| Matrix_113 | ABI5 | Not available | Upstream | -517 |
| Matrix_134 | ABF1 | Not available | Upstream | -518 |
| Matrix_145 | GBF4;AT5G44080 | Not available | Upstream | -517 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -517 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -521 |
| Matrix_296 | GBF2 | Not available | Upstream | -517 |
| Matrix_356 | PRR5 | Not available | Upstream | -525 |
| Matrix_403 | BZR1 | Not available | Upstream | -520 |
| Matrix_5 | AT5G51190;ERF104 | Not available | Upstream | -1464 |
| Matrix_55 | PIF3 | Not available | Upstream | -519 |
| Motif_174 | SREATMSD | sugar-repressive element (SRE) found in 272 of the 1592 down-regulated genes after main stem decapitation in Arabidopsis | Upstream | -1516 |
| Motif_321 | TATABOX5 | TATA box; TATA box found in the 5'upstream region of pea (Pisum sativum) glutamine synthetase gene; a functional TATA element by in vivo analysis | Upstream | -191 |
| | | Upstream | -186 |
| | | Upstream | -181 |
| Motif_342 | POLASIG1 | PolyA signal; poly A signal found in legA gene of pea, rice alpha-amylase; -10 to -30 in the case of animal genes. Near upstream elements (NUE) in Arabidopsis | Upstream | -190 |
| | | Upstream | -185 |
| | | Upstream | -180 |
| Motif_371 | DRE-like promoter motif | The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses | Upstream | -485 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -190 |
| | | Upstream | -185 |
| 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 | -515 |
| Motif_72 | GADOWNAT | Sequence present in 24 genes in the GA-down regulated d1 cluster (106 genes) found in Arabidopsis seed germination; This motif is similar to ABRE | Upstream | -515 |
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