| Matrix_10 | STY1 | Not available | Intron | 2158 |
| | | Intron | 2154 |
| | | Upstream | -608 |
| | | Upstream | -612 |
| Matrix_115 | AGL15 | Not available | Upstream | -669 |
| Matrix_123 | FUSCA3 | Not available | Intron | 2073 |
| | | Intron | 2069 |
| | | Upstream | -719 |
| Matrix_135 | ABI3 | Not available | Upstream | -720 |
| Matrix_148 | WRKY60 | Not available | Upstream | -886 |
| Matrix_153 | AP2 | Not available | Upstream | -1504 |
| | | Upstream | -1505 |
| Matrix_19 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -1505 |
| Matrix_197 | NAP | Not available | Upstream | -887 |
| Matrix_220 | WRKY18 | Not available | Upstream | -887 |
| Matrix_235 | WRKY67;WRKY64;WRKY63;WRKY66 | Not available | Upstream | -888 |
| Matrix_25 | AP3 | Not available | Upstream | -519 |
| Matrix_263 | WRKY33;WRKY19;WRKY32 | Not available | Upstream | -887 |
| Matrix_290 | AP2 | Not available | Upstream | -1633 |
| | | Upstream | -1634 |
| Matrix_3 | WRKY48 | Not available | Upstream | -887 |
| Matrix_370 | WRKY50;WRKY51 | Not available | Upstream | -887 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -753 |
| Matrix_39 | AP1 | Not available | Downstream | 3980 |
| | | Upstream | -525 |
| Matrix_396 | AP3 | Not available | Intron | 3819 |
| Matrix_414 | AGL15 | Not available | Upstream | -536 |
| Matrix_424 | MYB59 | Not available | Intron | 1056 |
| Matrix_470 | WRKY18 | Not available | Upstream | -887 |
| Matrix_48 | PI | Not available | Upstream | -527 |
| Matrix_497 | AP3 | Not available | Downstream | 4240 |
| Matrix_504 | WRKY40 | Not available | Upstream | -888 |
| Matrix_79 | FUS3 | Not available | Upstream | -720 |
| 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 | 4396 |
| | | Downstream | 4205 |
| | | Downstream | 4070 |
| | | Upstream | -1613 |
| 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 | Upstream | -1498 |
| 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 | -753 |
| 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 | 4270 |
| 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 | -1507 |
| Motif_16 | -300ELEMENT | Present upstream of the promoter from the B-hordein gene of barley and the alpha-gliadin, gamma-gliadin, and low molecular weight glutenin genes of wheat; See S000001 -300CORE; See S000002 -300MOTIF | Upstream | -692 |
| 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 | Downstream | 4151 |
| | | Upstream | -626 |
| 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 | -1507 |
| Motif_195 | TATABOX4 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation | Upstream | -1398 |
| Motif_22 | RYREPEATLEGUMINBOX | RY repeat (CATGCAY) or legumin box found in seed-storage protein genes in legume such as soybean | Upstream | -723 |
| | | Upstream | -724 |
| 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 | Downstream | 4151 |
| | | Upstream | -548 |
| | | Upstream | -559 |
| | | Upstream | -626 |
| | | Upstream | -928 |
| | | Upstream | -1402 |
| Motif_235 | C8GCARGAT | Binding site of plant MADS-domain protein AGL15; CArG motif with a longer A/T-rich core;A variant of CArG motif, with a longer A/T-rich core; Binding site for AGL15 (AGAMOUS-like 15) | Downstream | 3966 |
| 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 | Intron | 1055 |
| 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 | 3972 |
| | | Intron | 166 |
| | | Upstream | -553 |
| Motif_26 | GRF7 | Arabidopsis GROWTH-REGULATING FACTOR7 Functions as a Transcriptional Repressor of Abscisic Acid- and Osmotic Stress-Responsive Genes, Including DREB2A | Downstream | 4210 |
| Motif_263 | RYREPEATVFLEB4;ABI3 | RY repeat motif; quantitative seed expression; Gene: Vicia faba LeB4; Soybean glycinin (Gy2); other dicot and monocot seed protein genes; Sph box found in rice Osem gene promoter; Binding site of Arabidopsis B3-domain-containing transcription factor FUS3; TRAB1, bZIP transcription factor, interacts with VP1 and mediates abscisic acid-induced transcritption; FUS3 protein physically interact with two RY elements present in the AtGA3ox promoter;RY repeats are conserved in the 5 prime-flanking region of legume seed protein genes. Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene product | Upstream | -723 |
| 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 | Intron | 1051 |
| | | Upstream | -889 |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Downstream | 4331 |
| | | Downstream | 4323 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -1496 |
| | | Upstream | -1601 |
| 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 | 4276 |
| 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 | 4332 |
| | | Downstream | 4324 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Downstream | 4151 |
| | | Upstream | -626 |
