Matrix_104 | PI | Not available | Upstream | -710 |
Matrix_113 | ABI5 | Not available | Upstream | -710 |
| | | Upstream | -708 |
Matrix_119 | RRTF1 | Not available | Upstream | -389 |
Matrix_122 | ABF1;AREB2 | Not available | Upstream | -710 |
Matrix_129 | ABF1 | Not available | Upstream | -709 |
Matrix_134 | ABF1 | Not available | Upstream | -708 |
| | | Intron | 877 |
| | | Intron | 954 |
| | | Intron | 991 |
| | | Intron | 1016 |
Matrix_138 | RRTF1 | Not available | Upstream | -389 |
Matrix_145 | GBF4;AT5G44080 | Not available | Upstream | -708 |
Matrix_147 | ERF3;AT1G80580 | Not available | Upstream | -388 |
Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -713 |
Matrix_190 | ATERF1 | Not available | Upstream | -387 |
Matrix_192 | FHY3/FAR1 | Not available | Upstream | -712 |
| | | Upstream | -708 |
Matrix_194 | HYH;HY5 | Not available | Upstream | -712 |
Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -708 |
Matrix_234 | RAP2.3 | Not available | Upstream | -388 |
Matrix_24 | POC1 | Not available | Upstream | -713 |
Matrix_252 | RAP2.6 | Not available | Upstream | -388 |
Matrix_264 | ATAREB1 | Not available | Upstream | -712 |
| | | Upstream | -709 |
Matrix_288 | RAP2.3 | Not available | Upstream | -389 |
Matrix_295 | ERF1 | Not available | Upstream | -388 |
Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -708 |
Matrix_301 | PIL5 | Not available | Upstream | -714 |
Matrix_338 | AP2 | Not available | Upstream | -712 |
Matrix_343 | AT2G33710 | Not available | Upstream | -388 |
Matrix_355 | ERF10;ERF11 | Not available | Upstream | -389 |
Matrix_356 | PRR5 | Not available | Upstream | -716 |
| | | Upstream | -712 |
Matrix_363 | RAP2.3 | Not available | Upstream | -389 |
Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Intron | 929 |
| | | Intron | 938 |
| | | Intron | 944 |
| | | Intron | 952 |
Matrix_378 | ATERF1 | Not available | Upstream | -388 |
Matrix_403 | BZR1 | Not available | Upstream | -711 |
Matrix_406 | ATERF-7 | Not available | Upstream | -390 |
Matrix_420 | ANAC58 | Not available | Intron | 886 |
Matrix_443 | AGL15 | Not available | Upstream | -711 |
Matrix_45 | DRN | Not available | Upstream | -388 |
Matrix_462 | ATERF-8 | Not available | Upstream | -390 |
Matrix_473 | RRTF1 | Not available | Upstream | -388 |
Matrix_48 | PI | Not available | Intron | 1034 |
Matrix_484 | ATERF13 | Not available | Upstream | -388 |
Matrix_488 | ABF1 | Not available | Upstream | -717 |
| | | Upstream | -710 |
| | | Upstream | -387 |
Matrix_506 | DRNL;ATERF-4 | Not available | Upstream | -387 |
Matrix_517 | ERF12 | Not available | Upstream | -388 |
Matrix_55 | PIF3 | Not available | Upstream | -710 |
Matrix_7 | PIF4 | Not available | Upstream | -707 |
Matrix_77 | PRR5 | Not available | Upstream | -711 |
Matrix_91 | CRF3 | Not available | Upstream | -388 |
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 | -602 |
| | | Upstream | -273 |
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 | Upstream | -713 |
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 | -732 |
Motif_165 | AP3SV40 | AP-3 binding site consensus sequence in enhancer regions of SV40, MMTV, MLV, IL2 | Upstream | -631 |
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 | -707 |
Motif_193 | GLK1 | GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis | Upstream | -683 |
| | | Intron | 1015 |
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 | -707 |
| | | Upstream | -535 |
Motif_200 | GBOXLERBCS | G box; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis; Binding with GBF | Upstream | -708 |
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 | -708 |
| | | Upstream | -707 |
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 | Intron | 994 |
Motif_244 | ABRE-like binding site motif | Not available | Upstream | -709 |
| | | Upstream | -707 |
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 | -708 |
| | | Intron | 890 |
Motif_256 | RHE_element | Functional Conservation of a Root Hair Cell-Specific cis-Element in Angiosperms with Different Root Hair Distribution Patterns | Upstream | -717 |
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 | -593 |
| | | Upstream | -587 |
Motif_29 | GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -634 |
Motif_291 | ABFs binding site motif | Binding site of trans-acting factor EMBP-1; wheat Em gene;Binding site of ABFs; ABFs (ABRE binding factors) were isolated from Arabidopsis by a yeast one-hybrid screening system; Expression ABFs is induced by ABA and various stress treatment; ABFs belongs to a distinct subfamily of bZIP proteins; Involved in ABA-mediated stress-signaling pathway;A plant leucine zipper protein that recognizes an abscisic acid response element | Upstream | -707 |
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 | -387 |
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 | Intron | 997 |
Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -707 |
Motif_353 | HEXAMERATH4 | hexamer motif of Arabidopsis thaliana histone H4 promoter;Identification of cis-elements regulating the expression of an Arabidopsis histone H4 gene | Upstream | -689 |
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 | -593 |
| | | Upstream | -587 |
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 | -1818 |
| | | Upstream | -688 |
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 | Intron | 1017 |
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 | Upstream | -693 |
Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -504 |
| | | Downstream | 1931 |
Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -707 |
Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -714 |
| | | Intron | 890 |
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 | -535 |
Motif_490 | PROLAMINBOXOSGLUB1 | Prolamine box found in the rice GluB-1 gene promoter; Involved in quantitative regulation of the GluB-1 gene | Upstream | -735 |
Motif_542 | ABI5;AtMYC2;HY5 | A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth. Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. The homologous ABI5 and EEL transcription factors function antagonistically to fine-tune gene expression during late embryogenesis | Upstream | -709 |
Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -706 |
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 | Intron | 956 |
| | | Intron | 980 |
Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -528 |
Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Intron | 1018 |
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 | -709 |
| | | Upstream | -706 |
Motif_638 | ABRE binding site motif | Not available | Upstream | -707 |
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 | -749 |
Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -533 |
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 | -1769 |
| | | Upstream | -1756 |
| | | Upstream | -743 |
| | | Intron | 949 |
| | | Intron | 982 |
Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -528 |
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 | Upstream | -1756 |
| | | Intron | 949 |
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 | -608 |
| | | Upstream | -503 |
| | | Upstream | -501 |
| | | Upstream | -499 |
| | | Upstream | -497 |
| | | Downstream | 1932 |
| | | Downstream | 1934 |
| | | Downstream | 1936 |
| | | Downstream | 1938 |
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 | -709 |
Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Intron | 1015 |
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 | -601 |
Motif_92 | ABREATRD22 | ABRE (ABA responsive element) in Arabidopsis dehydration-responsive gene rd22 | Upstream | -708 |