Matrix_215 | ARF1 | ARF1, a transcription factor that binds to auxin response elements | Upstream | -277 |
Matrix_269 | FHY3/FAR1 | Not available | Upstream | -215 |
Matrix_430 | TOE2 | Not available | Upstream | -295 |
Matrix_452 | MYB46 | Not available | Upstream | -423 |
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 | -239 |
Motif_129 | GAGAGMGSA1 | GAGA element found in the promoter of the heme and chlorophyll synthesis gene Gsa1 in soybean; GAGA binding protein (GBP) binds to (GA)n/(CT)n DNA | Upstream | -234 |
| | | Upstream | -232 |
| | | Upstream | -230 |
| | | Upstream | -86 |
| | | Upstream | -84 |
| | | Upstream | -82 |
| | | Upstream | -80 |
| | | Upstream | -78 |
| | | Upstream | -76 |
| | | Upstream | -74 |
| | | Upstream | -72 |
| | | Upstream | -70 |
Motif_134 | ANAC092 | NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis | Upstream | -428 |
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 | Downstream | 1761 |
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 | -402 |
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 | -455 |
| | | Upstream | -432 |
| | | Upstream | -402 |
| | | Downstream | 1761 |
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 | -402 |
Motif_235 | C8GCARGAT | Binding site of plant MADS-domain protein AGL15; CArG motif with a longer A/T-rich core;A variant of CArG motif, with a longer A/T-rich core; Binding site for AGL15 (AGAMOUS-like 15) | Upstream | -291 |
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 | -317 |
Motif_274 | MYB1 binding site motif | Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein | Upstream | -425 |
Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Upstream | -151 |
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 | -423 |
| | | Upstream | -251 |
| | | Upstream | -136 |
Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -123 |
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 | -329 |
| | | Upstream | -324 |
| | | Downstream | 1783 |
Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -402 |
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 | -330 |
| | | Upstream | -325 |
| | | Upstream | -288 |
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 | -313 |
Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -234 |
| | | Upstream | -232 |
| | | Upstream | -230 |
| | | Upstream | -228 |
| | | Upstream | -86 |
| | | Upstream | -84 |
| | | Upstream | -82 |
| | | Upstream | -80 |
| | | Upstream | -78 |
| | | Upstream | -76 |
| | | Upstream | -74 |
| | | Upstream | -72 |
| | | Upstream | -70 |
| | | Upstream | -68 |
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 | Downstream | 1761 |
Motif_47 | CARGNCAT | Noncanonical CArG motif (CC-Wx8-GG) found in the promoter region of DTA1 (AtGA2ox6); A relevant cis element for the response to AGL15 (AGAMOUS-like 15) in vivo | Upstream | -292 |
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 | -455 |
Motif_527 | LFY | Structural basis for LEAFY floral switch function and similarity with helix-turn-helix proteins | Upstream | -322 |
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 | -1918 |
| | | Upstream | -461 |
Motif_564 | MYB98 | MYB98 positively regulates a battery of synergid-expressed genes encoding filiform apparatus localized proteins | Upstream | -252 |
Motif_579 | WRECSAA01 | Wound-responsive element (WRE) found in the promoter region of cucumber ascorbate oxidase gene, CsAAO1; Binding site of proteins in tobacco nuclear extracts | Upstream | -430 |
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 | Upstream | -415 |
| | | Upstream | -160 |
Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -191 |
Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -334 |
| | | Upstream | -329 |
Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Downstream | 1730 |
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 | Upstream | -426 |
Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -176 |
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 | -322 |
| | | Upstream | -321 |
Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -191 |
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 | -234 |
| | | Upstream | -232 |
| | | Upstream | -230 |
| | | Upstream | -228 |
| | | Upstream | -226 |
| | | Upstream | -224 |
| | | Upstream | -222 |
| | | Upstream | -220 |
| | | Upstream | -86 |
| | | Upstream | -84 |
| | | Upstream | -82 |
| | | Upstream | -80 |
| | | Upstream | -78 |
| | | Upstream | -76 |
| | | Upstream | -74 |
| | | Upstream | -72 |
| | | Upstream | -70 |
| | | Upstream | -68 |
| | | Upstream | -66 |
| | | Upstream | -64 |
| | | Upstream | -62 |
| | | Upstream | -60 |
Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Upstream | -432 |
| | | Upstream | -128 |
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 | -249 |