| Matrix_110 | ATABI4;AT3G57600 | Not available | Upstream | -369 |
| Matrix_138 | RRTF1 | Not available | Upstream | -368 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -20 |
| | | Upstream | -17 |
| Matrix_326 | AT5G07310;Rap2.6L;AT5G61890 | Not available | Upstream | -368 |
| Matrix_355 | ERF10;ERF11 | Not available | Upstream | -368 |
| Matrix_39 | AP1 | Not available | Upstream | -19 |
| Matrix_409 | DEAR3 | Not available | Upstream | -368 |
| Matrix_493 | AT1G22985;AT1G71130 | Not available | Upstream | -367 |
| Matrix_57 | WIN1;SHN3;SHN2 | Not available | Upstream | -368 |
| Matrix_91 | CRF3 | Not available | Upstream | -367 |
| Motif_116 | INRNTPSADB | Inr (initiator) elements found in the tobacco psaDb gene promoter without TATA boxes; Light-responsive transcription of psaDb depends on Inr, but not TATA box | Upstream | -44 |
| 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 | -360 |
| Motif_153 | MARABOX1 | A-box found in SAR(scaffold attachment region; or matrix attachment region, MAR) | Upstream | -613 |
| Motif_218 | ABRERATCAL | ABRE-related sequence or Repeated sequence motifs identified in the upstream regions of 162 Ca(2+)-responsive upregulated genes; see also ABRE | Upstream | -360 |
| Motif_332 | SV40COREENHAN | SV40 core enhancer; Similar sequences found in rbcS genes | Upstream | -46 |
| Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -361 |
| Motif_536 | TBOXATGAPB | Tbox found in the Arabidopsis thaliana GAPB gene promoter; Located between -94 and -89 (T1) and also between -84 and -79 (T2); Mutations in the Tbox resulted in reductions of light-activated gene transcription; GAPB encodes the B subunit of chloroplast glyceraldehyde-3-phosphate dehydrogenase(GADPH) of A.T.; Promoter analysis of the nuclear gene encoding the chloroplast glyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsis thaliana | Upstream | -86 |
| Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -21 |
| | | Upstream | -18 |
| 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 | -359 |
| 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 | -362 |
| Motif_570 | POLASIG2 | PolyA signal; poly A signal found in rice alpha-amylase; -10 to -30 in the case of animal genes | Upstream | -431 |
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