| Matrix_102 | WRKY21 | Not available | Upstream | -397 |
| Matrix_75 | WRKY29 | Not available | Upstream | -397 |
| 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 | -444 |
| | | Upstream | -442 |
| | | Upstream | -440 |
| | | Upstream | -438 |
| | | Upstream | -436 |
| | | Upstream | -434 |
| | | Upstream | -432 |
| | | Upstream | -430 |
| | | Upstream | -428 |
| | | Upstream | -426 |
| | | Upstream | -214 |
| | | Upstream | -212 |
| | | Upstream | -103 |
| | | Upstream | -101 |
| | | Upstream | -99 |
| | | Upstream | -97 |
| | | Upstream | -95 |
| 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 | -1674 |
| | | Upstream | -1667 |
| 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 | -336 |
| Motif_262 | WRKY70 | Identification of a novel type of WRKY transcription factor binding site in elicitor-responsive cis-sequences from Arabidopsis thaliana | Upstream | -408 |
| 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 | -452 |
| 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 | Upstream | -687 |
| 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 | -289 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -444 |
| | | Upstream | -442 |
| | | Upstream | -440 |
| | | Upstream | -438 |
| | | Upstream | -436 |
| | | Upstream | -434 |
| | | Upstream | -432 |
| | | Upstream | -430 |
| | | Upstream | -428 |
| | | Upstream | -426 |
| | | Upstream | -424 |
| | | Upstream | -214 |
| | | Upstream | -212 |
| | | Upstream | -210 |
| | | Upstream | -103 |
| | | Upstream | -101 |
| | | Upstream | -99 |
| | | Upstream | -97 |
| | | Upstream | -95 |
| | | Upstream | -93 |
| 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 | Upstream | -23 |
| Motif_453 | HEXMOTIFTAH3H4 | hexamer motif found in promoter of wheat histone genes H3 and H4; CaMV35S; NOS; Binding with HBP-1A and HBP-1B; Binding site of wheat nuclear protein HBP-1 (histone DNA binding protein-1); HBP-1 has a leucine zipper motif; hexamer motif in type 1 element may play important roles in regulation of replication- dependent but not of replication-independent expression of the wheat histone H3 gene;Rice OBF1-homodimer-binding site | Upstream | -390 |
| 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 | -361 |
| 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 | -294 |
| 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 | Upstream | -386 |
| 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 | Upstream | -390 |
| 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 | -445 |
| | | Upstream | -443 |
| | | Upstream | -441 |
| | | Upstream | -439 |
| | | Upstream | -437 |
| | | Upstream | -435 |
| | | Upstream | -433 |
| | | Upstream | -431 |
| | | Upstream | -429 |
| | | Upstream | -427 |
| | | Upstream | -425 |
| | | Upstream | -423 |
| | | Upstream | -421 |
| | | Upstream | -419 |
| | | Upstream | -417 |
| | | Upstream | -214 |
| | | Upstream | -212 |
| | | Upstream | -210 |
| | | Upstream | -208 |
| | | Upstream | -206 |
| | | Upstream | -204 |
| | | Upstream | -103 |
| | | Upstream | -101 |
| | | Upstream | -99 |
| | | Upstream | -97 |
| | | Upstream | -95 |
| | | Upstream | -93 |
| | | Upstream | -91 |
| | | Upstream | -89 |
| | | Upstream | -87 |
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