| Matrix_104 | PI | Not available | Upstream | -1524 |
| Matrix_105 | SPL14 | Not available | Upstream | -1517 |
| Matrix_113 | ABI5 | Not available | Upstream | -1524 |
| | | Upstream | -1522 |
| Matrix_122 | ABF1;AREB2 | Not available | Upstream | -1523 |
| Matrix_129 | ABF1 | Not available | Upstream | -1523 |
| Matrix_130 | TCP16 | Not available | Upstream | -1546 |
| Matrix_134 | ABF1 | Not available | Upstream | -1523 |
| Matrix_145 | GBF4;AT5G44080 | Not available | Upstream | -1522 |
| Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -1527 |
| Matrix_190 | ATERF1 | Not available | Upstream | -1530 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -1526 |
| | | Upstream | -1522 |
| Matrix_194 | HYH;HY5 | Not available | Upstream | -1526 |
| Matrix_216 | TCP16 | Not available | Upstream | -1546 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -1526 |
| Matrix_234 | RAP2.3 | Not available | Upstream | -1529 |
| Matrix_24 | POC1 | Not available | Upstream | -1527 |
| Matrix_264 | ATAREB1 | Not available | Upstream | -1526 |
| | | Upstream | -1523 |
| Matrix_266 | TCP16 | Determinants of the DNA binding specificity of class I and class II TCP transcription factors | Upstream | -1546 |
| Matrix_278 | AtbZIP44 | Not available | Upstream | -1419 |
| Matrix_281 | TCP13 | Not available | Upstream | -1546 |
| Matrix_288 | RAP2.3 | Not available | Upstream | -1528 |
| Matrix_294 | MEE35 | Not available | Upstream | -1546 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -1523 |
| Matrix_301 | PIL5 | Not available | Upstream | -1522 |
| Matrix_31 | SPL1 | Not available | Upstream | -1513 |
| Matrix_338 | AP2 | Not available | Upstream | -1526 |
| Matrix_342 | SPL14 | Identification of a Consensus DNA-Binding Site for the Arabidopsis thaliana SBP Domain Transcription Factor, AtSPL14, and Binding Kinetics by Surface Plasmon Resonance | Upstream | -1517 |
| Matrix_343 | AT2G33710 | Not available | Upstream | -1529 |
| Matrix_356 | PRR5 | Not available | Upstream | -1530 |
| Matrix_360 | ORA59 | Not available | Upstream | -1590 |
| Matrix_363 | RAP2.3 | Not available | Upstream | -1528 |
| Matrix_378 | ATERF1 | Not available | Upstream | -1529 |
| Matrix_40 | TCP2 | Not available | Upstream | -1546 |
| Matrix_403 | BZR1 | Not available | Upstream | -1525 |
| Matrix_443 | AGL15 | Not available | Upstream | -1525 |
| Matrix_473 | RRTF1 | Not available | Upstream | -1529 |
| Matrix_488 | ABF1 | Not available | Upstream | -1531 |
| Matrix_50 | ATERF14;AT5G43410 | Not available | Upstream | -1528 |
| Matrix_507 | TCP3 | Not available | Upstream | -1547 |
| Matrix_55 | PIF3 | Not available | Upstream | -1524 |
| Matrix_7 | PIF4 | Not available | Upstream | -1523 |
| Matrix_77 | PRR5 | Not available | Upstream | -1524 |
| Matrix_82 | TCP17 | Not available | Upstream | -1546 |
| Matrix_94 | TCP5 | Not available | Upstream | -1546 |
| 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 | -1521 |
| 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 | -1521 |
| 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 | -1523 |
| 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 | -1522 |
| | | Upstream | -1521 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -1523 |
| | | Upstream | -1521 |
| Motif_249 | DPBF1&2 binding site motif | A novel class of bZIP transcription factors, DPBF-1 and 2 (Dc3 promoter-binding factor-1 and 2) binding core sequence; Found in the carrot Dc3 gene promoter; Dc3 expression is normally embryo-specific, and also can be induced by ABA; The Arabidopsis abscisic acid response gene ABI5 encodes a bZIP transcription factor; abi5 mutant have a pleiotropic defects in ABA response; ABI5 regulates a subset of late embryogenesis-abundant genes; GIA1 (growth-insensitivity to ABA) is identical to ABI5; Isolation of a novel class of bZIP transcription factors that interact with ABA-responsive and embryo-specification elements in the Dc3 promoter using a modified yeast one-hybrid system | Upstream | -1521 |
| 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 | -1523 |
| Motif_313 | ERF1 BS in AtCHI-B | Core of GCC-box found in many pathogen-responsive genes such as PDF1.2, Thi2.1, and PR4; Has been shown to function as ethylene-responsive element; Appears to play important roles in regulating jasmonate-responsive gene expression; Tomato Pti4 (ERF) regulates defence-related gene expression via GCC box and non-GCC box cis elements (Myb1 (GTTAGTT) and G-box(CACGTG)); Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1;Molecular responses to dehydration and low temperature | Upstream | -1526 |
| Motif_320 | AGCBOXNPGLB | AGC box repeated twice in a 61 bp enhancer element in tobacco class I beta-1,3-glucanase (GLB) gene;GCC-box; Binding sequence of Arabidopsis AtERFs; AtERF1,2 and 5 functioned as activators of GCC box-dependent transcription; AtERF3 and 4 acted as repressors; AtERF proteins are stress signal-response factors; EREBP2 binding site; Conserved in most PR-protein genes; Rice MAPK (BWMK1) phosphorylates OS EREBP1, which enhance DNA-binding activity of the factor to the GCC box | Upstream | -1527 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -1521 |
| Motif_402 | AtTINY2 | Molecular cloning, phylogenetic analysis, expressional profiling and in vitro studies of TINY2 from Arabidopsis thaliana | Upstream | -1528 |
| Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -1522 |
| Motif_50 | AtERF-7;AtERF-4;AtERF-3;AtERF-1;AtERF-2;AtERF-5 | Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses | Upstream | -1528 |
| Motif_542 | ABI5;AtMYC2;HY5 | A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth. Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. The homologous ABI5 and EEL transcription factors function antagonistically to fine-tune gene expression during late embryogenesis | Upstream | -1523 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -1523 |
| Motif_619 | SITEIIBOSPCNA | Site IIb of rice PCNA (proliferating cell nuclear antigen) gene; Found at -178 to -169; Binding site for two nuclear proteins, PCF1 and PCF2; Suggested to be involved in meristematic tissue-specific expression; Resemble the conserved motif (T/GGTCCCAT) found in promoter regions of auxin-regulated genes | Upstream | -1545 |
| 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 | -1523 |
| | | Upstream | -1520 |
| Motif_638 | ABRE binding site motif | Not available | Upstream | -1523 |
| 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 | -1520 |
| Motif_92 | ABREATRD22 | ABRE (ABA responsive element) in Arabidopsis dehydration-responsive gene rd22 | Upstream | -1524 |
Expansion plot
Gene family finder
Ks-graphs
Skyline plot
Synteny plot
WGDotplot
Functional clusters
WGMapping
BLAST
Workbench