| Motif_166 | RAP2.2 | Transcription factor RAP2.2 and its interacting partner SINAT2: stable elements in the carotenogenesis of Arabidopsis leaves | | 77.78% |
| Motif_667 | TATABOXOSPAL | Binding site for OsTBP2, found in the promoter of rice pal gene encoding phenylalanine ammonia-lyase; OsTFIIB stimulated the DNA binding and bending activities of OsTBP2 and synergistically enhanced OsTBP2-mediated transcription from the pal promoter | | 72.22% |
| Motif_570 | POLASIG2 | PolyA signal; poly A signal found in rice alpha-amylase; -10 to -30 in the case of animal genes | | 66.67% |
| Motif_297 | Bellringer/replumless/pennywise BS1 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | | 66.67% |
| Motif_475 | GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | | 66.67% |
| Motif_575 | TATABOX3 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene | | 66.67% |
| Matrix_513 | SOL1; TSO1; TCX2 | Not Available | | 63.34% |
| Motif_673 | Bellringer/replumless/pennywise BS2 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | | 62.60% |
| Matrix_163 | AT2G20110 | Not Available | | 61.99% |
| 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 | | 61.11% |
| 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) | | 61.11% |
| 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 | | 61.11% |
| Matrix_474 | ANAC014; ANAC062; NTL9; TIP | Not Available | | 60.50% |
| Matrix_442 | AT5G62260 | Not Available | | 58.87% |
| Matrix_205 | AGL15 | Not Available | | 57.43% |
| Matrix_523 | FUSCA3 | Not Available | | 57.43% |
| 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 | | 57.04% |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | | 55.56% |
| 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 | | 55.56% |
| Motif_253 | S1FSORPL21 | S1F binding site (S1 site) in spinach (S.o.) RPL21 gene encoding the plastid ribosomal protein L21; Negative element; Might play a role in downregulating RPL21 promoter activity | | 55.56% |
| 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 | | 55.56% |
| Motif_138 | RAP2.2 | Transcription factor RAP2.2 and its interacting partner SINAT2: stable elements in the carotenogenesis of Arabidopsis leaves | | 55.56% |
| Motif_537 | CONSERVED11NTZMATP1 | Conserved 11 nt sequence found in the maize mitochondrial atp1 promoter; Located between -5 and +6; Essential for the expression | | 55.56% |
| Motif_187 | AT1BOX | AT-1 box (AT-rich element) found in the promoter region of the genes for tobacco chlorophyll a/b binding protein (cab) and small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS); Deletion of a region containing the AT-1 site in the tomato RBCS3A gene strongly inhibited reporter gene expression, whereas AT-1 site in N. plumbaginifolia CAB gene (cab-E) is in a negative element | | 55.56% |
| Motif_370 | TATABOX2 | TATA box; TATA box found in the 5'upstream region of pea legA gene; sporamin A of sweet potato; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation | | 55.56% |
| Motif_500 | D1GMAUX28 | D1; DNase I protected sequence found in the soybean auxin responsive gene, Aux28, promoter; D1 and D4 share a very similar core sequence TAGTXXCTGT and TAGTXCTGT, respectively; D1/D4-like sequence were identified in several other auxin-responsive genes; Binding site of GmGT-2 which is the GT-2 family of transcription factors; GmGT-2 are down-regulated by light in a phytochrome-dependent manner | | 55.56% |
| 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 | | 55.56% |
| 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 | | 55.56% |
| Motif_49 | TATAPVTRNALEU | TATA-like motif; A TATA-like sequence found in Phaseolus vulgaris tRNALeu gene promoter; Frequently observed upstream of plant tRNA genes; Found in maize glycolytic glyceraldehyde-3-phospate dehydrogenase 4 (GapC4) gene promoter; Binding site of TATA binding protein (TBP) | | 55.56% |
