| Matrix_346 | AtMYB70; MYB73 | Not Available | | 66.64% |
| Matrix_478 | AT1G01250 | Not Available | | 63.00% |
| Matrix_73 | DEAR3; RAP2.9; RAP2.10 | Not Available | | 61.91% |
| Matrix_5 | AT5G51190; ERF104 | Not Available | | 61.09% |
| Motif_483 | ABREMOTIFAOSOSEM | motif A ABRE-like sequence found in rice Osem gene promoter; Essential for activation by VP1; Important for regulation by ABA;TRAB1, bZIP transcription factor, interacts with VP1 and mediates abscisic acid-induced transcritption;ABRE motif A found in the promoter of the rice Osem gene; ACGT-containing ABRE; Required for ABA-responsiveness and VP1 activation; Binding site of TRAB1; Motif A and CE3 are functionally equivalent; TRAB1, bZIP transcription factor, interacts with VP1 and mediates abscisic acid-induced transcritption | | 61.02% |
| Motif_212 | GARE2OSREP1 | Gibberellin-responsive element (GARE) found in the promoter region of a cystein proteinase (REP-1) gene in rice | | 60.97% |
| Motif_626 | ACGTTBOX | T-box according to the nomenclature of ACGT elements; One of ACGT elements; See also ACGTABOX,ACGTCBOX, and CACGTGMOTIF | | 60.92% |
| Motif_86 | ACGTABOX | A-box according to the nomenclature of ACGT elements; One of ACGT elements; Found in ocs gene; RITA-1 binding site; G motif; G motif and TATCCAY motif (a GATA motif as its antisense sequence) are responsible for sugar repression | | 60.92% |
| Motif_407 | CE3OSOSEM | CE3 (Coupling Element 3) found in the promoter of the rice Osem gene; Required for ABA-responsiveness and VP1 activation; Binding site of TRAB1; Motif A and CE3 are functionally equivalent; TRAB1, bZIP transcription factor, interacts with VP1 and mediates abscisic acid-induced transcritption | | 60.80% |
| Matrix_490 | AtMYB77; ATMYB44 | Not Available | | 60.46% |
| Motif_244 | ABRE-like binding site motif | Not Available | | 60.36% |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | | 59.84% |
| Matrix_242 | AT2G25820; AT3G16280; AT4G32800; TINY2; tny | Not Available | | 59.02% |
| 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 | | 58.89% |
| Motif_37 | AtERF-4 | Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression | | 58.88% |
| Motif_421 | TAC1 | Regulation of telomerase in Arabidopsis by BT2, an apparent target of TELOMERASE ACTIVATOR1 | | 58.88% |
| Motif_251 | SUP | The Arabidopsis SUPERMAN protein is able to specifically bind DNA through its single Cys2-His2 zinc finger motif | | 58.88% |
| Motif_371 | DRE-like promoter motif | The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses | | 58.47% |
| Motif_24 | CAMTA3 | Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance | | 58.07% |
| Matrix_377 | AT1G75490; DREB2C; AT2G40350; AT5G18450 | Not Available | | 58.06% |
| Motif_567 | T/GBOXATPIN2 | T/G-box found in tomato proteinase inhibitor II (pin2) and leucine aminopeptidase (LAP) genes; Involved in jasmonate (JA) induction of these genes; bHLH-Leu zipper JAMYC2 and JAMYC10 proteins specifically recognize this motif | | 57.97% |
| Motif_344 | MSACRCYM | MSA (M-specific activator) motif in Catharanthus roseus B-type cyclin (CYM) promoter; Essential for M phase-specific expression; Found at -66 to -58 | | 57.95% |
| Matrix_344 | ATERF15; AT4G18450 | Not Available | | 57.15% |
| Motif_349 | QARBNEXTA | QAR (quantitative activator region) in promoter region of Brassica napus extA extensin gene | | 55.74% |
| Matrix_484 | ATERF13 | Not Available | | 55.71% |
| Motif_623 | MYBCOREATCYCB1 | Myb core in the 18 bp sequence which is able to activate reporter gene without leading to M-phase-specific expression, found in the promoter of Arabidopsis thaliana cyclin B1:1 gene; the 18 bp sequence share homology with a sequence found in the N. sylvestris cyclin B1 promoter | | 55.64% |
| Matrix_395 | AT1G19210; ORA47; AT4G31060; AT5G21960 | Not Available | | 55.58% |
