| Matrix_104 | PI | Not available | Upstream | -193 |
| Matrix_106 | AT5G47390 | Not available | Upstream | -240 |
| Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -193 |
| Matrix_109 | GBF3 | Not available | Upstream | -193 |
| | | Upstream | -191 |
| Matrix_113 | ABI5 | Not available | Upstream | -193 |
| | | Upstream | -191 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -196 |
| | | Upstream | -195 |
| Matrix_120 | BEE2 | Not available | Upstream | -192 |
| Matrix_122 | ABF1;AREB2 | Not available | Upstream | -192 |
| Matrix_129 | ABF1 | Not available | Upstream | -192 |
| Matrix_134 | ABF1 | Not available | Upstream | -192 |
| Matrix_14 | ZCW32;AT5G62610 | Not available | Upstream | -192 |
| Matrix_145 | GBF4;AT5G44080 | Not available | Upstream | -191 |
| Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -196 |
| Matrix_156 | POC1 | Not available | Upstream | -193 |
| | | Upstream | -191 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -195 |
| Matrix_194 | HYH;HY5 | Not available | Upstream | -195 |
| Matrix_200 | PIL5;AT4G28790;AT4G28800;AT4G28811;AT4G28815 | Not available | Upstream | -192 |
| Matrix_214 | AP1 | Not available | Upstream | -194 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -195 |
| Matrix_233 | MYC3 | Not available | Upstream | -191 |
| Matrix_247 | PIF3 | Not available | Upstream | -192 |
| Matrix_264 | ATAREB1 | Not available | Upstream | -192 |
| Matrix_296 | GBF2 | Not available | Upstream | -192 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -192 |
| | | Upstream | -191 |
| Matrix_305 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -194 |
| Matrix_331 | GBF1 | Not available | Upstream | -193 |
| | | Upstream | -191 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -192 |
| | | Upstream | -191 |
| Matrix_338 | AP2 | Not available | Upstream | -195 |
| Matrix_345 | POC1 | Not available | Upstream | -196 |
| | | Upstream | -195 |
| Matrix_356 | PRR5 | Not available | Upstream | -195 |
| Matrix_389 | ILR3 | Not available | Upstream | -192 |
| Matrix_403 | BZR1 | Not available | Upstream | -194 |
| Matrix_438 | AtbZIP63 | Not available | Upstream | -192 |
| Matrix_443 | AGL15 | Not available | Upstream | -194 |
| Matrix_488 | ABF1 | Not available | Upstream | -200 |
| Matrix_55 | PIF3 | Not available | Upstream | -193 |
| Matrix_64 | PIF5 | Not available | Upstream | -191 |
| Matrix_7 | PIF4 | Not available | Upstream | -192 |
| Matrix_77 | PRR5 | Not available | Upstream | -194 |
| Matrix_80 | BIM1 | Not available | Upstream | -193 |
| Motif_138 | RAP2.2 | Transcription factor RAP2.2 and its interacting partner SINAT2: stable elements in the carotenogenesis of Arabidopsis leaves | Upstream | -1545 |
| 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 | -209 |
| Motif_174 | SREATMSD | sugar-repressive element (SRE) found in 272 of the 1592 down-regulated genes after main stem decapitation in Arabidopsis | Upstream | -208 |
| 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 | -190 |
| Motif_181 | IBOXCORENT | I-box core motif in the CAMs (conserved DNA modular arrays) associated with light-responsive promoter regions | Upstream | -210 |
| 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 | -190 |
| 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 | -192 |
| 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 | -191 |
| | | Upstream | -190 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -192 |
| | | Upstream | -190 |
| 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 | Upstream | -175 |
| 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 | -192 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -190 |
| Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -191 |
| | | Upstream | -190 |
| Motif_459 | SORLIP1 | Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | Upstream | -120 |
| 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 | -191 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Upstream | -175 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -192 |
| Motif_599 | LREBOXIIPCCHS1;HY5 | BoxII; Light responsive element (LRE) found in the parsley CHS-1 (chalcone synthase-1) gene promoter; Required for light responsiveness; nuclear protein binding site; Highly conserved in various light inducible gene promoters; Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression | Upstream | -192 |
| Motif_603 | SITEIIATCYTC | Site II element found in the promoter regions of cytochrome genes (Cytc-1, Cytc-2) in Arabidopsis; Located between -147 and -156 from the translational starts sites;Overrepresented in the promoters of nuclear genes encoding components of the oxidative phosphorylation (OxPhos) machinery from both Arabidopsis and rice | Upstream | -133 |
| 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 | -192 |
| Motif_628 | TATCCAOSAMY | TATCCA element found in alpha-amylase promoters of rice at positions ca.90 to 150bp upstream of the transcription start sites; Binding sites of OsMYBS1, OsMYBS2 and OsMYBS3 which mediate sugar and hormone regulation of alpha-amylase gene expression; See also AMYBOX2 | Upstream | -207 |
| Motif_638 | ABRE binding site motif | Not available | Upstream | -192 |
| Motif_641 | LRENPCABE | LRE; A positive light regulatory element in tobacco CAB (cab-E) gene; Located at -241 | Upstream | -193 |
| Motif_79 | UPRMOTIFIIAT | Motif II in the conserved UPR (unfolded protein response) cis-acting element in Arabidopsis genes coding for SAR1B, HSP-90, SBR-like, Ca-ATPase 4, CNX1, PDI, etc | Upstream | -188 |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Upstream | -180 |
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