| Matrix_101 | ERF5 | Not available | Intron | 1424 |
| Matrix_110 | ATABI4;AT3G57600 | Not available | Intron | 1425 |
| Matrix_117 | ANT | Not available | Intron | 1459 |
| Matrix_123 | FUSCA3 | Not available | Intron | 2301 |
| Matrix_154 | AT1G22190;AT1G36060;AT1G64380;RAP2.4;AT2G20880;AT2G22200;AT4G13620;AT4G28140;AT4G39780;AT5G65130 | Not available | Intron | 1425 |
| Matrix_19 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Intron | 2681 |
| Matrix_215 | ARF1 | ARF1, a transcription factor that binds to auxin response elements | Upstream | -879 |
| Matrix_25 | AP3 | Not available | Intron | 1383 |
| Matrix_250 | ADAP;AT1G79700;WRI1;ANT | Not available | Intron | 1456 |
| Matrix_261 | ATERF-1 | Not available | Intron | 1424 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -698 |
| | | Upstream | -695 |
| Matrix_305 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -829 |
| Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Intron | 1427 |
| Matrix_39 | AP1 | Not available | Upstream | -888 |
| Matrix_395 | AT1G19210;ORA47;AT4G31060;AT5G21960 | Not available | Intron | 1426 |
| Matrix_396 | AP3 | Not available | Upstream | -1818 |
| Matrix_409 | DEAR3 | Not available | Intron | 1426 |
| Matrix_421 | GLK1 | Not available | Upstream | -807 |
| Matrix_48 | PI | Not available | Intron | 984 |
| Matrix_91 | CRF3 | Not available | Intron | 1424 |
| 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 | -980 |
| | | Intron | 1393 |
| Motif_125 | BOXIINTPATPB | Box II found in the tobacco plastid atpB gene promoter; Conserved in several NCII (nonconsensus type II) promoters of plastid genes; Important for the activity of this NCII promoter | Intron | 1718 |
| 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 | -747 |
| 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) | Intron | 2021 |
| 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 | Upstream | -862 |
| | | Intron | 1417 |
| Motif_150 | RBCSCONSENSUS | rbcS general consensus sequence; AATCCAA or AATCCAAC | Upstream | -803 |
| Motif_153 | MARABOX1 | A-box found in SAR(scaffold attachment region; or matrix attachment region, MAR) | Upstream | -938 |
| 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 | Intron | 1604 |
| Motif_171 | TCP binding consensus | found enriched in peaks in chip-seq data for SEP3 | Upstream | -1748 |
| Motif_174 | SREATMSD | sugar-repressive element (SRE) found in 272 of the 1592 down-regulated genes after main stem decapitation in Arabidopsis | Upstream | -830 |
| Motif_184 | PROXBBNNAPA | prox B (proximal portion of B-box) found in napA gene of Brassica napus; CA-rich sequence; Found between -130 and -124; Required for seed specific expression and ABA responsiveness; 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 | Intron | 1431 |
| 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 | -862 |
| | | Intron | 1417 |
| 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 | -1805 |
| 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 | -863 |
| | | Intron | 1417 |
| | | Intron | 2730 |
| | | Intron | 2751 |
| 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 | Intron | 2715 |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Upstream | -941 |
| | | Upstream | -929 |
| | | Upstream | -787 |
| | | Intron | 1621 |
| 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 | -476 |
| Motif_305 | SP1SV40 | SP-1 binding site (GC box) in enhancer regions of SV40 and human metallothionein IIA (hMT IIA) | Intron | 1427 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -492 |
| | | Upstream | -486 |
| | | Upstream | -480 |
| | | Intron | 1407 |
| | | Intron | 1443 |
| 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 | -935 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Intron | 2686 |
| 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 | -938 |
| | | Upstream | -934 |
| | | Intron | 2717 |
| 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 | -757 |
| 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 | -824 |
| Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | Upstream | -1816 |
| 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 | -475 |
| 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 | 1465 |
| 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 | Upstream | -654 |
| Motif_437 | ANAERO2CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1) | Intron | 2027 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -747 |
| | | Upstream | -745 |
| 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 | Upstream | -862 |
| | | Intron | 1417 |
| Motif_450 | E2FCONSENSUS | E2F consensus sequence of all different E2F-DP-binding motifs that were experimentally verified in plants | Upstream | -878 |
| 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 | Upstream | -806 |
| Motif_525 | CRTDREHVCBF2 | Preferred sequence for AP2 transcriptional activator HvCBF2 of barley; Core CRT/DRE motif; HvCBF2 bound to a (G/a)(T/c)CGAC core motif; DNA binding is regulated by temperature | Upstream | -822 |
| Motif_536 | TBOXATGAPB | Tbox found in the Arabidopsis thaliana GAPB gene promoter; Located between -94 and -89 (T1) and also between -84 and -79 (T2); Mutations in the Tbox resulted in reductions of light-activated gene transcription; GAPB encodes the B subunit of chloroplast glyceraldehyde-3-phosphate dehydrogenase(GADPH) of A.T.; Promoter analysis of the nuclear gene encoding the chloroplast glyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsis thaliana | Upstream | -799 |
| Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -695 |
| 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 | -873 |
| | | Intron | 2721 |
| Motif_570 | POLASIG2 | PolyA signal; poly A signal found in rice alpha-amylase; -10 to -30 in the case of animal genes | Upstream | -1915 |
| | | Intron | 1510 |
| Motif_591 | CBFHV | Binding site of barley CBF1, and also of barley CBF2; CBF = C-repeat (CRT) binding factors; CBFs are also known as dehydration-responsive element (DRE) binding proteins (DREBs) | Upstream | -822 |
| Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -653 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -843 |
| | | Upstream | -842 |
| | | Upstream | -841 |
| | | Upstream | -840 |
| | | Upstream | -839 |
| | | Upstream | -838 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Intron | 1464 |
| Motif_628 | TATCCAOSAMY | TATCCA element found in alpha-amylase promoters of rice at positions ca.90 to 150bp upstream of the transcription start sites; Binding sites of OsMYBS1, OsMYBS2 and OsMYBS3 which mediate sugar and hormone regulation of alpha-amylase gene expression; See also AMYBOX2 | Intron | 5078 |
| Motif_649 | 2SSEEDPROTBANAPA | Conserved in many storage-protein gene promoters; May be important for high activity of the napA promoter | Intron | 1432 |
| 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 | -981 |
| | | Upstream | -875 |
| | | Upstream | -831 |
| | | Upstream | -806 |
| | | Upstream | -679 |
| | | Upstream | -678 |
| | | Upstream | -657 |
| | | Intron | 1614 |
| | | Intron | 1615 |
| | | Intron | 2009 |
| 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 | Upstream | -992 |
| Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -653 |
| 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 | Intron | 2009 |
| 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 | -748 |
| | | Upstream | -746 |
| | | Upstream | -744 |
| | | Upstream | -742 |
| | | Upstream | -740 |
| | | Upstream | -738 |
| | | Intron | 1398 |
| | | Intron | 1400 |
| | | Intron | 1589 |
| | | Intron | 1732 |
| 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 | Intron | 1432 |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Intron | 1646 |
| 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 | -532 |
| 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 | -762 |
| | | Upstream | -648 |
| | | Intron | 2682 |
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