| Matrix_172 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -715 |
| Matrix_281 | TCP13 | Not available | Upstream | -1221 |
| Matrix_309 | FLC | Not available | Upstream | -798 |
| Matrix_36 | RAV1_1 | RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants | Upstream | -296 |
| Matrix_414 | AGL15 | Not available | Upstream | -797 |
| Motif_174 | SREATMSD | sugar-repressive element (SRE) found in 272 of the 1592 down-regulated genes after main stem decapitation in Arabidopsis | Upstream | -191 |
| Motif_181 | IBOXCORENT | I-box core motif in the CAMs (conserved DNA modular arrays) associated with light-responsive promoter regions | Upstream | -717 |
| Motif_603 | SITEIIATCYTC | Site II element found in the promoter regions of cytochrome genes (Cytc-1, Cytc-2) in Arabidopsis; Located between -147 and -156 from the translational starts sites;Overrepresented in the promoters of nuclear genes encoding components of the oxidative phosphorylation (OxPhos) machinery from both Arabidopsis and rice | Upstream | -1661 |
| | | Upstream | -1760 |
| | | Upstream | -1780 |
| | | Upstream | -1902 |
| Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Upstream | -826 |
| 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 | -103 |
| | | Upstream | -105 |
| Motif_94 | UP1ATMSD | Up1 motif found in 162 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | Upstream | -1780 |
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