of endosperm expression; This motif is the recognition site for a basic leucine zipper transcription factor that belongs to the group of maize Opaque-2 (O2)-like proteins; Although all the RISBZ proteins are able to interact with the GCN4 motif, only RISBZ1 is capable of activating the gene expression | | 55.56% |
| Motif_437 | ANAERO2CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1) | | 55.56% |
| Motif_122 | TGTCACACMCUCUMISIN | TGTCACA motif found in the region (from -254 to -215) of cucumisin (a subtilisin-like serine protease) in the fruit of melon; A novel enhancer element necessary for fruit-specific expression of the cucumisin gene | | 55.56% |
| Motif_233 | DRE1COREZMRAB17 | DRE1 core found in maize rab17 gene promoter; DRE1 was protected, in in vivo footprinting, by a protein in embryos specifically, but in leaves, was protected when was treated with ABA and drought; rab17 is expressed during late embryogenesis, and is induced by ABA | | 55.56% |
| Motif_405 | DREB2A; DREB1A | Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems. Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses | | 55.56% |
| Motif_311 | ANAC019; ANAC055; ANAC072 | Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter | | 55.56% |
| Motif_248 | L1-box | Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element | | 55.56% |
| Motif_351 | GARE1OSREP1 | Gibberellin-responsive element (GARE) found in the promoter region of a cystein proteinase (REP-1) gene in rice | | 55.56% |
| Motif_259 | AtSR1 | A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants | | 55.56% |
| Motif_238 | AtWER | Regulation of CAPRICE transcription by MYB proteins for root epidermis differentiation in Arabidopsis | | 55.56% |
| Motif_212 | GARE2OSREP1 | Gibberellin-responsive element (GARE) found in the promoter region of a cystein proteinase (REP-1) gene in rice | | 55.56% |
| 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 | | 55.56% |
| Motif_331 | AtWER | Regulation of CAPRICE transcription by MYB proteins for root epidermis differentiation in Arabidopsis | | 55.56% |
| Motif_140 | DREB2A; DREB1A | Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems;Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses | | 55.56% |
| Motif_106 | PR2GCNT | GC element conserved in the 5' upstream regions of group 2 PR protein genes (beta-1,3-glucanase (GLN2), chitinase (CHN17, CHN50)) of tobacco | | 55.56% |
| Motif_528 | ABI5 | The homologous ABI5 and EEL transcription factors function antagonistically to fine-tune gene expression during late embryogenesis | | 55.56% |
| Motif_628 | TATCCAOSAMY | TATCCA element found in alpha-amylase promoters of rice at positions ca.90 to 150bp upstream of the transcription start sites; Binding sites of OsMYBS1, OsMYBS2 and OsMYBS3 which mediate sugar and hormone regulation of alpha-amylase gene expression; See also AMYBOX2 | | 55.56% |
| 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 | | 55.56% |
| Motif_632 | EREGCC | GCC box in ERE (ethylene responsive element); Ethylene-responsive region of tobacco (N.t.) chitinase gene contains two copies of the GCC-box; ERF2 and ERF4 enhanced the GCC box-mediated transcription; ERF3 reduced the transcription of the reporter gene in tobacco protoplasts; Binding site of AtEBP; Pti4/5/6 proteins from tomato which belong to the ERF family activate the expression of GCC box-containing PR genes; ERF3 was found to interact with NtUBC2, a ubiquitin-conjugating enzyme; Identification of an ethylene-responsive region in the promoter of a tobacco class I chitinase gene | | 55.56% |
| Motif_534 | GBOXRELOSAMY3 | G box-related element found in Amy3D (amylase) promoter of rice; Similar to ABRE | | 55.56% |
| Motif_13 | E2F-varient binding site motif | A genome-wide identification of E2F-regulated genes in Arabidopsis | | 55.56% |
