| Matrix_268 | EMB2749;VND5;SMB;VND1;ANAC076;NAC101;ANAC105 | Not available | Upstream | -1233 |
| Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Upstream | -1172 |
| Matrix_463 | HAT3.1 | Not available | Upstream | -1264 |
| Matrix_48 | PI | Not available | Upstream | -1242 |
| Matrix_53 | MYC3 | Not available | Upstream | -1234 |
| Matrix_57 | WIN1;SHN3;SHN2 | Not available | Upstream | -1172 |
| Matrix_79 | FUS3 | Not available | Upstream | -1233 |
| Matrix_80 | BIM1 | Not available | Upstream | -1233 |
| Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -1253 |
| Motif_163 | BOXCPSAS1 | Box C in pea (P.s.) asparagine synthetase (AS1) gene; Found at -45; AS1 is negatively regulated by light; Box C binds with nuclear proteins, which was competed by a putative repressor element RE1 | Upstream | -1094 |
| Motif_292 | MYBPZM | Core of consensus maize P (myb homolog) binding site; 6 bp core; Maize P gene specifies red pigmentation of kernel pericarp, cob, and other floral organs; P binds to A1 gene, but not Bz1 gene; Maize C1 (myb homolog) activates both A1 and Bz1 genes | Upstream | -1127 |
| Motif_318 | CGCGBOXAT | CGCG box recognized by AtSR1-6 (Arabidopsis thaliana signal-responsive genes); Multiple CGCG elements are found in promoters of many genes; Ca2+/calmodulin binds to all AtSRs | Upstream | -1169 |
| Motif_329 | AMMORESIIUDCRNIA1 | Motifs (IIU and IID) found in the Chlamydomonas Nia1 gene promoter; Involved in ammonium-response; Located between -231 and -219 and also between -76 and -65; Involved in Nia1 transcription activation | Upstream | -1127 |
| Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -1232 |
| Motif_503 | EECCRCAH1 | EEC; Consensus motif of the two enhancer elements, EE-1 and EE-2, both found in the promoter region of the Chlamydomonas Cah1 (encoding a periplasmic carbonic anhydrase); Binding site of Myb transcription factor LCR1 | Upstream | -1253 |
| Motif_552 | MRE1 | MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1 | Upstream | -1262 |
| Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -1249 |
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