| Matrix_109 | GBF3 | Not available | Upstream | -1049 |
| | | Downstream | 1759 |
| Matrix_113 | ABI5 | Not available | Upstream | -859 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -1053 |
| Matrix_134 | ABF1 | Not available | Upstream | -859 |
| Matrix_14 | ZCW32;AT5G62610 | Not available | Upstream | -1049 |
| Matrix_147 | ERF3;AT1G80580 | Not available | Downstream | 1703 |
| Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -1054 |
| Matrix_155 | RAP2.6;ERF110;ABR1 | Not available | Downstream | 1702 |
| Matrix_156 | POC1 | Not available | Upstream | -1049 |
| Matrix_183 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Downstream | 1767 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -859 |
| | | Downstream | 1757 |
| Matrix_194 | HYH;HY5 | Not available | Upstream | -863 |
| Matrix_214 | AP1 | Not available | Upstream | -862 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -1049 |
| Matrix_232 | TCP23 | Not available | Upstream | -935 |
| Matrix_24 | POC1 | Not available | Upstream | -1054 |
| Matrix_264 | ATAREB1 | Not available | Upstream | -860 |
| Matrix_280 | TCP24;TCP1;BRC2;ATTCP18 | Not available | Upstream | -1046 |
| Matrix_296 | GBF2 | Not available | Upstream | -1049 |
| | | Downstream | 1760 |
| Matrix_297 | TCP15 | Not available | Upstream | -935 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -1049 |
| | | Downstream | 1760 |
| Matrix_301 | PIL5 | Not available | Upstream | -1049 |
| Matrix_331 | GBF1 | Not available | Upstream | -1049 |
| | | Downstream | 1759 |
| Matrix_344 | ATERF15;AT4G18450 | Not available | Downstream | 1703 |
| Matrix_348 | AT5G51910 | Not available | Upstream | -934 |
| Matrix_356 | PRR5 | Not available | Upstream | -867 |
| | | Downstream | 1757 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Downstream | 1273 |
| Matrix_414 | AGL15 | Not available | Upstream | -161 |
| Matrix_42 | AT2G45680 | Not available | Upstream | -934 |
| Matrix_433 | ATERF1 | Not available | Downstream | 1702 |
| Matrix_448 | ATERF6 | Not available | Downstream | 1702 |
| Matrix_45 | DRN | Not available | Downstream | 1703 |
| Matrix_462 | ATERF-8 | Not available | Downstream | 1703 |
| Matrix_488 | ABF1 | Not available | Downstream | 1759 |
| Matrix_5 | AT5G51190;ERF104 | Not available | Downstream | 1703 |
| Matrix_53 | MYC3 | Not available | Upstream | -1048 |
| Matrix_7 | PIF4 | Not available | Upstream | -1048 |
| Matrix_80 | BIM1 | Not available | Upstream | -1049 |
| Motif_153 | MARABOX1 | A-box found in SAR(scaffold attachment region; or matrix attachment region, MAR) | Upstream | -1249 |
| Motif_179 | CACGTGMOTIF;BES1;PIF4;PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling;A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana; CACGTG motif; G-box; Binding site of Arabidopsis GBF4; C. roseus G-box binding factor 1 (CrGBF1) and 1 (CrGBF2) can act as transcriptional repressors of the Str promoter via direct interaction with the G-box; Essential for expression of beta-phaseolin gene during embryogenesis in bean, tobacco, Arabidopsis; Tomato Pti4 (ERF) regulates defense-related gene expression via GCC box and non-GCC box cis-element (Myb1 (GTTAGTT) and G-box (CACGTG)); Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein; Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -858 |
| Motif_190 | WUSATAg | Target sequence of WUS in the intron of AGAMOUS gene in Arabidopsis | Upstream | -1888 |
| 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 | 1777 |
| Motif_200 | GBOXLERBCS | G box; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis; Binding with GBF | Upstream | -1049 |
| 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 | Downstream | 1714 |
| 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 | Downstream | 1786 |
| Motif_244 | ABRE-like binding site motif | Not available | Downstream | 1760 |
| Motif_286 | SEBFCONSSTPR10A | Binding site of the potato silencing element binding factor (SEBF) gene found in promoter of pathogenesis-related gene (PR-10a); Located between -45 and -39; Similar to the auxin response element | Downstream | 1735 |
