Matrix_104 | PI | Not available | Upstream | -876 |
| | | Upstream | -1768 |
Matrix_109 | GBF3 | Not available | Upstream | -901 |
| | | Upstream | -902 |
| | | Upstream | -1768 |
Matrix_111 | ABF3 | Not available | Upstream | -877 |
| | | Upstream | -878 |
Matrix_113 | ABI5 | Not available | Upstream | -876 |
| | | Upstream | -877 |
| | | Upstream | -878 |
| | | Upstream | -1768 |
| | | Upstream | -1770 |
Matrix_122 | ABF1;AREB2 | Not available | Upstream | -876 |
| | | Upstream | -877 |
| | | Upstream | -1769 |
Matrix_129 | ABF1 | Not available | Upstream | -877 |
| | | Upstream | -1769 |
Matrix_134 | ABF1 | Not available | Upstream | -877 |
| | | Upstream | -878 |
| | | Upstream | -1769 |
Matrix_146 | ORA47 | Not available | Upstream | -678 |
Matrix_147 | ERF3;AT1G80580 | Not available | Upstream | -678 |
Matrix_166 | TGA4 | Not available | Upstream | -899 |
| | | Upstream | -900 |
Matrix_192 | FHY3/FAR1 | Not available | Upstream | -874 |
| | | Upstream | -877 |
| | | Upstream | -878 |
| | | Upstream | -901 |
| | | Upstream | -902 |
| | | Upstream | -1766 |
Matrix_194 | HYH;HY5 | Not available | Upstream | -874 |
| | | Upstream | -1766 |
Matrix_214 | AP1 | Not available | Upstream | -1767 |
Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -901 |
| | | Upstream | -902 |
| | | Upstream | -1045 |
| | | Upstream | -1766 |
Matrix_224 | ERF1 | Not available | Upstream | -677 |
Matrix_23 | ANAC46 | Not available | Upstream | -906 |
Matrix_234 | RAP2.3 | Not available | Upstream | -674 |
| | | Upstream | -675 |
Matrix_261 | ATERF-1 | Not available | Upstream | -678 |
Matrix_264 | ATAREB1 | Not available | Upstream | -874 |
| | | Upstream | -877 |
| | | Upstream | -1766 |
| | | Upstream | -1769 |
Matrix_272 | DEAR4 | Not available | Upstream | -678 |
Matrix_278 | AtbZIP44 | Not available | Upstream | -899 |
| | | Upstream | -900 |
Matrix_284 | KAN2;KAN3;KAN;KAN4 | Not available | Downstream | 10052 |
Matrix_288 | RAP2.3 | Not available | Upstream | -677 |
Matrix_295 | ERF1 | Not available | Upstream | -678 |
Matrix_296 | GBF2 | Not available | Upstream | -901 |
| | | Upstream | -902 |
| | | Upstream | -1769 |
Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -901 |
| | | Upstream | -902 |
| | | Upstream | -1769 |
Matrix_301 | PIL5 | Not available | Upstream | -872 |
| | | Upstream | -1764 |
Matrix_306 | TGA1 | TGA1 and G-box binding factors: two distinct classes of Arabidopsis leucine zipper proteins compete for the G-box-like element TGACGTGG | Upstream | -897 |
| | | Upstream | -898 |
Matrix_326 | AT5G07310;Rap2.6L;AT5G61890 | Not available | Upstream | -677 |
Matrix_331 | GBF1 | Not available | Upstream | -901 |
| | | Upstream | -902 |
| | | Upstream | -1768 |
Matrix_334 | AT3G23230 | Not available | Upstream | -679 |
Matrix_338 | AP2 | Not available | Upstream | -874 |
| | | Upstream | -1766 |
Matrix_343 | AT2G33710 | Not available | Upstream | -674 |
| | | Upstream | -675 |
Matrix_355 | ERF10;ERF11 | Not available | Upstream | -677 |
Matrix_356 | PRR5 | Not available | Upstream | -870 |
| | | Upstream | -874 |
| | | Upstream | -1762 |
| | | Upstream | -1766 |
Matrix_359 | FLC | Not available | Upstream | -1767 |
Matrix_360 | ORA59 | Not available | Upstream | -678 |
Matrix_363 | RAP2.3 | Not available | Upstream | -677 |
Matrix_378 | ATERF1 | Not available | Upstream | -674 |
| | | Upstream | -675 |
Matrix_396 | AP3 | Not available | Upstream | -854 |
| | | Upstream | -855 |
Matrix_399 | TGA1 | Not available | Upstream | -898 |
| | | Upstream | -899 |
Matrix_403 | BZR1 | Not available | Upstream | -875 |
| | | Upstream | -1767 |
Matrix_405 | DREB2C | Not available | Upstream | -947 |
Matrix_406 | ATERF-7 | Not available | Upstream | -676 |
Matrix_409 | DEAR3 | Not available | Upstream | -677 |
Matrix_426 | CRF1;CRF2 | Not available | Upstream | -679 |
Matrix_429 | KAN4 | Not available | Downstream | 10052 |
Matrix_438 | AtbZIP63 | Not available | Upstream | -898 |
| | | Upstream | -899 |
| | | Upstream | -1769 |
Matrix_443 | AGL15 | Not available | Upstream | -875 |
| | | Upstream | -1767 |
Matrix_45 | DRN | Not available | Upstream | -678 |
Matrix_456 | bZIP60 | Not available | Upstream | -900 |
| | | Upstream | -901 |
Matrix_457 | TGA2 | Not available | Upstream | -898 |
| | | Upstream | -899 |
Matrix_462 | ATERF-8 | Not available | Upstream | -676 |
Matrix_471 | KAN4 | Not available | Downstream | 10051 |
Matrix_473 | RRTF1 | Not available | Upstream | -674 |
| | | Upstream | -675 |
Matrix_48 | PI | Not available | Upstream | -746 |
Matrix_480 | BES1 | Not available | Upstream | -1768 |
Matrix_484 | ATERF13 | Not available | Upstream | -678 |
Matrix_488 | ABF1 | Not available | Upstream | -900 |
| | | Upstream | -1043 |
| | | Upstream | -1761 |
