| Matrix_109 | GBF3 | Not available | Upstream | -1492 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -1495 |
| Matrix_14 | ZCW32;AT5G62610 | Not available | Upstream | -1491 |
| Matrix_156 | POC1 | Not available | Upstream | -1492 |
| Matrix_184 | AGL15 | Not available | Upstream | -1814 |
| Matrix_208 | AP1 | Not available | Upstream | -1381 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -1494 |
| Matrix_25 | AP3 | Not available | Upstream | -1172 |
| | | Upstream | -17 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -92 |
| | | Upstream | -89 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -1491 |
| Matrix_345 | POC1 | Not available | Upstream | -1495 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -1190 |
| Matrix_38 | SPL14 | Not available | Upstream | -766 |
| Matrix_43 | AG | Not available | Upstream | -485 |
| Matrix_445 | AG | Not available | Upstream | -485 |
| Matrix_55 | PIF3 | Not available | Upstream | -1492 |
| Matrix_7 | PIF4 | Not available | Upstream | -1491 |
| Matrix_77 | PRR5 | Not available | Upstream | -1492 |
| Matrix_98 | AG | Isolation and characterization of the binding sequences for the product of the Arabidopsis floral homeotic gene AGAMOUS | Upstream | -485 |
| 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 | -1247 |
| 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 | -1367 |
| | | Upstream | -1347 |
| | | Upstream | -229 |
| 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 | Upstream | -1206 |
| 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 | -459 |
| | | Downstream | 384 |
| 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 | 589 |
| | | Downstream | 597 |
| 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 | -1361 |
| | | Upstream | -281 |
| | | Upstream | -273 |
| | | Downstream | 445 |
| Motif_198 | CARGATCONSENSUS | CArG consensus sequence found in the promoter of Arabidopsis SOC1 which is the MADS-box flowering-time gene; FLC is a component of the vernalization (low-temperature) pathway binds directly to this site and blocks transcriptional activation of SOC1 by CONSTANS (CO) | Upstream | -481 |
| Motif_200 | GBOXLERBCS | G box; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis; Binding with GBF | Upstream | -1491 |
| Motif_213 | ZML2 | The CRYPTOCHROME1-Dependent Response to Excess Light Is Mediated through the Transcriptional Activators ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and ZML2 in Arabidopsis | Downstream | 458 |
| 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 | Upstream | -780 |
| | | Downstream | 589 |
| | | Downstream | 597 |
| 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 | Downstream | 471 |
| 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 | Upstream | -1299 |
| | | Upstream | -426 |
| Motif_261 | S1FBOXSORPS1L21 | S1F box conserved both in spinach RPS1 and RPL21 genes encoding the plastid ribosomal protein S1 and L21, respectively; Negative element; Might play a role in downregulating RPS1 and RPL21 promoter activity | Upstream | -393 |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Upstream | -433 |
| | | Upstream | -410 |
| | | Upstream | -407 |
| | | Upstream | -400 |
| | | Upstream | -382 |
| | | Upstream | -164 |
| 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 | -1380 |
| | | Upstream | -557 |
| | | Upstream | -287 |
| | | Upstream | -141 |
| Motif_291 | ABFs binding site motif | Binding site of trans-acting factor EMBP-1; wheat Em gene;Binding site of ABFs; ABFs (ABRE binding factors) were isolated from Arabidopsis by a yeast one-hybrid screening system; Expression ABFs is induced by ABA and various stress treatment; ABFs belongs to a distinct subfamily of bZIP proteins; Involved in ABA-mediated stress-signaling pathway;A plant leucine zipper protein that recognizes an abscisic acid response element | Upstream | -1491 |
| Motif_308 | SP8BFIBSP8AIB | One of SPBF binding site (SP8a); Found at -155 of gSPO-A1 (sporamin) gene, and also at -880 of gB-Amy (beta-amylase) gene in sweet potato; SP8BF recognizes both SP8a and SP8b sequences; See also SP8BFIBSP8BIB; SP8BF activity is also found in tobacco; SP8a found in the 5' upstream region of three differnt genes coding for sporamin and beta-amylase; Binding site of SPF1; SPF1 also binds to the SP8b | Downstream | 591 |
| 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 | -226 |
| 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 | -1829 |
| | | Upstream | -1370 |
| | | Upstream | -165 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Downstream | 589 |
| | | Downstream | 597 |
| 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 | -1828 |
| | | Upstream | -1369 |
| Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Upstream | -1321 |
| 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 | -1380 |
| | | Upstream | -556 |
| | | Upstream | -286 |
| | | Upstream | -140 |
| Motif_375 | ERELEE4 | ERE (ethylene responsive element) of tomato E4 and carnation GST1 genes; GST1 is related to senescence; Found in the 5'-LTR region of TLC1.1 retrotransposon family in Lycopersicon chilense; ERE motifs mediate ethylene-induced activation of the U3 promoter region | Upstream | -749 |
| Motif_377 | SURE2STPAT21 | Sucrose Responsive Element 2 (SURE2); A motif conserved among genes regulated by sucrose; See also SURE1ST; Found between -184 and -156 bp in the patatin (a major tuber protein) gene promoter of potato | Upstream | -439 |
