Matrix_10 | STY1 | Not available | Intron | 3870 |
| | | Intron | 1662 |
| | | Upstream | -667 |
Matrix_132 | SOC1 | Not available | Downstream | 4247 |
| | | Upstream | -641 |
| | | Upstream | -642 |
Matrix_196 | TCP20;AT5G41030 | Not available | Downstream | 4143 |
| | | Upstream | -1926 |
Matrix_25 | AP3 | Not available | Upstream | -1338 |
Matrix_269 | FHY3/FAR1 | Not available | Upstream | -932 |
| | | Upstream | -935 |
Matrix_327 | ARR11 | Not available | Intron | 3177 |
Matrix_348 | AT5G51910 | Not available | Upstream | -1924 |
Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Downstream | 4238 |
| | | Downstream | 4229 |
| | | Downstream | 4208 |
Matrix_396 | AP3 | Not available | Intron | 3866 |
Matrix_48 | PI | Not available | Upstream | -640 |
| | | Upstream | -641 |
Matrix_520 | ARR14 | Not available | Intron | 3178 |
Matrix_89 | SOC1 | Genome-wide identification of SOC1 and SVP targets during the floral transition in Arabidopsis | Upstream | -430 |
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 | -625 |
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 | Intron | 770 |
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 | Downstream | 4079 |
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 | 4219 |
Motif_150 | RBCSCONSENSUS | rbcS general consensus sequence; AATCCAA or AATCCAAC | Upstream | -758 |
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 | 3173 |
| | | Intron | 1733 |
Motif_165 | AP3SV40 | AP-3 binding site consensus sequence in enhancer regions of SV40, MMTV, MLV, IL2 | Upstream | -552 |
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 | -755 |
Motif_183 | TRANSINITDICOTS | Context sequence of translational initiation codon in dicots | Upstream | -544 |
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 | Intron | 1724 |
| | | Upstream | -424 |
| | | Upstream | -755 |
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 | Downstream | 4429 |
| | | Upstream | -885 |
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 | 4175 |
| | | Upstream | -626 |
| | | Upstream | -755 |
| | | Upstream | -854 |
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 | 4347 |
| | | Intron | 160 |
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 | 3021 |
Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Downstream | 4354 |
Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Downstream | 4035 |
| | | Downstream | 4029 |
| | | Intron | 1935 |
| | | Intron | 1731 |
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 | 4325 |
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 | 4360 |
| | | Downstream | 4355 |
| | | Downstream | 4233 |
| | | Downstream | 4126 |
| | | Upstream | -972 |
| | | Upstream | -979 |
Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -755 |
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 | 4359 |
| | | Downstream | 4234 |
| | | Downstream | 4125 |
| | | Intron | 2821 |
| | | Upstream | -978 |
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 | 3021 |
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 | Downstream | 4123 |
| | | Upstream | -622 |
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 | Intron | 765 |
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 | 4038 |
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 | Downstream | 4251 |
| | | Downstream | 4090 |
Motif_404 | AACACOREOSGLUB1 | Core of AACA motifs found in rice glutelin genes, involved in controlling the endosperm-specific expression; AACA is also closely associated with the GCN4 motif in all rice glutelin genes and together have been shown to confer endosperm-specific enhancement to the truncated -90 CaMV 35S promoter | Intron | 773 |
Motif_41 | ARR2 | Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators | Upstream | -870 |
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 | 4288 |
Motif_419 | MYB4 binding site motif | Not available | Intron | 773 |
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 | Upstream | -889 |
Motif_495 | TRANSINITMONOCOTS | Context sequence of translational initiation codon in monocots | Upstream | -544 |
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 | 4320 |
| | | Upstream | -761 |
Motif_552 | MRE1 | MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1 | Intron | 2816 |
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 | Downstream | 4244 |
| | | Intron | 3803 |
| | | Intron | 1855 |
| | | Upstream | -644 |
| | | Upstream | -650 |
| | | Upstream | -829 |
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 | 4038 |
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 | Downstream | 4137 |
Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 4288 |
| | | Intron | 773 |
Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Downstream | 4362 |
| | | Downstream | 4359 |
| | | Downstream | 4242 |
| | | Downstream | 4241 |
| | | Downstream | 4238 |
| | | Downstream | 4235 |
| | | Downstream | 4233 |
| | | Downstream | 4230 |
| | | Upstream | -407 |
| | | Upstream | -408 |
| | | Upstream | -409 |
| | | Upstream | -410 |
| | | Upstream | -411 |
| | | Upstream | -412 |
Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Downstream | 4250 |
Motif_626 | ACGTTBOX | T-box according to the nomenclature of ACGT elements; One of ACGT elements; See also ACGTABOX,ACGTCBOX, and CACGTGMOTIF | Downstream | 4462 |
| | | Upstream | -902 |
Motif_630 | WBOXNTCHN48 | W box identified in the region between -125 and -69 of a tobacco class I basic chitinase gene CHN48; NtWRKY1, NtWRKY2 and NtWRKY4 bound to W box; NtWRKYs possibly involved in elicitor-respsonsive transcription of defense genes in tobacco | Upstream | -633 |
Motif_645 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Intron | 1724 |
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 | 4458 |
| | | Downstream | 4457 |
| | | Downstream | 4319 |
| | | Downstream | 4225 |
| | | Downstream | 4203 |
| | | Downstream | 4128 |
| | | Downstream | 4034 |
| | | Intron | 1922 |
| | | Intron | 1730 |
| | | Intron | 1706 |
| | | Upstream | -406 |
| | | Upstream | -642 |
| | | Upstream | -648 |
| | | Upstream | -740 |
| | | Upstream | -762 |
Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 4288 |
| | | Intron | 773 |
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 | 4458 |
| | | Downstream | 4225 |
| | | Downstream | 4203 |
| | | Intron | 1706 |
| | | Upstream | -406 |
| | | Upstream | -642 |
| | | Upstream | -740 |
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 | -733 |
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 | Downstream | 4015 |
| | | Intron | 790 |
| | | Upstream | -420 |