| Motif_54 | LTREATLTI78 | Putative low temperature responsive element (LTRE); Found in Arabidopsis thaliana low-temperature-induced (lti) genes, lti78 and lti65; Repeated four times in lti78 which is also known as cor78 and rd29A; Found also in barley low temperature responsive genes, blt4.2, blt4.6, blt4.9 (lipid transfer genes); cold inducible; See LTRECORE; Also present in rab18, kin1, and kin2; Differential expression of two related, low-temperature-induced genes in Arabidopsis thaliana | | 55.14% |
| Motif_233 | DRE1COREZMRAB17 | DRE1 core found in maize rab17 gene promoter; DRE1 was protected, in in vivo footprinting, by a protein in embryos specifically, but in leaves, was protected when was treated with ABA and drought; rab17 is expressed during late embryogenesis, and is induced by ABA | | 55.14% |
| Motif_72 | GADOWNAT | Sequence present in 24 genes in the GA-down regulated d1 cluster (106 genes) found in Arabidopsis seed germination; This motif is similar to ABRE | | 55.14% |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | | 55.11% |
| 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 | | 55.09% |
| Motif_643 | DRE2COREZMRAB17 | DRE2 core found in maize rab17 gene promoter; DBF1 and DBF2 bound to DRE2; rab17 is expressed during late embryogenesis, and is induced by ABA | | 55.09% |
| 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 | | 55.03% |
| Motif_574 | MYB2 binding site motif | MYB transcription factors in plants | | 54.77% |
| Matrix_45 | DRN | Not Available | | 54.47% |
| Motif_141 | BP5OSWX | OsBP-5 (a MYC protein) binding site in Wx promoter | | 54.35% |
| Motif_179 | CACGTGMOTIF; BES1; PIF4; PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling;A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana; CACGTG motif; G-box; Binding site of Arabidopsis GBF4; C. roseus G-box binding factor 1 (CrGBF1) and 1 (CrGBF2) can act as transcriptional repressors of the Str promoter via direct interaction with the G-box; Essential for expression of beta-phaseolin gene during embryogenesis in bean, tobacco, Arabidopsis; Tomato Pti4 (ERF) regulates defense-related gene expression via GCC box and non-GCC box cis-element (Myb1 (GTTAGTT) and G-box (CACGTG)); Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein; Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | | 54.30% |
| 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 | | 54.30% |
| Motif_218 | ABRERATCAL | ABRE-related sequence or Repeated sequence motifs identified in the upstream regions of 162 Ca(2+)-responsive upregulated genes; see also ABRE | | 54.00% |
| Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | | 52.64% |
| Matrix_147 | ERF3; AT1G80580 | Not Available | | 52.57% |
| Matrix_295 | ERF1 | Not Available | | 52.43% |
| Motif_65 | BS1EGCCR | BS1 (binding site 1) found in E. gunnii Cinnamoyl-CoA reductase (CCR) gene promoter; nuclear protein binding site; Required for vascular expression | | 52.13% |
| Motif_63 | ABRELATERD1 | ABRE-like sequence (from -199 to -195) required for etiolation-induced expression of erd1 (early responsive to dehydration) in Arabidopsis | | 52.08% |
| Matrix_371 | MYB7; AtMYB6; AtMYB32; ATMYB4 | Not Available | | 51.80% |
| Matrix_360 | ORA59 | Not Available | | 51.12% |
| Matrix_243 | RAP2.12; RAP2.2 | Not Available | | 50.93% |
| Matrix_164 | AT1G02030; AT2G45120; AZF2; AT3G60580 | Not Available | | 50.82% |
| Matrix_436 | AT3G49930; AZF1 | Not Available | | 50.70% |
| Matrix_7 | PIF4 | Not Available | | 50.70% |
| Motif_454 | DRECRTCOREAT | Core motif of DRE/CRT (dehydration-responsive element/C-repeat) cis-acting element found in many genes in Arabidopsis and in rice; Os DREB1A bound to GCCGAC more preferentially than to ACCGAC whereas At DREB1A bound to both GCCGAC and ACCGAC efficiently; Maize ZmDREB1A bound to DRE; HaDREB2 in Helianthus annuus (sunflower) | | 50.65% |
| Matrix_321 | HRD | Not Available | | 50.57% |
| 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 | | 50.19% |
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