| Matrix_104 | PI | Not available | Upstream | -1148 |
| Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -1148 |
| | | Upstream | -708 |
| Matrix_109 | GBF3 | Not available | Upstream | -1146 |
| Matrix_113 | ABI5 | Not available | Upstream | -1148 |
| | | Upstream | -1146 |
| Matrix_120 | BEE2 | Not available | Upstream | -1147 |
| Matrix_122 | ABF1;AREB2 | Not available | Upstream | -1148 |
| Matrix_129 | ABF1 | Not available | Upstream | -1147 |
| Matrix_134 | ABF1 | Not available | Upstream | -1146 |
| Matrix_143 | GATA14;GATA6;GATA5 | Not available | Intron | 246 |
| Matrix_153 | AP2 | Not available | Upstream | -1148 |
| Matrix_156 | POC1 | Not available | Upstream | -1146 |
| | | Upstream | -708 |
| Matrix_186 | FHY3 | Not available | Upstream | -166 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -1146 |
| Matrix_194 | HYH;HY5 | Not available | Upstream | -1150 |
| Matrix_196 | TCP20;AT5G41030 | Not available | Upstream | -679 |
| Matrix_200 | PIL5;AT4G28790;AT4G28800;AT4G28811;AT4G28815 | Not available | Upstream | -1147 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -1150 |
| | | Upstream | -1146 |
| Matrix_232 | TCP23 | Not available | Upstream | -680 |
| Matrix_247 | PIF3 | Not available | Upstream | -1147 |
| Matrix_260 | CAMTA3 | Not available | Upstream | -1151 |
| Matrix_264 | ATAREB1 | Not available | Upstream | -1150 |
| Matrix_296 | GBF2 | Not available | Upstream | -1146 |
| Matrix_297 | TCP15 | Not available | Upstream | -680 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -1146 |
| Matrix_301 | PIL5 | Not available | Upstream | -1152 |
| Matrix_323 | BIM3 | Not available | Upstream | -1147 |
| Matrix_331 | GBF1 | Not available | Upstream | -1146 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -1146 |
| Matrix_338 | AP2 | Not available | Upstream | -1150 |
| Matrix_339 | bHLH104 | Not available | Upstream | -1147 |
| Matrix_345 | POC1 | Not available | Upstream | -1151 |
| Matrix_369 | AT2G18300 | Not available | Upstream | -1149 |
| Matrix_389 | ILR3 | Not available | Upstream | -1147 |
| Matrix_403 | BZR1 | Not available | Upstream | -1149 |
| Matrix_42 | AT2G45680 | Not available | Upstream | -681 |
| Matrix_438 | AtbZIP63 | Not available | Upstream | -1149 |
| Matrix_443 | AGL15 | Not available | Upstream | -1149 |
| Matrix_449 | BIM2 | Not available | Upstream | -1147 |
| Matrix_452 | MYB46 | Not available | Upstream | -242 |
| Matrix_456 | bZIP60 | Not available | Upstream | -1147 |
| Matrix_48 | PI | Not available | Upstream | -307 |
| Matrix_49 | FHY3/FAR1 | Not available | Upstream | -169 |
| Matrix_514 | DYT1 | Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development | Upstream | -1149 |
| Matrix_55 | PIF3 | Not available | Upstream | -1148 |
| | | Upstream | -708 |
| Matrix_56 | BZIP17;BZIP28;BZIP49 | Not available | Upstream | -1151 |
| | | Upstream | -1148 |
| Matrix_64 | PIF5 | Not available | Upstream | -1146 |
| Matrix_65 | POC1;PIL1 | Not available | Upstream | -1145 |
| Matrix_7 | PIF4 | Not available | Upstream | -1145 |
| Matrix_77 | PRR5 | Not available | Upstream | -1149 |
| | | Upstream | -1148 |
| | | Upstream | -167 |
| Matrix_80 | BIM1 | Not available | Upstream | -1148 |
| Motif_139 | RHERPATEXPA7 | Right part of RHEs (Root Hair-specific cis-Elements) conserved among the Arabidopsis thaliana A7 (AtEXPA7) orthologous (and paralogous) genes from diverse angiosperm species with different hair distribution patterns | Upstream | -1146 |
| Motif_165 | AP3SV40 | AP-3 binding site consensus sequence in enhancer regions of SV40, MMTV, MLV, IL2 | Upstream | -187 |
| 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 | -1145 |
| 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 | -1145 |
| | | Downstream | 11395 |
| Motif_216 | PYRIMIDINEBOXHVEPB1 | Pyrimidine box found in the barley EPB-1 (cysteine proteinase) gene promoter; Located between -120 to -113; Required for GA induction | Upstream | -172 |
| 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 | -1145 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -1145 |
| Motif_261 | S1FBOXSORPS1L21 | S1F box conserved both in spinach RPS1 and RPL21 genes encoding the plastid ribosomal protein S1 and L21, respectively; Negative element; Might play a role in downregulating RPS1 and RPL21 promoter activity | Upstream | -379 |
| 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 | -1145 |
| 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 | -1151 |
| Motif_332 | SV40COREENHAN | SV40 core enhancer; Similar sequences found in rbcS genes | Upstream | -1350 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -1145 |
| 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 | Upstream | -26 |
| Motif_382 | CATATGGMSAUR | Sequence found in NDE element in soybean SAUR (Small Auxin-Up RNA) 15A gene promoter; Involved in auxin responsiveness | Downstream | 11395 |
| Motif_419 | MYB4 binding site motif | Not available | Upstream | -238 |
| | | Upstream | -180 |
| Motif_437 | ANAERO2CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1) | Upstream | -11 |
| Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -1145 |
| 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 | -1142 |
| Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -164 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -1144 |
| Motif_563 | PYRIMIDINEBOXOSRAMY1A | Pyrimidine box found in rice alpha-amylase (RAmy1A) gene; Gibberellin-respons cis-element of GARE and pyrimidine box are partially involved in sugar repression; Found in the promoter of barley alpha-amylase (Amy2/32b) gene which is induced in the aleurone layers in response to GA; BPBF protein binds specifically to this site | Upstream | -303 |
| | | Upstream | -174 |
| 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 | -1144 |
| Motif_638 | ABRE binding site motif | Not available | Upstream | -1145 |
| Motif_653 | INTRONLOWER | 3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns | Upstream | -74 |
| 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 | -385 |
| | | Upstream | -377 |
| | | Upstream | -316 |
| | | Upstream | -306 |
| | | Upstream | -305 |
| | | Upstream | -251 |
| | | Upstream | -250 |
| | | Upstream | -171 |
| | | Upstream | -170 |
| | | Downstream | 11373 |
| 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 | -305 |
| | | Upstream | -171 |
| 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 | -40 |
| | | Upstream | -38 |
| | | Upstream | -36 |
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