| Matrix_396 | AP3 | Not available | Upstream | -601 |
| Matrix_424 | MYB59 | Not available | Downstream | 3725 |
| Matrix_505 | GATA8 | Not available | Upstream | -548 |
| Motif_254 | MYB46;MYB83 | MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes | Downstream | 3727 |
| Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | Upstream | -600 |
| Motif_411 | PRECONSCRHSP70A | Consensus sequence of PRE (plastid response element) in the promoters of HSP70A in Chlamydomonas; Involved in induction of HSP70A gene by both MgProto and light | Upstream | -576 |
| Motif_419 | MYB4 binding site motif | Not available | Downstream | 3727 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Downstream | 3726 |
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