| Matrix_109 | GBF3 | Not available | Upstream | -934 |
| Matrix_113 | ABI5 | Not available | Upstream | -934 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -325 |
| Matrix_122 | ABF1;AREB2 | Not available | Upstream | -935 |
| Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -931 |
| Matrix_156 | POC1 | Not available | Upstream | -934 |
| Matrix_183 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -327 |
| | | Upstream | -1038 |
| Matrix_186 | FHY3 | Not available | Upstream | -326 |
| | | Upstream | -1038 |
| Matrix_301 | PIL5 | Not available | Upstream | -767 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -935 |
| Matrix_345 | POC1 | Not available | Upstream | -325 |
| Matrix_356 | PRR5 | Not available | Upstream | -932 |
| Matrix_369 | AT2G18300 | Not available | Upstream | -1042 |
| Matrix_403 | BZR1 | Not available | Upstream | -933 |
| Matrix_449 | BIM2 | Not available | Upstream | -772 |
| Matrix_476 | bHLH115;bHLH34 | Not available | Upstream | -329 |
| Matrix_480 | BES1 | Not available | Upstream | -328 |
| | | Upstream | -934 |
| Matrix_49 | FHY3/FAR1 | Not available | Upstream | -324 |
| Matrix_55 | PIF3 | Not available | Upstream | -934 |
| Matrix_7 | PIF4 | Not available | Upstream | -935 |
| Matrix_77 | PRR5 | Not available | Upstream | -326 |
| | | Upstream | -934 |
| 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 | -332 |
| Motif_210 | REBETALGLHCB21 | REbeta found in Lemna gibba Lhcb21 gene promoter; Located at -114 to -109; A GATA sequence created at a position six nucleotides upstream could replace the function of REbeta; Required for phytochrome regulation | Upstream | -239 |
| Motif_218 | ABRERATCAL | ABRE-related sequence or Repeated sequence motifs identified in the upstream regions of 162 Ca(2+)-responsive upregulated genes; see also ABRE | Upstream | -328 |
| | | Upstream | -935 |
| | | Upstream | -936 |
| | | Upstream | -1039 |
| 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 | -326 |
| | | Upstream | -328 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -408 |
| Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -762 |
| Motif_552 | MRE1 | MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1 | Upstream | -763 |
| | | Upstream | -802 |
| Motif_627 | ACGTABREMOTIFA2OSEM | Experimentally determined sequence requirement of ACGT-core of motif A in ABRE of the rice gene, OSEM; DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A in Arabidopsis | Upstream | -934 |
| Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -1280 |
| | | Upstream | -1396 |
| 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 | -407 |
| | | Upstream | -409 |
| | | Upstream | -411 |
| | | Upstream | -413 |
| | | Upstream | -415 |
| | | Upstream | -747 |
| | | Upstream | -749 |
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