| Matrix_183 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -1536 |
| Matrix_186 | FHY3 | Not available | Upstream | -1536 |
| Matrix_237 | MYB55 | Not available | Upstream | -1452 |
| Matrix_352 | LEC2 | Not available | Upstream | -1046 |
| Matrix_414 | AGL15 | Not available | Intron | 2371 |
| Matrix_476 | bHLH115;bHLH34 | Not available | Upstream | -1537 |
| Matrix_48 | PI | Not available | Intron | 2380 |
| Matrix_49 | FHY3/FAR1 | Not available | Upstream | -1533 |
| Matrix_84 | AtGRF6 | Not available | Upstream | -1452 |
| Motif_119 | ABI3 | Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene product | Upstream | -1047 |
| 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 | -1456 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -304 |
| Motif_484 | RAV1-B binding site motif | Binding consensus sequence of an Arabidopsis transcription factor, RAV1; RAV1 specifically binds to DNA with bipartite sequence motifs of RAV1-A (CAACA) and RAV1-B (CACCTG); RAV1 protein contain AP2-like and B3-like domains; The AP2-like and B3-like domains recognize the CAACA and CACCTG motifs, respectively; The expression level of RAV1 were relatively high in rosette leaves and roots; RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants | Upstream | -1456 |
| Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Upstream | -697 |
| 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 | Intron | 2385 |
| | | Intron | 2383 |
| | | Intron | 2381 |
| | | Upstream | -304 |
| | | Upstream | -306 |
| | | Upstream | -308 |
| | | Upstream | -310 |
| | | Upstream | -312 |
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