| Matrix_101 | ERF5 | Not available | Downstream | 1819 |
| Matrix_119 | RRTF1 | Not available | Downstream | 1818 |
| Matrix_138 | RRTF1 | Not available | Downstream | 1818 |
| Matrix_146 | ORA47 | Not available | Downstream | 1819 |
| Matrix_147 | ERF3;AT1G80580 | Not available | Downstream | 1817 |
| Matrix_155 | RAP2.6;ERF110;ABR1 | Not available | Downstream | 1818 |
| Matrix_190 | ATERF1 | Not available | Downstream | 1819 |
| Matrix_211 | MYB3 | Not available | Upstream | -1237 |
| Matrix_224 | ERF1 | Not available | Downstream | 1818 |
| Matrix_234 | RAP2.3 | Not available | Downstream | 1819 |
| Matrix_243 | RAP2.12;RAP2.2 | Not available | Downstream | 1818 |
| Matrix_248 | ZFP5 | Not available | Downstream | 2133 |
| Matrix_25 | AP3 | Not available | Upstream | -1168 |
| Matrix_252 | RAP2.6 | Not available | Downstream | 1819 |
| Matrix_26 | ATMYB3;MYB24 | Not available | Upstream | -1240 |
| | | Upstream | -1241 |
| Matrix_261 | ATERF-1 | Not available | Downstream | 1818 |
| Matrix_272 | DEAR4 | Not available | Downstream | 1819 |
| Matrix_287 | ERF2 | Not available | Downstream | 1819 |
| Matrix_288 | RAP2.3 | Not available | Downstream | 1818 |
| Matrix_295 | ERF1 | Not available | Downstream | 1817 |
| Matrix_30 | AtSPL8 | Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains | Upstream | -1658 |
| Matrix_315 | MYB111 | Not available | Upstream | -1238 |
| | | Upstream | -1239 |
| Matrix_321 | HRD | Not available | Downstream | 1818 |
| Matrix_326 | AT5G07310;Rap2.6L;AT5G61890 | Not available | Downstream | 1818 |
| Matrix_334 | AT3G23230 | Not available | Downstream | 1818 |
| Matrix_343 | AT2G33710 | Not available | Downstream | 1819 |
| Matrix_355 | ERF10;ERF11 | Not available | Downstream | 1818 |
| Matrix_360 | ORA59 | Not available | Downstream | 1817 |
| Matrix_363 | RAP2.3 | Not available | Downstream | 1818 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -1160 |
| Matrix_374 | AT5G07580;AT5G61590 | Not available | Downstream | 1818 |
| Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Downstream | 1818 |
| Matrix_378 | ATERF1 | Not available | Downstream | 1819 |
| Matrix_395 | AT1G19210;ORA47;AT4G31060;AT5G21960 | Not available | Downstream | 1817 |
| Matrix_406 | ATERF-7 | Not available | Downstream | 1817 |
| Matrix_409 | DEAR3 | Not available | Downstream | 1818 |
| Matrix_414 | AGL15 | Not available | Upstream | -1100 |
| | | Upstream | -1167 |
| | | Upstream | -1172 |
| Matrix_426 | CRF1;CRF2 | Not available | Downstream | 1818 |
| Matrix_448 | ATERF6 | Not available | Downstream | 1818 |
| Matrix_45 | DRN | Not available | Downstream | 1817 |
| Matrix_454 | AT1G77200;ATERF38;AT4G16750;AT5G52020 | Not available | Downstream | 1818 |
| Matrix_462 | ATERF-8 | Not available | Downstream | 1817 |
| Matrix_473 | RRTF1 | Not available | Downstream | 1819 |
| Matrix_484 | ATERF13 | Not available | Downstream | 1817 |
| Matrix_493 | AT1G22985;AT1G71130 | Not available | Downstream | 1818 |
| Matrix_50 | ATERF14;AT5G43410 | Not available | Downstream | 1818 |
| Matrix_506 | DRNL;ATERF-4 | Not available | Downstream | 1818 |
| Matrix_517 | ERF12 | Not available | Downstream | 1817 |
| Matrix_57 | WIN1;SHN3;SHN2 | Not available | Downstream | 1818 |
| Matrix_84 | AtGRF6 | Not available | Upstream | -1191 |
| | | Upstream | -1192 |
| | | Upstream | -1225 |
| | | Upstream | -1226 |
| Matrix_86 | CRF5;CRF6;CRF4 | Not available | Downstream | 1818 |
| Matrix_91 | CRF3 | Not available | Downstream | 1818 |
| Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -1114 |
| 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 | -1109 |
| 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 | -984 |
| | | Upstream | -986 |
| | | Upstream | -988 |
| | | Upstream | -990 |
| | | Upstream | -992 |
| 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 | -669 |
| 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 | -764 |
| 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 | Downstream | 2205 |
| | | Upstream | -669 |
| | | Upstream | -764 |
| Motif_22 | RYREPEATLEGUMINBOX | RY repeat (CATGCAY) or legumin box found in seed-storage protein genes in legume such as soybean | Upstream | -666 |
| 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 | -764 |
| | | Upstream | -1251 |
