| Matrix_147 | ERF3;AT1G80580 | Not available | Upstream | -417 |
| Matrix_203 | GATA9;GATA12 | Not available | Upstream | -29 |
| Matrix_242 | AT2G25820;AT3G16280;AT4G32800;TINY2;tny | Not available | Upstream | -435 |
| | | Upstream | -441 |
| Matrix_244 | DREB2C | Not available | Upstream | -434 |
| | | Upstream | -440 |
| Matrix_246 | ARR10 | Molecular structure of the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators | Upstream | -409 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -162 |
| | | Upstream | -165 |
| | | Upstream | -168 |
| | | Upstream | -171 |
| | | Upstream | -174 |
| | | Upstream | -177 |
| | | Upstream | -180 |
| Matrix_277 | RAP2.6 | Not available | Upstream | -1840 |
| Matrix_385 | DEAR4 | Not available | Upstream | -434 |
| | | Upstream | -440 |
| Matrix_39 | AP1 | Not available | Upstream | -178 |
| Matrix_394 | DREB_U | Not available | Upstream | -434 |
| | | Upstream | -440 |
| Matrix_406 | ATERF-7 | Not available | Upstream | -417 |
| Matrix_408 | GATA12 | Not available | Upstream | -29 |
| Matrix_45 | DRN | Not available | Upstream | -417 |
| Matrix_454 | AT1G77200;ATERF38;AT4G16750;AT5G52020 | Not available | Upstream | -434 |
| Matrix_462 | ATERF-8 | Not available | Upstream | -417 |
| Matrix_478 | AT1G01250 | Not available | Upstream | -435 |
| | | Upstream | -441 |
| Matrix_73 | DEAR3;RAP2.9;RAP2.10 | Not available | Upstream | -435 |
| | | Upstream | -441 |
| Matrix_92 | AT1G33760 | Not available | Upstream | -434 |
| | | Upstream | -440 |
| Motif_125 | BOXIINTPATPB | Box II found in the tobacco plastid atpB gene promoter; Conserved in several NCII (nonconsensus type II) promoters of plastid genes; Important for the activity of this NCII promoter | Upstream | -161 |
| Motif_168 | IBOX | I box; I-box; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis; I box; Binding site of LeMYB1, that is a member of a novel class of myb-like proteins; LeMYBI act as a transcriptional activator; An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene | Upstream | -233 |
| Motif_258 | -10PEHVPSBD | -10 promoter element found in the barley (H.v.) chloroplast psbD gene promoter; Involved in the expression of the plastid gene psbD which encodes a photosystem II reaction center chlorophyll-binding protein that is activated by blue, white or UV-A light | Downstream | 10515 |
| Motif_292 | MYBPZM | Core of consensus maize P (myb homolog) binding site; 6 bp core; Maize P gene specifies red pigmentation of kernel pericarp, cob, and other floral organs; P binds to A1 gene, but not Bz1 gene; Maize C1 (myb homolog) activates both A1 and Bz1 genes | Upstream | -961 |
| | | Upstream | -1485 |
| | | Upstream | -1855 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -232 |
| Motif_391 | REALPHALGLHCB21 | REalpha found in Lemna gibba Lhcb21 gene promoter; Located at -134 to -129; Binding site of proteins of whole-cell extracts; The DNA binding activity is high in etiolated plants but much lower in green plants; Required for phytochrome regulation | Upstream | -269 |
| | | Upstream | -466 |
| | | Upstream | -554 |
| Motif_416 | MYB80 | The MYB80 transcription factor is required for pollen development and the regulation of tapetal programmed cell death in Arabidopsis thaliana | Upstream | -463 |
| Motif_502 | MYB98 | The MYB98 subcircuit of the synergid gene regulatory network includes genes directly and indirectly regulated by MYB98 | Downstream | 10525 |
| Motif_54 | LTREATLTI78 | Putative low temperature responsive element (LTRE); Found in Arabidopsis thaliana low-temperature-induced (lti) genes, lti78 and lti65; Repeated four times in lti78 which is also known as cor78 and rd29A; Found also in barley low temperature responsive genes, blt4.2, blt4.6, blt4.9 (lipid transfer genes); cold inducible; See LTRECORE; Also present in rab18, kin1, and kin2; Differential expression of two related, low-temperature-induced genes in Arabidopsis thaliana | Upstream | -435 |
| | | Upstream | -441 |
| Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -164 |
| | | Upstream | -167 |
| | | Upstream | -170 |
| | | Upstream | -173 |
| | | Upstream | -176 |
| | | Upstream | -179 |
| Motif_643 | DRE2COREZMRAB17 | DRE2 core found in maize rab17 gene promoter; DBF1 and DBF2 bound to DRE2; rab17 is expressed during late embryogenesis, and is induced by ABA | Upstream | -435 |
| | | Upstream | -441 |
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