| Matrix_199 | AT1G69170; SPL9; SPL15; SPL13A; SPL13B | Not Available | | 67.36% |
| Matrix_512 | HAT3 | Not Available | | 67.06% |
| Matrix_85 | SPL5 | Not Available | | 64.92% |
| Matrix_504 | WRKY40 | Not Available | | 63.45% |
| Matrix_137 | SPL1; SPL12 | Not Available | | 63.13% |
| Motif_443 | KN1; BP | The knotted1-like homeobox gene BREVIPEDICELLUS regulates cell differentiation by modulating metabolic pathways. Selective interaction of plant homeodomain proteins mediates high DNA-binding affinity | | 62.64% |
| Matrix_243 | RAP2.12; RAP2.2 | Not Available | | 62.18% |
| Matrix_312 | ARF11; MP; ARF6; IAA21; ARF8; ARF4 | Not Available | | 62.07% |
| Matrix_256 | IXR11; KNAT5; KNAT4; KNAT3 | Not Available | | 62.07% |
| Matrix_334 | AT3G23230 | Not Available | | 61.61% |
| 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 | | 61.21% |
| Matrix_347 | WOX14; WOX10 | Not Available | | 60.90% |
| Matrix_281 | TCP13 | Not Available | | 60.12% |
| 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 | | 60.08% |
| Matrix_460 | NAM; anac025; ATNAC2 | Not Available | | 59.75% |
| Matrix_275 | ZAP1 | Characterization of a zinc-dependent transcriptional activator from Arabidopsis | | 59.32% |
| Matrix_177 | ADOF2 | Not Available | | 59.30% |
| Matrix_418 | KNAT6; KNAT2 | Not Available | | 59.07% |
| Motif_576 | TGACGTVMAMY | TGACGT motif found in the Vigna mungo alpha-Amylase (Amy) gene promoter; Located between -128 and -123; Required for high level expression of alpha-Amylase in the cotyledons of the germinated seeds | | 59.05% |
| 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 | | 58.87% |
| Matrix_325 | WRKY4; WRKY3; WRKY58; ATWRKY34; WRKY20; ATWRKY2 | Not Available | | 58.63% |
| Matrix_411 | DOF5.6 | Not Available | | 58.54% |
| Matrix_425 | TIFY2A | Not Available | | 58.44% |
| Matrix_303 | ATWOX13 | Not Available | | 57.79% |
| Matrix_218 | TIFY2B; TIFY1 | Not Available | | 57.64% |
| Matrix_235 | WRKY67; WRKY64; WRKY63; WRKY66 | Not Available | | 57.61% |
| Motif_26 | GRF7 | Arabidopsis GROWTH-REGULATING FACTOR7 Functions as a Transcriptional Repressor of Abscisic Acid- and Osmotic Stress-Responsive Genes, Including DREB2A | | 57.41% |
| Matrix_78 | AT3G45610 | Not Available | | 57.32% |
| Motif_132 | PIATGAPB | PI found in the Arabidopsis thaliana GAPB gene promoter; Located between -157 and -150; Mutations in the PI 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 | | 57.17% |
| Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | | 57.08% |
| Matrix_319 | TEM1 | Not Available | | 57.03% |
| Matrix_505 | GATA8 | Not Available | | 56.73% |
| Matrix_368 | ATWRKY56; WRKY45; WRKY75; WRKY24 | Not Available | | 56.63% |
| Motif_186 | WBOXNTERF3 | W box found in the promoter region of a transcriptional repressor ERF3 gene in tobacco; May be involved in activation of ERF3 gene by wounding | | 56.58% |
| Matrix_519 | ATDOF2.4 | Not Available | | 56.47% |
| Motif_250 | ACGTOSGLUB1 | ACGT motif found in GluB-1 gene in rice; Required for endosperm-specific expression; Conserved in the 5'-flanking region of glutelin genes; Combination of GCN4, AACA and ACGT motifs was found sufficient to confer a detectable level of endosperm expression | | 56.35% |
| Motif_586 | ASF1MOTIFCAMV | ASF-1 binding site in CaMV 35S promoter; ASF-1 binds to two TGACG motifs; Found in HBP-1 binding site of wheat histone H3 gene; TGACG motifs are found in many promoters and are involved in transcriptional activation of several genes by auxin and/or salicylic acid; May be relevant to light regulation; Binding site of tobacco TGA1a; TGA1a and b show homology to CREB; TGA6 is a new member of the TGA family; Abiotic and biotic stress differentially stimulate as-1 element activity | | 56.34% |
| Matrix_94 | TCP5 | Not Available | | 56.33% |
| Matrix_37 | GATA27 | Not Available | | 56.08% |
| Matrix_289 | WRKY25 | Not Available | | 56.05% |
| Matrix_294 | MEE35 | Not Available | | 55.58% |
| Matrix_159 | TEM2 | Not Available | | 55.58% |
| Motif_502 | MYB98 | The MYB98 subcircuit of the synergid gene regulatory network includes genes directly and indirectly regulated by MYB98 | | 55.40% |
| Matrix_506 | DRNL; ATERF-4 | Not Available | | 55.31% |
| Motif_648 | ARE2 | ARE (antioxidant response element); antioxidant response element of mouse metallothionein-I (MT-I) gene; Consensus sequence of mouse MT-I and MT-II genes, and MT genes isolated from rat, hamster, human, sheep, chicken, Drosophila melanogaster, C. elegans; See ARE1 | | 55.27% |
| Matrix_482 | AT2G25650; AT4G00270 | Not Available | | 55.16% |