| 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 | 4328 |
| | | Upstream | -903 |
| | | Upstream | -911 |
| Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Intron | 185 |
| | | Intron | 180 |
| | | Upstream | -885 |
| | | Upstream | -1596 |
| 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 | Intron | 3308 |
| Motif_351 | GARE1OSREP1 | Gibberellin-responsive element (GARE) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -1402 |
| Motif_357 | NTBBF1ARROLB | NtBBF1(Dof protein from tobacco) binding site in Agrobacterium rhizogenes rolB gene; Found in regulatory domain B (-341 to -306); Required for tissue-specific expression and auxin induction | Upstream | -46 |
| | | Upstream | -622 |
| 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 | Downstream | 4010 |
| 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 | 3960 |
| | | Upstream | -770 |
| Motif_419 | MYB4 binding site motif | Not available | Intron | 1055 |
| Motif_425 | ANAC013;ANAC016;ANAC017;ANAC053;ANAC078 | A membrane-bound NAC transcription factor is a regulator of mitochondrial retrograde regulation involved in oxidative stress responses in Arabidopsis thaliana | Upstream | -1599 |
| 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 | 4197 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -94 |
| | | Upstream | -753 |
| | | Upstream | -755 |
| 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 | -1507 |
| Motif_469 | QELEMENTZMZM13 | Q(quantitative)-element in maize ZM13 gene promoter; Found at -107 to -102; Involved in expression enhancing activity; ZM13 is a maize homolog of tomato LAT52 gene; ZM13 is a pollen-specific maize gene | Intron | 1052 |
| Motif_470 | MYB98 | MYB98 positively regulates a battery of synergid-expressed genes encoding filiform apparatus localized proteins | Upstream | -1584 |
| Motif_476 | XYLAT | cis-element identified among the promoters of the core xylem gene set | Upstream | -772 |
| Motif_495 | TRANSINITMONOCOTS | Context sequence of translational initiation codon in monocots | Downstream | 4188 |
| 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 | -599 |
| | | Upstream | -1501 |
| Motif_511 | RYREPEATGMGY2 | RY repeat motif (CATGCAT); Present in the 5' region of the soybean glycinin gene (Gy2) | Upstream | -723 |
| | | Upstream | -724 |
| Motif_520 | AMYBOX1 | amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barley | Upstream | -1402 |
| 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 | Intron | 3327 |
| | | Intron | 1059 |
| 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 | 3304 |
| | | Upstream | -1489 |
| 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 | Downstream | 4010 |
| Motif_596 | WRKY11 | Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function | Intron | 1053 |
| Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 4157 |
| | | Downstream | 3960 |
| | | Intron | 179 |
| | | Upstream | -771 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Downstream | 4331 |
| | | Downstream | 4328 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Downstream | 4061 |
| | | Intron | 1914 |
| 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 | -723 |
| | | Upstream | -725 |
| 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 | 4071 |
| | | Downstream | 3985 |
| | | Downstream | 3984 |
| | | Upstream | -535 |
| | | Upstream | -588 |
| | | Upstream | -643 |
| | | Upstream | -660 |
| | | Upstream | -797 |
| | | Upstream | -1486 |
| | | Upstream | -1487 |
| | | Upstream | -1602 |
| | | Upstream | -1611 |
| | | Upstream | -1612 |
| Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 4157 |
| | | Downstream | 3960 |
| | | Intron | 179 |
| | | Upstream | -771 |
| 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 | Downstream | 3985 |
| | | Upstream | -643 |
| | | Upstream | -797 |
| | | Upstream | -1487 |
| 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 | -94 |
| | | Upstream | -96 |
| | | Upstream | -98 |
| | | Upstream | -100 |
| | | Upstream | -752 |
| | | Upstream | -754 |
| | | Upstream | -756 |
| | | Upstream | -758 |
| | | Upstream | -760 |
| | | Upstream | -762 |
| 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 | -677 |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Downstream | 4009 |
| 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 | Downstream | 4204 |
| Motif_88 | MYB2AT | Binding site for ATMYB2, an Arabidopsis MYB homolog; ATMYB2 binds oligonucleotides that contained a consensus MYB recognition sequence (TAACTG), such as is in the SV40 enhancer and the maize bronze-1 promoter; ATMYB2 is involved in regulation of genes that are responsive to water stress in Arabidopsis | Upstream | -626 |
| 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 | -1584 |
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