| 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 | -1240 |
| Motif_292 | MYBPZM | Core of consensus maize P (myb homolog) binding site; 6 bp core; Maize P gene specifies red pigmentation of kernel pericarp, cob, and other floral organs; P binds to A1 gene, but not Bz1 gene; Maize C1 (myb homolog) activates both A1 and Bz1 genes | Upstream | -1713 |
| Motif_313 | ERF1 BS in AtCHI-B | Core of GCC-box found in many pathogen-responsive genes such as PDF1.2, Thi2.1, and PR4; Has been shown to function as ethylene-responsive element; Appears to play important roles in regulating jasmonate-responsive gene expression; Tomato Pti4 (ERF) regulates defence-related gene expression via GCC box and non-GCC box cis elements (Myb1 (GTTAGTT) and G-box(CACGTG)); Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1;Molecular responses to dehydration and low temperature | Downstream | 1816 |
| 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 | Downstream | 2140 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -764 |
| Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Upstream | -1092 |
| 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 | -1126 |
| Motif_419 | MYB4 binding site motif | Not available | Upstream | -1240 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -327 |
| | | Upstream | -984 |
| | | Upstream | -986 |
| | | Upstream | -988 |
| | | Upstream | -990 |
| | | Upstream | -992 |
| | | Upstream | -994 |
| 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 | -669 |
| Motif_470 | MYB98 | MYB98 positively regulates a battery of synergid-expressed genes encoding filiform apparatus localized proteins | Upstream | -1241 |
| Motif_476 | XYLAT | cis-element identified among the promoters of the core xylem gene set | Upstream | -1729 |
| Motif_495 | TRANSINITMONOCOTS | Context sequence of translational initiation codon in monocots | Downstream | 2057 |
| | | Upstream | -896 |
| Motif_502 | MYB98 | The MYB98 subcircuit of the synergid gene regulatory network includes genes directly and indirectly regulated by MYB98 | Upstream | -1089 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Upstream | -1239 |
| Motif_520 | AMYBOX1 | amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barley | Downstream | 2140 |
| 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 | -1265 |
| 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 | Downstream | 2142 |
| Motif_552 | MRE1 | MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1 | Upstream | -664 |
| 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 | -477 |
| | | Upstream | -582 |
| | | Upstream | -602 |
| | | Upstream | -610 |
| | | Upstream | -1175 |
| Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 2140 |
| 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 | Downstream | 2140 |
| 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 | -667 |
| Motif_649 | 2SSEEDPROTBANAPA | Conserved in many storage-protein gene promoters; May be important for high activity of the napA promoter | Downstream | 2172 |
| 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 | 1830 |
| | | Downstream | 1826 |
| | | Downstream | 1809 |
| | | Upstream | -895 |
| | | Upstream | -1100 |
| | | Upstream | -1738 |
| Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Downstream | 2140 |
| 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 | -1100 |
| Motif_688 | AMMORESIVDCRNIA1 | Motif (IVD) found in the Chlamydomonas Nia1 gene promoter; Located between -51 and -42; Involved in Nia1 transcription repression | Downstream | 2134 |
| 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 | -328 |
| | | Upstream | -330 |
| | | Upstream | -332 |
| | | Upstream | -334 |
| | | Upstream | -983 |
| | | Upstream | -985 |
| | | Upstream | -987 |
| | | Upstream | -989 |
| | | Upstream | -991 |
| | | Upstream | -993 |
| | | Upstream | -995 |
| | | Upstream | -997 |
| | | Upstream | -999 |
| | | Upstream | -1001 |
| | | Upstream | -1159 |
| | | Upstream | -1161 |
| 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 | Downstream | 2172 |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Upstream | -834 |
| 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 | 1757 |
| | | Upstream | -1244 |
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