| Matrix_82 | TCP17 | Not Available | | 55.11% |
| Motif_80 | AP1SV40 | AP-1 binding site in enhancer regions of SV40 and human metallothionein IIA (hMT IIA) | | 55.11% |
| Motif_189 | CMSRE1IBSPOA | CMSRE-1 (Carbohydrate Metabolite Signal Responsive Element 1) found in the promoter of sweet potato sporamin A gene | | 54.96% |
| Matrix_126 | RBE | Not Available | | 54.92% |
| Matrix_379 | RHL41 | Not Available | | 54.68% |
| Matrix_86 | CRF5; CRF6; CRF4 | Not Available | | 54.52% |
| Matrix_291 | EDF3 | Not Available | | 54.42% |
| Motif_351 | GARE1OSREP1 | Gibberellin-responsive element (GARE) found in the promoter region of a cystein proteinase (REP-1) gene in rice | | 54.15% |
| Matrix_152 | EIL1; AT5G65100 | Not Available | | 54.14% |
| Motif_520 | AMYBOX1 | amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barley | | 54.10% |
| Motif_661 | WBOXATNPR1 | W-box found in promoter of Arabidopsis thaliana NPR1 gene; Located between +70 and +79 in tandem; They were recognized specifically by salicylic acid (SA)-induced WRKY DNA binding proteins; A cluster of WRKY binding sites act as negative regulatory elements for the inducible expression of AtWRKY18; Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expression | | 53.88% |
| Matrix_503 | AT2G37430; AT3G53600 | Not Available | | 53.87% |
| Matrix_197 | NAP | Not Available | | 53.80% |
| Motif_196 | WBOXHVISO1 | SUSIBA2 bind to W-box element in barley iso1 (encoding isoamylase1) promoter | | 53.65% |
| Motif_33 | ACGTCBOX | C-box according to the nomenclature of ACGT elements; One of ACGT elements; Factors groups 1, 2 and 3 have affinity for C-box;RITA-1 binding site | | 53.64% |
| Matrix_100 | AT1G48610 | Not Available | | 53.57% |
| Matrix_198 | STZ; C2H2; AZF3 | Not Available | | 53.31% |
| Motif_440 | TGA1 binding site motif | Hex motif; Binding site of Arabidopsis bZIP protein TGA1 and G box binding factor GBF1; TGA1 and members of the GBF family differ in their DNA binding properties; G-Box-like element;TGA1 and G-box binding factors: two distinct classes of Arabidopsis leucine zipper proteins compete for the G-box-like element TGACGTGG | | 53.28% |
| Matrix_239 | AT5G04390 | Not Available | | 53.09% |
| Matrix_164 | AT1G02030; AT2G45120; AZF2; AT3G60580 | Not Available | | 53.08% |
| Matrix_245 | WRKY62; WRKY38 | Not Available | | 52.98% |
| Motif_685 | PALINDROMICCBOXGM | Palindromic C-box in soybean;bZIP factors, STGA1 and STFs (STF1 and STF2) found in soybean apical hypocotyl, bind to this sequence | | 52.95% |
| Matrix_283 | GATA15; GATA17; AT4G16141; GATA22; GATA23; GATA16; GNC | Not Available | | 52.80% |
| 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 | | 52.73% |
| Matrix_35 | YAB5; YAB3 | Not Available | | 52.72% |
| Motif_437 | ANAERO2CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1) | | 52.48% |
| Matrix_282 | bZIP60 | Not Available | | 52.31% |
| Matrix_426 | CRF1; CRF2 | Not Available | | 52.27% |
| Matrix_415 | WRKY27 | Not Available | | 52.24% |
| Matrix_202 | WRKY71; WRKY28; WRKY8 | Not Available | | 52.23% |
| 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 | | 52.14% |
| Motif_318 | CGCGBOXAT | CGCG box recognized by AtSR1-6 (Arabidopsis thaliana signal-responsive genes); Multiple CGCG elements are found in promoters of many genes; Ca2+/calmodulin binds to all AtSRs | | 52.08% |
| Motif_684 | MNF1ZMPPC1 | MNF1 binding site in maize Ppc1 (phosphoenolpyruvate carboxylase) gene promoter; Involved in light induction | | 52.06% |
| Matrix_188 | SPL4 | Not Available | | 51.96% |
| Matrix_221 | SPL7 | Not Available | | 51.96% |
| Matrix_248 | ZFP5 | Not Available | | 51.95% |
| Matrix_436 | AT3G49930; AZF1 | Not Available | | 51.94% |
| Matrix_182 | ATHB6 | Not Available | | 51.84% |
| 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 | | 51.83% |
| Matrix_515 | ddf2; ATCBF3; CBF1; CBF4 | Not Available | | 51.76% |
| Matrix_96 | TMO6 | Not Available | | 51.56% |
| Matrix_44 | CUC3; anac046; NAC3; ANAC087; ATNAC6; CUC2 | Not Available | | 51.50% |
| Matrix_228 | TGA2 | Not Available | | 51.20% |
| Matrix_14 | ZCW32; AT5G62610 | Not Available | | 50.81% |
| Motif_552 | MRE1 | MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1 | | 50.67% |
| Matrix_374 | AT5G07580; AT5G61590 | Not Available | | 50.64% |
| Matrix_261 | ATERF-1 | Not Available | | 50.58% |
| Matrix_274 | EDF3 | Not Available | | 50.43% |
| Motif_332 | SV40COREENHAN | SV40 core enhancer; Similar sequences found in rbcS genes | | 50.35% |
| Matrix_84 | AtGRF6 | Not Available | | 50.21% |
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