Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -677 |
| | | Upstream | -678 |
Matrix_153 | AP2 | Not available | Upstream | -677 |
| | | Upstream | -678 |
Matrix_184 | AGL15 | Not available | Upstream | -401 |
| | | Upstream | -603 |
Matrix_19 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -784 |
Matrix_196 | TCP20;AT5G41030 | Not available | Downstream | 1963 |
| | | Upstream | -731 |
| | | Upstream | -732 |
| | | Upstream | -787 |
| | | Upstream | -788 |
Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -675 |
Matrix_232 | TCP23 | Not available | Upstream | -732 |
| | | Upstream | -733 |
| | | Upstream | -788 |
| | | Upstream | -789 |
Matrix_24 | POC1 | Not available | Upstream | -674 |
Matrix_297 | TCP15 | Not available | Upstream | -732 |
| | | Upstream | -733 |
| | | Upstream | -788 |
| | | Upstream | -789 |
Matrix_301 | PIL5 | Not available | Upstream | -679 |
| | | Upstream | -680 |
Matrix_305 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -676 |
| | | Upstream | -677 |
Matrix_348 | AT5G51910 | Not available | Upstream | -733 |
| | | Upstream | -734 |
| | | Upstream | -789 |
| | | Upstream | -790 |
Matrix_396 | AP3 | Not available | Downstream | 1511 |
Matrix_403 | BZR1 | Not available | Upstream | -676 |
| | | Upstream | -677 |
Matrix_42 | AT2G45680 | Not available | Upstream | -733 |
| | | Upstream | -734 |
| | | Upstream | -789 |
| | | Upstream | -790 |
Matrix_438 | AtbZIP63 | Not available | Upstream | -678 |
| | | Upstream | -679 |
Matrix_467 | RAV1 | Not available | Downstream | 1990 |
Matrix_477 | RAV1 | Not available | Downstream | 1990 |
Matrix_507 | TCP3 | Not available | Upstream | -732 |
| | | Upstream | -788 |
Matrix_55 | PIF3 | Not available | Upstream | -677 |
| | | Upstream | -678 |
Matrix_64 | PIF5 | Not available | Upstream | -679 |
| | | Upstream | -680 |
Matrix_65 | POC1;PIL1 | Not available | Upstream | -679 |
Matrix_80 | BIM1 | Not available | Upstream | -679 |
| | | Upstream | -680 |
Motif_1 | GT1CORE | Critical for GT-1 binding to box II of rbcS; Transcriptional activation by Arabidopsis GT-1 may be through interaction with TFIIA-TBP-TATA complex | Downstream | 1429 |
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 | 1849 |
| | | Upstream | -704 |
| | | Upstream | -756 |
| | | Upstream | -817 |
| | | Upstream | -1249 |
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 | 1411 |
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 | 1337 |
| | | Upstream | -681 |
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 | 1300 |
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 | Upstream | -331 |
| | | Upstream | -777 |
Motif_165 | AP3SV40 | AP-3 binding site consensus sequence in enhancer regions of SV40, MMTV, MLV, IL2 | Downstream | 1428 |
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 | 1977 |
| | | Downstream | 1582 |
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 | -680 |
Motif_181 | IBOXCORENT | I-box core motif in the CAMs (conserved DNA modular arrays) associated with light-responsive promoter regions | Downstream | 1977 |
| | | Downstream | 1582 |
Motif_192 | BOXLCOREDCPAL | Consensus of the putative core sequences of box-L-like sequences in carrot; PAL1 promoter region; DCMYB1 bound to these sequences in vitro | Downstream | 1957 |
Motif_193 | GLK1 | GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis | Upstream | -740 |
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 | 2059 |
| | | Downstream | 2013 |
| | | Downstream | 1988 |
| | | Downstream | 1300 |
| | | Upstream | -680 |
| | | Upstream | -786 |
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 | -679 |
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 | 2056 |
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 | -362 |
| | | Upstream | -641 |
| | | Upstream | -752 |
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 | 1510 |
Motif_244 | ABRE-like binding site motif | Not available | Upstream | -678 |
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 | 1989 |
| | | Downstream | 1301 |
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 | 1312 |
Motif_258 | -10PEHVPSBD | -10 promoter element found in the barley (H.v.) chloroplast psbD gene promoter; Involved in the expression of the plastid gene psbD which encodes a photosystem II reaction center chlorophyll-binding protein that is activated by blue, white or UV-A light | Upstream | -282 |
Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Downstream | 1352 |
| | | Downstream | 1349 |
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 | -652 |
Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Downstream | 1583 |
| | | Upstream | -333 |
| | | Upstream | -698 |
| | | Upstream | -782 |
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 | 1414 |
| | | Downstream | 1408 |
Motif_323 | MYB1LEPR | Tomato Pti4(ERF) regulates defence-related gene expression via GCC box and non-GCC box cis elements (Myb1(GTTAGTT), G box (CACGTG)) | Downstream | 2054 |
Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Downstream | 1336 |
| | | Upstream | -680 |
Motif_341 | NAM | Molecular characterization of AtNAM: a member of the Arabidopsis NAC domain superfamily | Downstream | 1817 |
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 | 1413 |
| | | Upstream | -644 |
Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Upstream | -794 |
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 | Upstream | -749 |
Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | Downstream | 1510 |
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 | 2033 |
| | | Upstream | -667 |
Motif_410 | ANAERO1CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1); Arbitrary named ANAERO1CONSENSUS by the PLACEdb curator | Downstream | 1377 |
| | | Upstream | -855 |
Motif_419 | MYB4 binding site motif | Not available | Downstream | 2054 |
| | | Downstream | 1312 |
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 | 2015 |
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 | 1300 |
Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -679 |
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 | 1335 |
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 | 2059 |
| | | Downstream | 1988 |
| | | Upstream | -786 |
Motif_491 | GT-1 | Molecular dissection of GT-1 from Arabidopsis | Downstream | 1431 |
Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Downstream | 1313 |
Motif_517 | LEAFYATAG | Target sequence of LEAFY in the intron of AGAMOUS gene in Arabidopsis | Downstream | 2036 |
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 | 1812 |
| | | Upstream | -640 |
Motif_570 | POLASIG2 | PolyA signal; poly A signal found in rice alpha-amylase; -10 to -30 in the case of animal genes | Upstream | -1235 |
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 | 1335 |
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 | -338 |
Motif_590 | MYB3 binding site motif | Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses | Downstream | 2054 |
Motif_606 | NAPINMOTIFBN | Sequence found in 5' upstream region (-6, -95, -188) of napin (2S albumin) gene in Brassica napus; Interact with a protein present in crude nuclear extracts from developing B. napus seeds | Downstream | 1302 |
Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 1376 |
| | | Upstream | -328 |
| | | Upstream | -400 |
| | | Upstream | -855 |
Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Downstream | 1503 |
Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Downstream | 2032 |
| | | Downstream | 2020 |
| | | Downstream | 1428 |
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 | 1614 |
| | | Upstream | -334 |
| | | Upstream | -697 |
| | | Upstream | -781 |
Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Downstream | 1313 |
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 | 1537 |
Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 1376 |
| | | Upstream | -328 |
| | | Upstream | -400 |
| | | Upstream | -855 |
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 | -276 |
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 | 1992 |
Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Upstream | -261 |