| Motif_291 | ABFs binding site motif | Binding site of trans-acting factor EMBP-1; wheat Em gene;Binding site of ABFs; ABFs (ABRE binding factors) were isolated from Arabidopsis by a yeast one-hybrid screening system; Expression ABFs is induced by ABA and various stress treatment; ABFs belongs to a distinct subfamily of bZIP proteins; Involved in ABA-mediated stress-signaling pathway;A plant leucine zipper protein that recognizes an abscisic acid response element | Upstream | -1048 |
| 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 | Downstream | 1714 |
| | | Downstream | 1770 |
| | | Downstream | 1772 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Downstream | 1762 |
| Motif_365 | ARF1 binding site motif | ARF (auxin response factor) binding site found in the promoters of primary/early auxin response genes of Arabidopsis thaliana; AuxRE;Binding site of Arabidopsis ARF1 (Auxin response factor1); Sequence found in NDE element in Soybean SAUR (Small Auxin-Up RNA) 15A gene promoter;Found in D1 or D4 element in Soybean GH3 promoter; This element was enriched in the 5'-flanking region of genes up-regulated by both IAA and BL;Dimerization and DNA binding of auxin response factors | Downstream | 1735 |
| 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 | 1764 |
| Motif_450 | E2FCONSENSUS | E2F consensus sequence of all different E2F-DP-binding motifs that were experimentally verified in plants | Downstream | 1705 |
| Motif_473 | ABREOSRGA1 | ABRE (ABA responsive element) in rice RGA1 encoding a G protein alpha subunit;ABRE; ABA and water-stress responses; Found in maize rab28; maize rab28 is ABA-inducible in embryos and vegetative tissues; Found in the Arabidopsis (A.t.) alcohol dehydrogenase (Adh) gene promoter; ABRE2; Found in the maize (Z.m.) Cat1 gene promoter; Responsible for the induction by ABA; Binding site of CBF2; Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance; The CBF genes do not appear to be autoregulated through the CRT/DRE sequence;The cis-regulatory element CCACGTGG is involved in ABA and water-stress responses of the maize gene rab28. Characterization of a maize G-box binding factor that is induced by hypoxia | Upstream | -1049 |
| Motif_552 | MRE1 | MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1 | Downstream | 1772 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -1047 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Downstream | 1275 |
| | | Downstream | 1276 |
| | | Downstream | 1277 |
| | | Downstream | 1278 |
| | | Downstream | 1279 |
| | | Downstream | 1280 |
| | | Downstream | 1281 |
| Motif_627 | ACGTABREMOTIFA2OSEM | Experimentally determined sequence requirement of ACGT-core of motif A in ABRE of the rice gene, OSEM; DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A in Arabidopsis | Upstream | -857 |
| | | Downstream | 1760 |
| Motif_638 | ABRE binding site motif | Not available | Upstream | -1048 |
| Motif_640 | RYREPEATBNNAPA | RY repeat found in RY/G box (the complex containing the two RY repeats and the G-box) of napA gene in Brassica napus; Found between -78 and -50; Required for seed specific expression;dist B ABRE mediated transactivation by ABI3 adn ABI3-dependent response to ABA; a tetramer of the composite RY/G complex mediated only ABA-independent transactivation by ABI3; B2 domain of ABI3 is necessary for ABA-independent and ABA-dependent activation through the dist B ABRE | Upstream | -86 |
| Motif_641 | LRENPCABE | LRE; A positive light regulatory element in tobacco CAB (cab-E) gene; Located at -241 | Upstream | -1047 |
| 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 | 1749 |
| Motif_72 | GADOWNAT | Sequence present in 24 genes in the GA-down regulated d1 cluster (106 genes) found in Arabidopsis seed germination; This motif is similar to ABRE | Upstream | -857 |
| | | Downstream | 1760 |
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