Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -527 |
| | | Upstream | -528 |
Matrix_153 | AP2 | Not available | Upstream | -527 |
| | | Upstream | -528 |
Matrix_170 | AT5G47660 | Not available | Downstream | 1798 |
Matrix_172 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -199 |
| | | Upstream | -200 |
Matrix_184 | AGL15 | Not available | Upstream | -78 |
Matrix_196 | TCP20;AT5G41030 | Not available | Downstream | 2233 |
| | | Downstream | 2047 |
| | | Downstream | 2005 |
| | | Upstream | -580 |
| | | Upstream | -581 |
Matrix_216 | TCP16 | Not available | Upstream | -582 |
| | | Upstream | -583 |
Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -525 |
Matrix_232 | TCP23 | Not available | Upstream | -581 |
| | | Upstream | -582 |
Matrix_266 | TCP16 | Determinants of the DNA binding specificity of class I and class II TCP transcription factors | Upstream | -582 |
| | | Upstream | -583 |
Matrix_269 | FHY3/FAR1 | Not available | Upstream | -310 |
Matrix_297 | TCP15 | Not available | Downstream | 2048 |
| | | Upstream | -581 |
| | | Upstream | -582 |
Matrix_301 | PIL5 | Not available | Upstream | -529 |
| | | Upstream | -530 |
Matrix_305 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -526 |
| | | Upstream | -527 |
Matrix_34 | RAV1_2 | RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants | Downstream | 2041 |
Matrix_348 | AT5G51910 | Not available | Downstream | 2049 |
| | | Upstream | -582 |
| | | Upstream | -583 |
| | | Upstream | -638 |
| | | Upstream | -639 |
Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -77 |
| | | Upstream | -1447 |
Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Downstream | 2001 |
Matrix_381 | ATHB9 | Not available | Upstream | -654 |
Matrix_387 | ORA47 | Not available | Downstream | 2000 |
Matrix_395 | AT1G19210;ORA47;AT4G31060;AT5G21960 | Not available | Downstream | 2000 |
Matrix_396 | AP3 | Not available | Downstream | 1464 |
Matrix_40 | TCP2 | Not available | Upstream | -582 |
Matrix_403 | BZR1 | Not available | Upstream | -526 |
| | | Upstream | -527 |
Matrix_42 | AT2G45680 | Not available | Upstream | -582 |
| | | Upstream | -583 |
| | | Upstream | -638 |
| | | Upstream | -639 |
Matrix_438 | AtbZIP63 | Not available | Upstream | -528 |
| | | Upstream | -529 |
Matrix_459 | ATHB9;CNA;PHB;ATHB-8;REV | Not available | Upstream | -654 |
Matrix_467 | RAV1 | Not available | Downstream | 2041 |
| | | Downstream | 2029 |
Matrix_477 | RAV1 | Not available | Downstream | 2041 |
| | | Downstream | 2029 |
Matrix_48 | PI | Not available | Downstream | 1447 |
| | | Upstream | -113 |
| | | Upstream | -191 |
| | | Upstream | -192 |
Matrix_480 | BES1 | Not available | Downstream | 1369 |
Matrix_488 | ABF1 | Not available | Upstream | -208 |
Matrix_55 | PIF3 | Not available | Upstream | -527 |
| | | Upstream | -528 |
Matrix_64 | PIF5 | Not available | Upstream | -529 |
| | | Upstream | -530 |
Matrix_65 | POC1;PIL1 | Not available | Upstream | -529 |
Matrix_80 | BIM1 | Not available | Upstream | -529 |
| | | Upstream | -530 |
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 | Downstream | 1395 |
| | | Upstream | -188 |
| | | Upstream | -553 |
| | | Upstream | -605 |
Motif_134 | ANAC092 | NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis | Downstream | 2088 |
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) | Downstream | 1974 |
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 | Downstream | 1792 |
| | | Downstream | 1367 |
| | | Upstream | -531 |
Motif_153 | MARABOX1 | A-box found in SAR(scaffold attachment region; or matrix attachment region, MAR) | Downstream | 1403 |
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 | Downstream | 2191 |
| | | Upstream | -240 |
| | | Upstream | -626 |
Motif_168 | IBOX | I box; I-box; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis; I box; Binding site of LeMYB1, that is a member of a novel class of myb-like proteins; LeMYBI act as a transcriptional activator; An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene | Downstream | 2016 |
| | | Downstream | 1572 |
| | | Upstream | -202 |
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 | Downstream | 1366 |
| | | Upstream | -530 |
Motif_181 | IBOXCORENT | I-box core motif in the CAMs (conserved DNA modular arrays) associated with light-responsive promoter regions | Downstream | 2016 |
| | | Downstream | 1572 |
| | | Upstream | -202 |
| | | Upstream | -1100 |
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 | Downstream | 2173 |
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 | Downstream | 2173 |
| | | Downstream | 2099 |
| | | Downstream | 2039 |
| | | Downstream | 2027 |
| | | Downstream | 1471 |
| | | Downstream | 1366 |
| | | Upstream | -530 |
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 | Downstream | 1366 |
| | | Upstream | -529 |
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 | Downstream | 2173 |
| | | Downstream | 1734 |
| | | Upstream | -318 |
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 | -271 |
