| Matrix_104 | PI | Not available | Upstream | -611 |
| Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -611 |
| Matrix_109 | GBF3 | Not available | Upstream | -611 |
| Matrix_113 | ABI5 | Not available | Upstream | -611 |
| Matrix_120 | BEE2 | Not available | Upstream | -610 |
| Matrix_122 | ABF1;AREB2 | Not available | Upstream | -611 |
| Matrix_129 | ABF1 | Not available | Upstream | -610 |
| Matrix_134 | ABF1 | Not available | Upstream | -610 |
| Matrix_14 | ZCW32;AT5G62610 | Not available | Upstream | -610 |
| | | Upstream | -609 |
| Matrix_145 | GBF4;AT5G44080 | Not available | Upstream | -609 |
| Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -614 |
| Matrix_156 | POC1 | Not available | Upstream | -611 |
| | | Upstream | -609 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -613 |
| Matrix_200 | PIL5;AT4G28790;AT4G28800;AT4G28811;AT4G28815 | Not available | Upstream | -610 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -613 |
| Matrix_233 | MYC3 | Not available | Upstream | -609 |
| Matrix_24 | POC1 | Not available | Upstream | -614 |
| Matrix_247 | PIF3 | Not available | Upstream | -610 |
| Matrix_264 | ATAREB1 | Not available | Upstream | -610 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -397 |
| Matrix_296 | GBF2 | Not available | Upstream | -610 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -610 |
| Matrix_301 | PIL5 | Not available | Upstream | -615 |
| Matrix_331 | GBF1 | Not available | Upstream | -611 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -610 |
| | | Upstream | -609 |
| Matrix_356 | PRR5 | Not available | Upstream | -613 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -1870 |
| Matrix_389 | ILR3 | Not available | Upstream | -610 |
| Matrix_403 | BZR1 | Not available | Upstream | -612 |
| Matrix_480 | BES1 | Not available | Upstream | -611 |
| Matrix_488 | ABF1 | Not available | Upstream | -611 |
| Matrix_53 | MYC3 | Not available | Upstream | -612 |
| Matrix_55 | PIF3 | Not available | Upstream | -611 |
| Matrix_56 | BZIP17;BZIP28;BZIP49 | Not available | Upstream | -611 |
| Matrix_60 | AT1G01260;AT5G57150 | Not available | Upstream | -609 |
| Matrix_64 | PIF5 | Not available | Upstream | -609 |
| Matrix_7 | PIF4 | Not available | Upstream | -610 |
| Matrix_77 | PRR5 | Not available | Upstream | -611 |
| Matrix_80 | BIM1 | Not available | Upstream | -611 |
| 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 | -608 |
| 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 | Upstream | -608 |
| 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 | -610 |
| 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 | -609 |
| | | Upstream | -608 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -610 |
| Motif_252 | GBOXPC | G box; Binding site of parsley cytosolic G-box binding factors (cytosolic GBFs); Cytosolic G-Box binding activity is modulated by light; DNA binding activity of cytosolic GBFs is regulated by cytosolic phosphorylation/dephospholylation activities; Cytosolic GBFs are translocated to the nucleus in a light-regulated manner | Upstream | -610 |
| 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 | -610 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -608 |
| Motif_388 | CPRFPCCHS;AtbZIP1 | BoxII; Binding site of CPRF-1, -2, -3 and -4(Common Plant Regulatory Factor) in the parsley light responsive chalcone synthase (CHS) gene promoter; CPRF proteins are bZIP class transcription factors; CPRF proteins participates in the light-mediated activation of the CHS gene in parsley; ACE; The proline-rich domains of CPRF1 and 4 activate transcription; CPRF1-containing bZIP heterodimer interacts with ACE in vivo; ACE; Binding site of parsley bZIP factors CPRF1 and 4; Found in the parsley light responsive chalcone synthase (CHS) gene promoter; The proline-rich domains of CPRF1 and 4 activate transcription; CPRF1-containing bZIP heterodimer interacts with ACE in vivo; The arabidopsis bZIP1 transcription factor is involved in sugar signaling, protein networking, and DNA binding | Upstream | -611 |
| Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -609 |
| | | Upstream | -608 |
| 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 | -609 |
| Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -397 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -610 |
| 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 | -611 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -1871 |
| | | Upstream | -1870 |
| | | Upstream | -1859 |
| | | Upstream | -1858 |
| | | Upstream | -1857 |
| | | Upstream | -1856 |
| | | Upstream | -1855 |
| | | Upstream | -1854 |
| | | Upstream | -1853 |
| 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 | -610 |
| Motif_638 | ABRE binding site motif | Not available | Upstream | -610 |
| 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 | Upstream | -1865 |
| 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 | -1865 |
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