| Motif_32 | DREB2A; DREB1A; AtTINY2; DREB1C; DREB1B | Molecular cloning, phylogenetic analysis, expressional profiling and in vitro studies of TINY2 from Arabidopsis thaliana. Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems.Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression.Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit.Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses | | 55.56% |
| Motif_607 | DREB2A; DREB1A | Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems.Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses | | 55.56% |
| Motif_17 | AUXRETGA1GMGH3 | TGA-box #1 in putative auxin-resonsive element (AUXRE) of soybean GH3 promoter; Strong binding site for proteins in plant nuclear extracts | | 55.56% |
| Motif_619 | SITEIIBOSPCNA | Site IIb of rice PCNA (proliferating cell nuclear antigen) gene; Found at -178 to -169; Binding site for two nuclear proteins, PCF1 and PCF2; Suggested to be involved in meristematic tissue-specific expression; Resemble the conserved motif (T/GGTCCCAT) found in promoter regions of auxin-regulated genes | | 55.56% |
| Motif_509 | AtTINY2 | Molecular cloning, phylogenetic analysis, expressional profiling and in vitro studies of TINY2 from Arabidopsis thaliana | | 55.56% |
| Motif_543 | TATCCACHVAL21 | TATCCAC box is a part of the conserved cis-acting response complex (GARC) that most often contain three sequence motifs, the TAACAAA box, or GA-responsive element (GARE); the pyrimidine box, CCTTTT (see S000259); and the TATCCAC box, which are necessary for a full GA response | | 55.56% |
| Motif_80 | AP1SV40 | AP-1 binding site in enhancer regions of SV40 and human metallothionein IIA (hMT IIA) | | 55.56% |
| Motif_552 | MRE1 | MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1 | | 54.31% |
| Matrix_223 | MYB60; ATMYB31; ATMYB30; MYB94; MYBCOV1 | Not Available | | 54.24% |
| Matrix_61 | ATCBF3 | Not Available | | 53.88% |
| Matrix_454 | AT1G77200; ATERF38; AT4G16750; AT5G52020 | Not Available | | 53.67% |
| Matrix_409 | DEAR3 | Not Available | | 53.66% |
| Motif_371 | DRE-like promoter motif | The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses | | 53.45% |
| Matrix_11 | TRFL5 | Not Available | | 51.77% |
| Matrix_287 | ERF2 | Not Available | | 51.70% |
| Matrix_395 | AT1G19210; ORA47; AT4G31060; AT5G21960 | Not Available | | 51.13% |
| Matrix_394 | DREB_U | Not Available | | 51.11% |
| Matrix_326 | AT5G07310; Rap2.6L; AT5G61890 | Not Available | | 51.05% |
| Matrix_355 | ERF10; ERF11 | Not Available | | 50.96% |
| Matrix_244 | DREB2C | Not Available | | 50.87% |
| Matrix_285 | DDF1 | Not Available | | 50.85% |
| Matrix_387 | ORA47 | Not Available | | 50.28% |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | | 50.00% |
| Motif_393 | AUXREPSIAA4 | AuxRE (Auxine responsive element ) of pea PS-IAA4/5 gene; Indoleacetic acid-inducible genes; domain A; TGA1a is preferentially expressed in root tip meristems; TGA1a may contribute to the expression of GST isoenzymes, especially in root tip meristems | | 50.00% |
| Motif_307 | TATCCAYMOTIFOSRAMY3D | TATCCAY motif found in rice RAmy3D alpha-amylase gene promoter; a GATA motif as its antisense sequence; TATCCAY motif and G motif are responsible for sugar repression | | 50.00% |
| 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) | | 50.00% |
| Motif_580 | L1BOXATPDF1 | L1 box found in promoter of Arabidopsis thaliana PROTODERMAL FACTOR1 (PDF1) gene; Located between -134 and -127; Involved in L1 layer-specific expression; L1-specific homeodomain protein ATML can bind to the L1 box; Y=C/T; A cotton fiber gene, RD22-like 1 (RDL1), contains a homeodomain binding L1 box and a MYB binding motif ; HDZip IV; Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein | | 50.00% |
| 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 | | 50.00% |
| Motif_520 | AMYBOX1 | amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barley | | 50.00% |
Expansion plot
Gene family finder
Ks-graphs
Skyline plot
Synteny plot
WGDotplot
Functional clusters
WGMapping
BLAST
Workbench