| Motif_108 | ROOTMOTIFTAPOX1 | Motif found both in promoters of rolD | | 55.56% |
| 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 | | 55.56% |
| Motif_295 | HY5 | Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression | | 55.56% |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | | 55.56% |
| Matrix_51 | LFY | Not Available | | 55.11% |
| Matrix_354 | AHL12 | Not Available | | 54.59% |
| Matrix_168 | AHL25 | Not Available | | 54.47% |
| Matrix_341 | HMGA | Not Available | | 54.39% |
| Matrix_430 | TOE2 | Not Available | | 53.33% |
| Matrix_29 | AP1 | Not Available | | 53.16% |
| Matrix_262 | ATGRP2B; CSDP2 | Not Available | | 52.43% |
| Matrix_81 | YAB1 | Not Available | | 51.91% |
| Matrix_391 | AHL20 | Not Available | | 51.72% |
| Matrix_204 | WOX13 | Not Available | | 51.58% |
| Motif_158 | ZDNAFORMINGATCAB1 | Z-DNA-forming sequence found in the Arabidopsis chlorophyll a/b binding protein gene (cab1) promoter; Involved in light-dependent developmental expression of the gene; Z-box; Activation of Z-box containing promoters is regulated by downstream regulatory components, COP1 and HY5; phyB and CRY1 photoreceptors act redundantly to induce Z-box containing promoters in white light; Identification of upstream regulatory elements involved in the developmental expression of the Arabidopsis thaliana cab1 gene | | 51.49% |
| Motif_521 | RBCSBOX3PS | rbcS box III; 5' upstream region (-114) of pea rbcS gene; binding with trans factor GT-1; one of GT-1 boxes | | 51.49% |
| 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 | | 51.49% |
| Motif_547 | AG BS in AP3 | The CArG boxes in the promoter of the Arabidopsis floral organ identity gene APETALA3 mediate diverse regulatory effects | | 51.49% |
| Motif_590 | MYB3 binding site motif | Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses | | 51.49% |
| 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 | | 51.49% |
| Matrix_390 | GT-1 | Not Available | | 51.40% |
| Matrix_157 | LHY; RVE2 | Not Available | | 51.35% |
| Matrix_479 | TOE1 | Not Available | | 51.30% |
| Matrix_318 | ATHB16 | Not Available | | 51.21% |
| Matrix_54 | AHL20 | Not Available | | 51.01% |
| Matrix_46 | AT4G21895 | Not Available | | 50.30% |
| Matrix_444 | AT1G19485; AT4G17950 | Not Available | | 50.12% |
| Motif_165 | AP3SV40 | AP-3 binding site consensus sequence in enhancer regions of SV40, MMTV, MLV, IL2 | | 50.00% |
| Motif_533 | Bellringer/replumless/pennywise BS3 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | | 50.00% |
| Motif_222 | AGMOTIFNTMYB2 | AG-motif found at -114 of the promoter of NtMyb2 gene; NtMyb2 is a regulator of the tobacco retrotransposon Tto1 and the defence-related gene phenylalanine ammonia lyase (PAL), which are induced by various stress such as wounding or elicitor treatment; AGP1 (GATA-type zinc finger protein) binding site | | 50.00% |
| Motif_15 | AMYBOX2 | amylase box; amylase element; Conserved sequence found in 5'upstream region of alpha-amylase gene of rice, wheat, barley | | 50.00% |
| 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 | | 50.00% |
| Motif_307 | TATCCAYMOTIFOSRAMY3D | TATCCAY motif found in rice RAmy3D alpha-amylase gene promoter; a GATA motif as its antisense sequence; TATCCAY motif and G motif are responsible for sugar repression | | 50.00% |
| Motif_150 | RBCSCONSENSUS | rbcS general consensus sequence; AATCCAA or AATCCAAC | | 50.00% |
| Motif_153 | MARABOX1 | A-box found in SAR(scaffold attachment region; or matrix attachment region, MAR) | | 50.00% |
| 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 | | 50.00% |
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