| Matrix_25 | AP3 | Not available | Upstream | -301 |
| Matrix_399 | TGA1 | Not available | Upstream | -449 |
| Matrix_414 | AGL15 | Not available | Upstream | -833 |
| Matrix_457 | TGA2 | Not available | Upstream | -450 |
| Matrix_48 | PI | Not available | Upstream | -165 |
| Motif_1 | GT1CORE | Critical for GT-1 binding to box II of rbcS; Transcriptional activation by Arabidopsis GT-1 may be through interaction with TFIIA-TBP-TATA complex | Upstream | -363 |
| | | Upstream | -380 |
| 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 | -198 |
| | | Upstream | -200 |
| | | Upstream | -202 |
| | | Upstream | -204 |
| | | Upstream | -206 |
| | | Upstream | -208 |
| | | Upstream | -210 |
| | | Upstream | -212 |
| | | Upstream | -214 |
| | | Upstream | -216 |
| | | Upstream | -218 |
| | | Upstream | -220 |
| | | Upstream | -222 |
| | | Upstream | -224 |
| | | Upstream | -226 |
| | | Upstream | -228 |
| 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 | -106 |
| | | Upstream | -430 |
| 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 | -315 |
| | | Upstream | -340 |
| Motif_34 | LECPLEACS2 | Core element in LeCp (tomato Cys protease) binding cis-element (from -715 to -675) in LeAcs2 gene | Upstream | -596 |
| 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 | -316 |
| | | Upstream | -341 |
| Motif_391 | REALPHALGLHCB21 | REalpha found in Lemna gibba Lhcb21 gene promoter; Located at -134 to -129; Binding site of proteins of whole-cell extracts; The DNA binding activity is high in etiolated plants but much lower in green plants; Required for phytochrome regulation | Upstream | -320 |
| | | Upstream | -345 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -198 |
| | | Upstream | -200 |
| | | Upstream | -202 |
| | | Upstream | -204 |
| | | Upstream | -206 |
| | | Upstream | -208 |
| | | Upstream | -210 |
| | | Upstream | -212 |
| | | Upstream | -214 |
| | | Upstream | -216 |
| | | Upstream | -218 |
| | | Upstream | -220 |
| | | Upstream | -222 |
| | | Upstream | -224 |
| | | Upstream | -226 |
| | | Upstream | -228 |
| | | Upstream | -230 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Upstream | -1070 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Upstream | -319 |
| | | Upstream | -344 |
| Motif_645 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -106 |
| | | Upstream | -430 |
| Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Upstream | -320 |
| | | Upstream | -345 |
| | | Upstream | -885 |
| 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 | Upstream | -313 |
| | | Upstream | -338 |
| | | Upstream | -758 |
| 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 | -197 |
| | | Upstream | -199 |
| | | Upstream | -201 |
| | | Upstream | -203 |
| | | Upstream | -205 |
| | | Upstream | -207 |
| | | Upstream | -209 |
| | | Upstream | -211 |
| | | Upstream | -213 |
| | | Upstream | -215 |
| | | Upstream | -217 |
| | | Upstream | -219 |
| | | Upstream | -221 |
| | | Upstream | -223 |
| | | Upstream | -225 |
| | | Upstream | -227 |
| | | Upstream | -229 |
| | | Upstream | -231 |
| | | Upstream | -233 |
| | | Upstream | -235 |
| | | Upstream | -237 |
| Motif_98 | SEF3MOTIFGM | SEF3 binding site; Soybean consensus sequence found in the 5' upstream region of beta-conglycinin (7S globulin) gene; AACCCA(-27bp-)AACCCA; SEF=soybean embryo factor; SEF2; SEF3; SEF4 | Upstream | -461 |
| | | Upstream | -882 |
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