Matrix_130 | TCP16 | Not available | Upstream | -630 |
| | | Upstream | -631 |
Matrix_144 | AT5G08330;AT5G23280 | Not available | Upstream | -630 |
| | | Upstream | -631 |
| | | Upstream | -632 |
| | | Upstream | -652 |
Matrix_154 | AT1G22190;AT1G36060;AT1G64380;RAP2.4;AT2G20880;AT2G22200;AT4G13620;AT4G28140;AT4G39780;AT5G65130 | Not available | Upstream | -619 |
| | | Upstream | -620 |
Matrix_179 | AtMYB84;MYB36;MYB68;O49746_ARATH | Not available | Upstream | -621 |
| | | Upstream | -622 |
Matrix_196 | TCP20;AT5G41030 | Not available | Upstream | -628 |
| | | Upstream | -629 |
| | | Upstream | -633 |
| | | Upstream | -634 |
| | | Upstream | -650 |
Matrix_216 | TCP16 | Not available | Upstream | -630 |
| | | Upstream | -631 |
Matrix_232 | TCP23 | Not available | Upstream | -629 |
| | | Upstream | -630 |
| | | Upstream | -632 |
| | | Upstream | -633 |
| | | Upstream | -651 |
Matrix_25 | AP3 | Not available | Upstream | -399 |
| | | Upstream | -400 |
Matrix_26 | ATMYB3;MYB24 | Not available | Upstream | -550 |
| | | Upstream | -551 |
Matrix_266 | TCP16 | Determinants of the DNA binding specificity of class I and class II TCP transcription factors | Upstream | -630 |
| | | Upstream | -631 |
Matrix_269 | FHY3/FAR1 | Not available | Upstream | -177 |
Matrix_280 | TCP24;TCP1;BRC2;ATTCP18 | Not available | Upstream | -630 |
| | | Upstream | -631 |
| | | Upstream | -632 |
| | | Upstream | -652 |
Matrix_281 | TCP13 | Not available | Upstream | -630 |
Matrix_290 | AP2 | Not available | Upstream | -627 |
Matrix_294 | MEE35 | Not available | Upstream | -630 |
| | | Upstream | -631 |
Matrix_297 | TCP15 | Not available | Upstream | -629 |
| | | Upstream | -630 |
| | | Upstream | -632 |
| | | Upstream | -633 |
| | | Upstream | -651 |
Matrix_348 | AT5G51910 | Not available | Upstream | -630 |
| | | Upstream | -631 |
| | | Upstream | -632 |
| | | Upstream | -652 |
Matrix_352 | LEC2 | Not available | Upstream | -613 |
| | | Upstream | -614 |
Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Upstream | -621 |
| | | Upstream | -622 |
Matrix_395 | AT1G19210;ORA47;AT4G31060;AT5G21960 | Not available | Upstream | -620 |
| | | Upstream | -621 |
Matrix_40 | TCP2 | Not available | Upstream | -630 |
Matrix_401 | MYB55 | Not available | Upstream | -624 |
| | | Upstream | -625 |
Matrix_409 | DEAR3 | Not available | Upstream | -620 |
| | | Upstream | -621 |
Matrix_42 | AT2G45680 | Not available | Upstream | -630 |
| | | Upstream | -631 |
| | | Upstream | -632 |
| | | Upstream | -652 |
Matrix_48 | PI | Not available | Upstream | -177 |
| | | Upstream | -389 |
| | | Upstream | -390 |
| | | Upstream | -921 |
Matrix_496 | ATMYB15 | Not available | Upstream | -621 |
| | | Upstream | -622 |
Matrix_507 | TCP3 | Not available | Upstream | -629 |
| | | Upstream | -630 |
| | | Upstream | -632 |
| | | Upstream | -633 |
| | | Upstream | -651 |
Matrix_510 | AtMYB84 | More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -621 |
| | | Upstream | -622 |
Matrix_79 | FUS3 | Not available | Upstream | -615 |
| | | Upstream | -616 |
Matrix_82 | TCP17 | Not available | Upstream | -630 |
Matrix_94 | TCP5 | Not available | Upstream | -630 |
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 | Upstream | -421 |
Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Downstream | 1122 |
| | | Upstream | -410 |
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 | 1059 |
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 | Upstream | -698 |
| | | Upstream | -700 |
| | | Upstream | -702 |
| | | Upstream | -704 |
| | | Upstream | -706 |
| | | Upstream | -708 |
| | | Upstream | -710 |
| | | Upstream | -712 |
| | | Upstream | -714 |
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 | 1022 |
| | | Upstream | -221 |
Motif_223 | LTRE1HVBLT49 | LTRE-1 (low-temperature-responsive element) in barley (H.v.) blt4.9 gene promoter; A new LTRE; A previously known LTRE is CCGAC | Downstream | 1153 |
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 | Upstream | -552 |