Matrix_50 | ATERF14;AT5G43410 | Not available | Upstream | -677 |
Matrix_506 | DRNL;ATERF-4 | Not available | Upstream | -679 |
Matrix_517 | ERF12 | Not available | Upstream | -678 |
Matrix_56 | BZIP17;BZIP28;BZIP49 | Not available | Upstream | -899 |
| | | Upstream | -900 |
Matrix_57 | WIN1;SHN3;SHN2 | Not available | Upstream | -677 |
Matrix_7 | PIF4 | Not available | Upstream | -1769 |
Matrix_86 | CRF5;CRF6;CRF4 | Not available | Upstream | -679 |
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 | Intron | 9142 |
Motif_131 | P1BS | PHR1-binding sequence found in the upstream regions of phosphate starvation responsive genes from several plant species; phr1 (phosphate starvation response 1) gene codes for PHR1 protein related to PSR1 gene in C. reinhardtii | Downstream | 10051 |
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 | -345 |
| | | Upstream | -878 |
| | | Upstream | -1770 |
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 | -823 |
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 | -823 |
| | | Upstream | -878 |
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 | -877 |
| | | Upstream | -878 |
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 | -823 |
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 | Upstream | -855 |
Motif_244 | ABRE-like binding site motif | Not available | Upstream | -876 |
| | | Upstream | -878 |
| | | Upstream | -902 |
| | | Upstream | -1045 |
| | | Upstream | -1768 |
| | | Upstream | -1770 |
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 | -877 |
| | | Upstream | -878 |
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 | Downstream | 10052 |
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 | -846 |
Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Downstream | 10113 |
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 | -678 |
Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -823 |
Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -878 |
| | | Upstream | -902 |
Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Downstream | 10080 |
Motif_347 | OPAQUE2ZMB32 | opaque-2 binding site of maize b-32 (type I ribosome-inactivating protein gene); O2; O2S; O2S and GARE form a gibberellin response complex (GARC) | Upstream | -899 |
Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | Upstream | -855 |
Motif_399 | UPRMOTIFIAT | Motif I in the conserved UPR (unfolded protein response) cis-acting element in Arabidopsis genes coding for SAR1B, HSP-90, SBR-like, Ca-ATPase 4, CNX1, PDI, etc. | Upstream | -901 |
Motif_437 | ANAERO2CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1) | Upstream | -87 |
Motif_440 | TGA1 binding site motif | Hex motif; Binding site of Arabidopsis bZIP protein TGA1 and G box binding factor GBF1; TGA1 and members of the GBF family differ in their DNA binding properties; G-Box-like element;TGA1 and G-box binding factors: two distinct classes of Arabidopsis leucine zipper proteins compete for the G-box-like element TGACGTGG | Upstream | -901 |
Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Intron | 9142 |
| | | Intron | 9140 |
Motif_450 | E2FCONSENSUS | E2F consensus sequence of all different E2F-DP-binding motifs that were experimentally verified in plants | Downstream | 10047 |
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 | Upstream | -901 |
Motif_489 | SORLREP3AT | one of Sequences Over-Represented in Light-Repressed Promoters (SORLREPs) in Arabidopsis; Computationally identified phyA-repressed motifs; See also all SORLREPs and also all SORLIPs;Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | Downstream | 10060 |
Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -903 |
| | | Upstream | -1046 |
| | | Upstream | -1768 |
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 | Upstream | -901 |
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 | -892 |
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 | -876 |
| | | Upstream | -879 |
| | | Upstream | -903 |
| | | Upstream | -1046 |
| | | Upstream | -1768 |
Motif_652 | AUXRETGA2GMGH3 | TGA-box #2 in putative auxin-resonsive element (AUXRE) E1 of soybean GH3 promoter; Strong binding site for proteins in plant nuclear extracts; Hex-like element; E1 element=-249 to -203; E2 element=-241 to -224 | Upstream | -901 |
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 | Intron | 9143 |
| | | Intron | 9141 |
| | | Intron | 9139 |
| | | Intron | 9137 |
| | | Intron | 9135 |
| | | Intron | 9133 |
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 | -876 |
| | | Upstream | -879 |
Motif_95 | UPRE2AT | XBP1 binding site-like sequence found in the plant UPRE (unfolded protein response element) in Arabidopsis thaliana;Either of ERSEII or XBP1 binding sites is essential and sufficient for the UPR | Upstream | -899 |