| Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Intron | 2356 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Intron | 2358 |
| | | Intron | 906 |
| Matrix_135 | ABI3 | Not available | Intron | 2662 |
| | | Intron | 2661 |
| | | Intron | 2160 |
| Matrix_247 | PIF3 | Not available | Intron | 2355 |
| Matrix_252 | RAP2.6 | Not available | Upstream | -889 |
| Matrix_334 | AT3G23230 | Not available | Upstream | -887 |
| Matrix_345 | POC1 | Not available | Intron | 2359 |
| | | Intron | 2358 |
| | | Intron | 934 |
| | | Intron | 906 |
| Matrix_355 | ERF10;ERF11 | Not available | Upstream | -887 |
| Matrix_378 | ATERF1 | Not available | Upstream | -889 |
| Matrix_406 | ATERF-7 | Not available | Upstream | -888 |
| Matrix_426 | CRF1;CRF2 | Not available | Upstream | -887 |
| Matrix_433 | ATERF1 | Not available | Upstream | -887 |
| Matrix_462 | ATERF-8 | Not available | Upstream | -888 |
| Matrix_473 | RRTF1 | Not available | Upstream | -889 |
| Matrix_506 | DRNL;ATERF-4 | Not available | Upstream | -887 |
| Matrix_507 | TCP3 | Not available | Intron | 898 |
| Motif_171 | TCP binding consensus | found enriched in peaks in chip-seq data for SEP3 | Upstream | -38 |
| | | Upstream | -130 |
| Motif_184 | PROXBBNNAPA | prox B (proximal portion of B-box) found in napA gene of Brassica napus; CA-rich sequence; Found between -130 and -124; Required for seed specific expression and ABA responsiveness; dist B ABRE mediated transactivation by ABI3 adn ABI3-dependent response to ABA; a tetramer of the composite RY/G complex mediated only ABA-independent transactivation by ABI3; B2 domain of ABI3 is necessary for ABA-independent and ABA-dependent activation through the dist B ABRE | Upstream | -167 |
| Motif_286 | SEBFCONSSTPR10A | Binding site of the potato silencing element binding factor (SEBF) gene found in promoter of pathogenesis-related gene (PR-10a); Located between -45 and -39; Similar to the auxin response element | Intron | 1560 |
| Motif_297 | Bellringer/replumless/pennywise BS1 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | Upstream | -423 |
| | | Upstream | -428 |
| Motif_34 | LECPLEACS2 | Core element in LeCp (tomato Cys protease) binding cis-element (from -715 to -675) in LeAcs2 gene | Upstream | -1217 |
| | | Upstream | -1265 |
| Motif_365 | ARF1 binding site motif | ARF (auxin response factor) binding site found in the promoters of primary/early auxin response genes of Arabidopsis thaliana; AuxRE;Binding site of Arabidopsis ARF1 (Auxin response factor1); Sequence found in NDE element in Soybean SAUR (Small Auxin-Up RNA) 15A gene promoter;Found in D1 or D4 element in Soybean GH3 promoter; This element was enriched in the 5'-flanking region of genes up-regulated by both IAA and BL;Dimerization and DNA binding of auxin response factors | Intron | 1560 |
| Motif_570 | POLASIG2 | PolyA signal; poly A signal found in rice alpha-amylase; -10 to -30 in the case of animal genes | Upstream | -423 |
| | | Upstream | -428 |
| Motif_667 | TATABOXOSPAL | Binding site for OsTBP2, found in the promoter of rice pal gene encoding phenylalanine ammonia-lyase; OsTFIIB stimulated the DNA binding and bending activities of OsTBP2 and synergistically enhanced OsTBP2-mediated transcription from the pal promoter | Upstream | -191 |
| | | Upstream | -392 |
| | | Upstream | -421 |
| | | Upstream | -1102 |
| | | Upstream | -1514 |
| 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 | 1569 |
| | | Intron | 1567 |
| | | Intron | 1565 |
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