Motif_305 | SP1SV40 | SP-1 binding site (GC box) in enhancer regions of SV40 and human metallothionein IIA (hMT IIA) | Upstream | -621 |
Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Downstream | 1298 |
Motif_310 | ANAERO3CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1); Arbitrary named ANAERO3CONSENSUS by the PLACEdb curator | Downstream | 1049 |
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 | 1019 |
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 | 1018 |
Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Upstream | -153 |
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 | -696 |
Motif_370 | TATABOX2 | TATA box; TATA box found in the 5'upstream region of pea legA gene; sporamin A of sweet potato; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation | Downstream | 1139 |
Motif_383 | UPRE-III(bZIP60) | The plant-specific transcription factor NAC103 is induced by bZIP60 through a new cis-regulatory element to modulate the unfolded protein response in Arabidopsis | Upstream | -573 |
| | | Upstream | -580 |
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 | 977 |
Motif_419 | MYB4 binding site motif | Not available | Upstream | -552 |
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 | 1228 |
| | | Downstream | 1225 |
Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Downstream | 1261 |
| | | Upstream | -698 |
| | | Upstream | -700 |
| | | Upstream | -702 |
| | | Upstream | -704 |
| | | Upstream | -706 |
| | | Upstream | -708 |
| | | Upstream | -710 |
| | | Upstream | -712 |
| | | Upstream | -714 |
| | | Upstream | -716 |
Motif_470 | MYB98 | MYB98 positively regulates a battery of synergid-expressed genes encoding filiform apparatus localized proteins | Upstream | -537 |
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 | Downstream | 1280 |
Motif_552 | MRE1 | MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1 | Upstream | -613 |
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 | -165 |
Motif_584 | UPRE-III(bZIP60) | The plant-specific transcription factor NAC103 is induced by bZIP60 through a new cis-regulatory element to modulate the unfolded protein response in Arabidopsis | Upstream | -573 |
| | | Upstream | -580 |
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 | -631 |
Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 976 |
Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Downstream | 1021 |
| | | Downstream | 1018 |
Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -809 |
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 | 1299 |
| | | Downstream | 1287 |
| | | Downstream | 1151 |
| | | Upstream | -598 |
Motif_662 | MYB26PS | Myb26 binding site; Myb26 recognizes the c-Myb and P-box-like binding sites representing cis-elements in the promoter regions of several phenylpropanoid biosynthetic genes; Identical to P-box in maize, and to Myb305 binding site in snapdragon | Upstream | -552 |
Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Upstream | -552 |
Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 976 |
Motif_676 | RNFG1OS | RNFG1 binding site; Box I; RNFG1 is one of two Rice Nuclear Factors required for phloem-specific gene expression of Rice Tungro Bacilliform Virus (RTBV); Box I is found at -3 to +8 of RTBV promoter; See also RNFG2OS | Upstream | -570 |
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 | Downstream | 1260 |
| | | Downstream | 1258 |
| | | Downstream | 1256 |
| | | Downstream | 1254 |
| | | Upstream | -698 |
| | | Upstream | -700 |
| | | Upstream | -702 |
| | | Upstream | -704 |
| | | Upstream | -706 |
| | | Upstream | -708 |
| | | Upstream | -710 |
| | | Upstream | -712 |
| | | Upstream | -714 |
| | | Upstream | -716 |
| | | Upstream | -718 |
| | | Upstream | -720 |
| | | Upstream | -722 |
| | | Upstream | -724 |
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 | -415 |
Motif_98 | SEF3MOTIFGM | SEF3 binding site; Soybean consensus sequence found in the 5' upstream region of beta-conglycinin (7S globulin) gene; AACCCA(-27bp-)AACCCA; SEF=soybean embryo factor; SEF2; SEF3; SEF4 | Upstream | -419 |
| | | Upstream | -537 |