| Matrix_183 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -231 |
| Matrix_186 | FHY3 | Not available | Upstream | -231 |
| Matrix_208 | AP1 | Not available | Intron | 9706 |
| | | Intron | 6174 |
| Matrix_209 | RAP2.6 | Not available | Upstream | -132 |
| Matrix_222 | AGL2 | DNA binding properties of two Arabidopsis MADS domain proteins: binding consensus and dimer formation | Intron | 11369 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -274 |
| | | Upstream | -275 |
| Matrix_46 | AT4G21895 | Not available | Intron | 265 |
| Matrix_476 | bHLH115;bHLH34 | Not available | Upstream | -232 |
| Matrix_48 | PI | Not available | Upstream | -143 |
| | | Upstream | -144 |
| Matrix_77 | PRR5 | Not available | Upstream | -230 |
| 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 | -129 |
| 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 | -232 |
| | | Upstream | -274 |
| | | Upstream | -275 |
| Motif_318 | CGCGBOXAT | CGCG box recognized by AtSR1-6 (Arabidopsis thaliana signal-responsive genes); Multiple CGCG elements are found in promoters of many genes; Ca2+/calmodulin binds to all AtSRs | Upstream | -233 |
| Motif_34 | LECPLEACS2 | Core element in LeCp (tomato Cys protease) binding cis-element (from -715 to -675) in LeAcs2 gene | Upstream | -657 |
| | | Upstream | -1190 |
| | | Upstream | -1591 |
| Motif_349 | QARBNEXTA | QAR (quantitative activator region) in promoter region of Brassica napus extA extensin gene | Intron | 2548 |
| Motif_375 | ERELEE4 | ERE (ethylene responsive element) of tomato E4 and carnation GST1 genes; GST1 is related to senescence; Found in the 5'-LTR region of TLC1.1 retrotransposon family in Lycopersicon chilense; ERE motifs mediate ethylene-induced activation of the U3 promoter region | Upstream | -705 |
| Motif_395 | RHE_element | Functional Conservation of a Root Hair Cell-Specific cis-Element in Angiosperms with Different Root Hair Distribution Patterns | Upstream | -129 |
| 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 | Upstream | -91 |
| | | Upstream | -140 |
| | | Upstream | -142 |
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