| Matrix_29 | AP1 | Not available | Upstream | -201 |
| Matrix_396 | AP3 | Not available | Upstream | -20 |
| | | Upstream | -21 |
| Matrix_56 | BZIP17;BZIP28;BZIP49 | Not available | Upstream | -707 |
| 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 | -204 |
| Motif_153 | MARABOX1 | A-box found in SAR(scaffold attachment region; or matrix attachment region, MAR) | Upstream | -197 |
| 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 | Upstream | -208 |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Upstream | -193 |
| 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 | -194 |
| | | Upstream | -198 |
| | | Upstream | -202 |
| 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 | Upstream | -197 |
| | | Upstream | -201 |
| Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | Upstream | -21 |
| Motif_450 | E2FCONSENSUS | E2F consensus sequence of all different E2F-DP-binding motifs that were experimentally verified in plants | Upstream | -8 |
| 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) | Upstream | -207 |
| Motif_652 | AUXRETGA2GMGH3 | TGA-box #2 in putative auxin-resonsive element (AUXRE) E1 of soybean GH3 promoter; Strong binding site for proteins in plant nuclear extracts; Hex-like element; E1 element=-249 to -203; E2 element=-241 to -224 | Upstream | -705 |
| 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 | -28 |
| | | Upstream | -30 |
| | | Upstream | -32 |
| | | Upstream | -34 |
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