| Matrix_169 | E2F1 | Not available | Upstream | -485 |
| Matrix_183 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -454 |
| | | Upstream | -487 |
| Matrix_186 | FHY3 | Not available | Upstream | -453 |
| | | Upstream | -486 |
| Matrix_232 | TCP23 | Not available | Downstream | 2423 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -38 |
| Matrix_380 | ATMYR1 | Not available | Upstream | -6 |
| Matrix_77 | PRR5 | Not available | Upstream | -453 |
| | | Upstream | -486 |
| Motif_129 | GAGAGMGSA1 | GAGA element found in the promoter of the heme and chlorophyll synthesis gene Gsa1 in soybean; GAGA binding protein (GBP) binds to (GA)n/(CT)n DNA | Upstream | -119 |
| | | Upstream | -121 |
| | | Upstream | -123 |
| | | Upstream | -125 |
| | | Upstream | -127 |
| | | Upstream | -129 |
| | | Upstream | -131 |
| Motif_150 | RBCSCONSENSUS | rbcS general consensus sequence; AATCCAA or AATCCAAC | Downstream | 2221 |
| Motif_182 | MYB2CONSENSUSAT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; see MYB2 and MYBATRD22 | Upstream | -53 |
| | | Upstream | -211 |
| | | Upstream | -340 |
| Motif_194 | EBOXBNNAPA | E-box of napA storage-protein gene of Brassica napus;This sequence is also known as RRE (R response element); MYC recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; Binding site of ATMYC2 (previously known as rd22BP1); see E-box and MYCATRD22; MYC recognition sequence in CBF3 promoter; Binding site of ICE1 (inducer of CBF expression 1) that regulates the transcription of CBF/DREB1 genes in the cold in Arabidopsis; ICE1 | Downstream | 2415 |
| 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 | -455 |
| | | Upstream | -488 |
| Motif_221 | MYBCORE | Binding site for all animal MYB and at least two plant MYB proteins ATMYB1 and ATMYB2, both isolated from Arabidopsis; ATMYB2 is involved in regulation of genes that are responsive to water stress in Arabidopsis; A petunia MYB protein (MYB.Ph3) is involved in regulation of flavonoid biosynthesis | Upstream | -53 |
| | | Upstream | -211 |
| Motif_254 | MYB46;MYB83 | MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes | Downstream | 2194 |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Downstream | 2127 |
| | | Downstream | 2124 |
| | | Downstream | 2121 |
| | | Downstream | 2118 |
| | | Downstream | 2115 |
| 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 | -455 |
| | | Upstream | -488 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -53 |
| | | Upstream | -211 |
| | | Upstream | -340 |
| Motif_342 | POLASIG1 | PolyA signal; poly A signal found in legA gene of pea, rice alpha-amylase; -10 to -30 in the case of animal genes. Near upstream elements (NUE) in Arabidopsis | Downstream | 2207 |
| Motif_371 | DRE-like promoter motif | The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses | Downstream | 2411 |
| Motif_419 | MYB4 binding site motif | Not available | Downstream | 2194 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -119 |
| | | Upstream | -121 |
| | | Upstream | -123 |
| | | Upstream | -125 |
| | | Upstream | -127 |
| | | Upstream | -129 |
| | | Upstream | -131 |
| | | Upstream | -133 |
| Motif_450 | E2FCONSENSUS | E2F consensus sequence of all different E2F-DP-binding motifs that were experimentally verified in plants | Upstream | -214 |
| Motif_454 | DRECRTCOREAT | Core motif of DRE/CRT (dehydration-responsive element/C-repeat) cis-acting element found in many genes in Arabidopsis and in rice; Os DREB1A bound to GCCGAC more preferentially than to ACCGAC whereas At DREB1A bound to both GCCGAC and ACCGAC efficiently; Maize ZmDREB1A bound to DRE; HaDREB2 in Helianthus annuus (sunflower) | Downstream | 2410 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Downstream | 2194 |
| 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 | Downstream | 2411 |
| Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -40 |
| Motif_591 | CBFHV | Binding site of barley CBF1, and also of barley CBF2; CBF = C-repeat (CRT) binding factors; CBFs are also known as dehydration-responsive element (DRE) binding proteins (DREBs) | Downstream | 2410 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Downstream | 2393 |
| 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 | Downstream | 2410 |
| Motif_649 | 2SSEEDPROTBANAPA | Conserved in many storage-protein gene promoters; May be important for high activity of the napA promoter | Downstream | 2217 |
| Motif_658 | GT1CONSENSUS | Consensus GT-1 binding site in many light-regulated genes, e.g., RBCS from many species, PHYA from oat and rice, spinach RCA and PETA, and bean CHS15; GT-1 can stabilize the TFIIA-TBP-DNA (TATA box) complex; The activation mechanism of GT-1 may be achieved through direct interaction between TFIIA and GT-1; Binding of GT-1-like factors to the PR-1a promoter influences the level of SA-inducible gene expression | Downstream | 2407 |
| | | Upstream | -46 |
| Motif_682 | GT1GMSCAM4 | GT-1 motif found in the promoter of soybean CaM isoform, SCaM-4; Plays a role in pathogen- and salt-induced SCaM-4 gene expression | Upstream | -46 |
| 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 | -118 |
| | | Upstream | -120 |
| | | Upstream | -122 |
| | | Upstream | -124 |
| | | Upstream | -126 |
| | | Upstream | -128 |
| | | Upstream | -130 |
| | | Upstream | -132 |
| | | Upstream | -134 |
| | | Upstream | -136 |
| | | Upstream | -138 |
| | | Upstream | -140 |
| Motif_70 | CANBNNAPA | Core of (CA)n element in storage protein genes in Brasica napus; embryo- and endosperm-specific transcription of napin (storage protein) gene, napA; seed specificity; activator and repressor | Downstream | 2217 |
| Motif_88 | MYB2AT | Binding site for ATMYB2, an Arabidopsis MYB homolog; ATMYB2 binds oligonucleotides that contained a consensus MYB recognition sequence (TAACTG), such as is in the SV40 enhancer and the maize bronze-1 promoter; ATMYB2 is involved in regulation of genes that are responsive to water stress in Arabidopsis | Upstream | -53 |
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