Motif_243 | TELOBOXATEEF1AA1 | telo-box (telomere motif) found in the Arabidopsis (A.t.) eEF1AA1 gene promoter; Conserved in all known plant eEF1A gene promoters; Found in the 5' region of numerous genes encoding components of the translational apparatus; Required for the activation of expression in root primordia; Acts co-operatively with tef-box; Binding site of AtPur alpha-1; Plant interstitial telomere mitifs participate in the control of gene expression in root meristems | Downstream | 1463 |
Motif_244 | ABRE-like binding site motif | Not available | Upstream | -528 |
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 | Downstream | 2028 |
| | | Downstream | 1366 |
| | | Downstream | 1364 |
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 | Downstream | 1732 |
| | | Downstream | 1375 |
Motif_270 | ELRECOREPCRP1 | ElRE (Elicitor Responsive Element) core of parsley PR1 genes; consensus sequence of elements W1 and W2 of parsley PR1-1 and PR1-2 promoters; Box W1 and W2 are the binding site of WRKY1 and WRKY2, respectively; ERE; WA box; One of the W boxes found in the Parsley WRKY1 gene promoter; Required for elicitor responsiveness; WC box WB box and WC box constitute a palindrome; WRKY1 protein binding site; W-box found in thioredoxin h5 gene in Arabidopsis | Downstream | 2007 |
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 | 1728 |
| | | Upstream | -502 |
Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Downstream | 1993 |
| | | Downstream | 1573 |
| | | Upstream | -201 |
| | | Upstream | -242 |
| | | Upstream | -547 |
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 | Downstream | 1400 |
Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Downstream | 2173 |
Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Downstream | 1366 |
| | | Upstream | -530 |
Motif_341 | NAM | Molecular characterization of AtNAM: a member of the Arabidopsis NAC domain superfamily | Downstream | 1806 |
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 | Downstream | 1403 |
| | | Downstream | 1399 |
| | | Upstream | -494 |
Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Upstream | -643 |
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 | Downstream | 2008 |
Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | Downstream | 1463 |
Motif_371 | DRE-like promoter motif | The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses | Upstream | -671 |
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 | Downstream | 2073 |
| | | Downstream | 1376 |
| | | Upstream | -517 |
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 | Downstream | 1998 |
Motif_419 | MYB4 binding site motif | Not available | Downstream | 1732 |
| | | Downstream | 1375 |
Motif_43 | CCA1 binding site motif | CCA1 binding site; CCA1 protein (myb-related transcription factor) interact with two imperfect repeats of AAMAATCT in Lhcb1*3 gene of Arabidopsis thaliana; Related to regulation by phytochrome;A myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene | Downstream | 1973 |
Motif_437 | ANAERO2CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1) | Downstream | 2055 |
Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -529 |
Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Downstream | 1793 |
| | | Downstream | 1364 |
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 | Downstream | 2099 |
| | | Downstream | 2039 |
| | | Downstream | 2027 |
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 | -1475 |
Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Downstream | 1732 |
Motif_517 | LEAFYATAG | Target sequence of LEAFY in the intron of AGAMOUS gene in Arabidopsis | Downstream | 2076 |
Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -310 |
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 | Downstream | 1801 |
| | | Upstream | -1451 |
Motif_575 | TATABOX3 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene | Downstream | 1433 |
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 | -247 |
Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -237 |
| | | Upstream | -1454 |
Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Downstream | 1524 |
| | | Downstream | 1523 |
| | | Downstream | 1522 |
| | | Downstream | 1521 |
Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Downstream | 2072 |
| | | Downstream | 2060 |
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 | -637 |
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 | 2140 |
| | | Downstream | 2130 |
| | | Downstream | 1798 |
| | | Downstream | 1594 |
| | | Downstream | 1531 |
| | | Upstream | -243 |
| | | Upstream | -546 |
| | | Upstream | -630 |
Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Downstream | 1376 |
Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -237 |
| | | Upstream | -1454 |
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 | 2140 |
| | | Downstream | 2130 |
| | | Downstream | 1594 |
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 | 2031 |
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 | -189 |