| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -766 |
| Matrix_156 | POC1 | Not available | Upstream | -769 |
| Matrix_290 | AP2 | Not available | Upstream | -706 |
| Matrix_296 | GBF2 | Not available | Upstream | -792 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -792 |
| Matrix_472 | ZN_C2_H2 | Not available | Intron | 1810 |
| Matrix_55 | PIF3 | Not available | Upstream | -769 |
| Matrix_73 | DEAR3;RAP2.9;RAP2.10 | Not available | Upstream | -810 |
| Motif_139 | RHERPATEXPA7 | Right part of RHEs (Root Hair-specific cis-Elements) conserved among the Arabidopsis thaliana A7 (AtEXPA7) orthologous (and paralogous) genes from diverse angiosperm species with different hair distribution patterns | Upstream | -551 |
| | | Upstream | -772 |
| Motif_192 | BOXLCOREDCPAL | Consensus of the putative core sequences of box-L-like sequences in carrot; PAL1 promoter region; DCMYB1 bound to these sequences in vitro | Upstream | -109 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -769 |
| Motif_353 | HEXAMERATH4 | hexamer motif of Arabidopsis thaliana histone H4 promoter;Identification of cis-elements regulating the expression of an Arabidopsis histone H4 gene | Upstream | -790 |
| 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 | -394 |
| Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -770 |
| Motif_567 | T/GBOXATPIN2 | T/G-box found in tomato proteinase inhibitor II (pin2) and leucine aminopeptidase (LAP) genes; Involved in jasmonate (JA) induction of these genes; bHLH-Leu zipper JAMYC2 and JAMYC10 proteins specifically recognize this motif | Upstream | -550 |
| Motif_57 | ABREOSRAB21 | ABA responsive element (ABRE) of wheat Em and rice rab21 genes; Proposed consensus sequence for the repeated motif (Em1a and Em1b) of wheat Em gene | Upstream | -551 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -643 |
| | | Upstream | -644 |
| | | Upstream | -645 |
| | | Upstream | -646 |
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