| Motif_382 | CATATGGMSAUR | Sequence found in NDE element in soybean SAUR (Small Auxin-Up RNA) 15A gene promoter; Involved in auxin responsiveness | Upstream | -281 |
| 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 | -735 |
| Motif_411 | PRECONSCRHSP70A | Consensus sequence of PRE (plastid response element) in the promoters of HSP70A in Chlamydomonas; Involved in induction of HSP70A gene by both MgProto and light | Upstream | -1232 |
| Motif_422 | SP8BFIBSP8BIB | One of SPBF binding site (SP8b); Found at -330, -220, and -200 of gSPO-B1 (sporamin) gene, and also at -80 of gB-Amy (beta-amylase) gene; SP8BF recognizes both SP8a and SP8b sequences; See also SP8BFIBSP8AIB; SP8BF activity is also found in tobacco; SP8b found in the 5' upstream region of three differnt genes coding for sporamin and beta-amylase; Binding site of SPF1; SPF1 also binds to the SP8b | Upstream | -388 |
| Motif_437 | ANAERO2CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1) | Upstream | -250 |
| 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 | Upstream | -311 |
| Motif_484 | RAV1-B binding site motif | Binding consensus sequence of an Arabidopsis transcription factor, RAV1; RAV1 specifically binds to DNA with bipartite sequence motifs of RAV1-A (CAACA) and RAV1-B (CACCTG); RAV1 protein contain AP2-like and B3-like domains; The AP2-like and B3-like domains recognize the CAACA and CACCTG motifs, respectively; The expression level of RAV1 were relatively high in rosette leaves and roots; RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants | Upstream | -1361 |
| Motif_495 | TRANSINITMONOCOTS | Context sequence of translational initiation codon in monocots | Upstream | -567 |
| 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 | -1428 |
| | | Upstream | -1143 |
| | | Upstream | -746 |
| | | Upstream | -542 |
| | | Downstream | 481 |
| Motif_520 | AMYBOX1 | amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barley | Upstream | -226 |
| 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 | -435 |
| | | Upstream | -158 |
| | | Downstream | 493 |
| Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -92 |
| | | Upstream | -89 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -1491 |
| Motif_560 | GLUTECOREOS | Core site required for binding of the trans-acting factor in the promoter region of rice glutelin (type 2 glutelin gene family) | Upstream | -770 |
| 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 | -1181 |
| | | Upstream | -490 |
| | | Upstream | -481 |
| Motif_575 | TATABOX3 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene | Upstream | -405 |
| Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -735 |
| | | Upstream | -226 |
| | | Upstream | -75 |
| Motif_614 | MYBGAHV | Central element of gibberellin (GA) response complex (GARC) in high-pI alpha-amylase gene in barley; Similar to c-myb and v-myb consensus binding site; GAmyb binds specifically to the TAACAAA box in vitro; GAmyb is the sole GA-regulated transcriptional factor required for transcriptional activation of the high-pI alpha-amylase; GARC consist of the pyrimidine, TAACAAA and TATCCAC boxes; GARE in RAmy1A gene; GARE and pyrimidine box in RAmy1A are partially involved in sugar repression | Upstream | -226 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -1828 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Upstream | -50 |
| Motif_626 | ACGTTBOX | T-box according to the nomenclature of ACGT elements; One of ACGT elements; See also ACGTABOX,ACGTCBOX, and CACGTGMOTIF | Upstream | -753 |
| 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 | -35 |
| Motif_638 | ABRE binding site motif | Not available | Upstream | -1491 |
| Motif_641 | LRENPCABE | LRE; A positive light regulatory element in tobacco CAB (cab-E) gene; Located at -241 | Upstream | -1492 |
| Motif_649 | 2SSEEDPROTBANAPA | Conserved in many storage-protein gene promoters; May be important for high activity of the napA promoter | Upstream | -1439 |
| Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -64 |
| 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 | -1179 |
| | | Upstream | -1165 |
| | | Upstream | -1157 |
| | | Upstream | -1156 |
| | | Upstream | -1142 |
| | | Upstream | -473 |
| | | Upstream | -458 |
| | | Upstream | -391 |
| | | Upstream | -23 |
| | | Upstream | -11 |
| | | Downstream | 385 |
| | | Downstream | 436 |
| Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -735 |
| | | Upstream | -226 |
| | | Upstream | -75 |
| 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 | -1179 |
| | | Upstream | -1165 |
| | | Upstream | -458 |
| | | Upstream | -23 |
| | | Upstream | -11 |
| | | Downstream | 385 |
| 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 | -1288 |
| | | Upstream | -1264 |
| 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 | -1439 |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Downstream | 605 |
| 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 | Downstream | 589 |
| | | Downstream | 597 |
| Motif_93 | RGATAOS | R-GATA (GATA motif binding factor) binding site; GATA motif is found at -143 to -135 of RTBV promoter; GATA motif is required for phloem-specific gene expression of Rice Tungro Bacilliform Virus (RTBV); See also RNFG1OS, RNFG2OS, and ABFOS | Upstream | -563 |
| 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 | -320 |
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