| Matrix_130 | TCP16 | Not available | Upstream | -753 |
| | | Downstream | 1187 |
| Matrix_132 | SOC1 | Not available | Upstream | -847 |
| Matrix_141 | AT3G25990 | Not available | Upstream | -698 |
| Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -714 |
| Matrix_171 | LBD3;LBD4 | Not available | Upstream | -750 |
| Matrix_179 | AtMYB84;MYB36;MYB68;O49746_ARATH | Not available | Upstream | -278 |
| | | Upstream | -277 |
| | | Upstream | -276 |
| | | Upstream | -275 |
| | | Upstream | -274 |
| | | Upstream | -273 |
| Matrix_191 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -713 |
| Matrix_197 | NAP | Not available | Downstream | 1204 |
| Matrix_206 | CUC1;ANAC100 | Not available | Upstream | -778 |
| Matrix_210 | ARR1 | Not available | Upstream | -659 |
| Matrix_216 | TCP16 | Not available | Upstream | -753 |
| | | Downstream | 1187 |
| Matrix_257 | NAC050;ANAC051;anac057;NAC2 | Not available | Upstream | -778 |
| Matrix_260 | CAMTA3 | Not available | Upstream | -747 |
| Matrix_266 | TCP16 | Determinants of the DNA binding specificity of class I and class II TCP transcription factors | Upstream | -753 |
| | | Downstream | 1187 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -251 |
| Matrix_294 | MEE35 | Not available | Upstream | -753 |
| | | Downstream | 1187 |
| Matrix_352 | LEC2 | Not available | Upstream | -587 |
| Matrix_396 | AP3 | Not available | Downstream | 868 |
| Matrix_4 | ARR14 | Not available | Upstream | -659 |
| Matrix_40 | TCP2 | Not available | Upstream | -753 |
| Matrix_41 | anac058 | Not available | Upstream | -778 |
| Matrix_420 | ANAC58 | Not available | Upstream | -777 |
| Matrix_44 | CUC3;anac046;NAC3;ANAC087;ATNAC6;CUC2 | Not available | Upstream | -777 |
| Matrix_499 | ARR18 | Not available | Upstream | -659 |
| Matrix_511 | AT1G05805;AT1G35460;AT1G51140;AT2G42280;AT2G43140;AT4G09180 | Not available | Upstream | -710 |
| Matrix_82 | TCP17 | Not available | Upstream | -753 |
| | | Downstream | 1187 |
| Matrix_94 | TCP5 | Not available | Upstream | -753 |
| Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -568 |
| 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 | -340 |
| Motif_122 | TGTCACACMCUCUMISIN | TGTCACA motif found in the region (from -254 to -215) of cucumisin (a subtilisin-like serine protease) in the fruit of melon; A novel enhancer element necessary for fruit-specific expression of the cucumisin gene | Downstream | 1237 |
| 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 | 152 |
| | | Intron | 154 |
| | | Intron | 156 |
| | | Intron | 158 |
| 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) | Upstream | -925 |
| 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 | 1235 |
| 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 | Upstream | -322 |
| 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 | -722 |
| | | Upstream | -708 |
| | | Upstream | -581 |
| | | Downstream | 1235 |
| Motif_22 | RYREPEATLEGUMINBOX | RY repeat (CATGCAY) or legumin box found in seed-storage protein genes in legume such as soybean | Upstream | -585 |
| 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 | 1205 |
| 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 | 868 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -789 |
| Motif_317 | GAREAT | GARE (GA-responsive element); Occurrence of GARE in GA-inducible, GA-responsible, and GA-nonresponsive genes found in Arabidopsis seed germination was 20, 18, and 12%, respectively | Upstream | -609 |
| Motif_318 | CGCGBOXAT | CGCG box recognized by AtSR1-6 (Arabidopsis thaliana signal-responsive genes); Multiple CGCG elements are found in promoters of many genes; Ca2+/calmodulin binds to all AtSRs | Upstream | -747 |
| 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 | -922 |
| | | Intron | 290 |
| Motif_329 | AMMORESIIUDCRNIA1 | Motifs (IIU and IID) found in the Chlamydomonas Nia1 gene promoter; Involved in ammonium-response; Located between -231 and -219 and also between -76 and -65; Involved in Nia1 transcription activation | Downstream | 868 |
| Motif_34 | LECPLEACS2 | Core element in LeCp (tomato Cys protease) binding cis-element (from -715 to -675) in LeAcs2 gene | Upstream | -959 |
| 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 | -921 |
| Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | Upstream | -621 |
| | | Downstream | 870 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Intron | 152 |
| | | Intron | 154 |
| | | Intron | 156 |
| | | Intron | 158 |
| | | Intron | 160 |
| 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 | 1235 |
| Motif_459 | SORLIP1 | Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | Upstream | -711 |
| | | Intron | 301 |
| Motif_530 | CPBCSPOR | The sequence critical for Cytokinin-enhanced Protein Binding in vitro, found in -490 to -340 of the promoter of the cucumber POR (NADPH-protochlorophyllide reductase) gene | Upstream | -735 |
| 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 | -844 |
| Motif_575 | TATABOX3 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene | Upstream | -615 |
| | | Upstream | -614 |
| 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 | -781 |
| | | Upstream | -599 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -924 |
| Motif_640 | RYREPEATBNNAPA | RY repeat found in RY/G box (the complex containing the two RY repeats and the G-box) of napA gene in Brassica napus; Found between -78 and -50; Required for seed specific expression;dist B ABRE mediated transactivation by ABI3 adn ABI3-dependent response to ABA; a tetramer of the composite RY/G complex mediated only ABA-independent transactivation by ABI3; B2 domain of ABI3 is necessary for ABA-independent and ABA-dependent activation through the dist B ABRE | Upstream | -585 |
| Motif_645 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -708 |
| | | Upstream | -581 |
| 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 | -847 |
| | | Intron | 292 |
| 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 | -847 |
| 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 | 152 |
| | | Intron | 154 |
| | | Intron | 156 |
| | | Intron | 158 |
| | | Intron | 160 |
| | | Intron | 162 |
| | | Intron | 164 |
| | | Intron | 166 |
| 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 | Upstream | -562 |
| 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 | -340 |
Expansion plot
Gene family finder
Ks-graphs
Skyline plot
Synteny plot
WGDotplot
Functional clusters
WGMapping
BLAST
Workbench