| Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -557 |
| Matrix_109 | GBF3 | Not available | Upstream | -557 |
| Matrix_113 | ABI5 | Not available | Upstream | -557 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -559 |
| Matrix_120 | BEE2 | Not available | Upstream | -556 |
| Matrix_129 | ABF1 | Not available | Upstream | -556 |
| Matrix_134 | ABF1 | Not available | Upstream | -556 |
| Matrix_147 | ERF3;AT1G80580 | Not available | Upstream | -586 |
| Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -560 |
| Matrix_150 | UNE10;PIF7 | Not available | Upstream | -555 |
| Matrix_153 | AP2 | Not available | Upstream | -557 |
| Matrix_156 | POC1 | Not available | Upstream | -557 |
| Matrix_19 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -559 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -559 |
| Matrix_200 | PIL5;AT4G28790;AT4G28800;AT4G28811;AT4G28815 | Not available | Upstream | -556 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -559 |
| Matrix_24 | POC1 | Not available | Upstream | -560 |
| Matrix_247 | PIF3 | Not available | Upstream | -556 |
| Matrix_264 | ATAREB1 | Not available | Upstream | -559 |
| Matrix_296 | GBF2 | Not available | Upstream | -556 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -556 |
| Matrix_301 | PIL5 | Not available | Upstream | -561 |
| | | Upstream | -555 |
| Matrix_331 | GBF1 | Not available | Upstream | -557 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -556 |
| Matrix_345 | POC1 | Not available | Upstream | -559 |
| Matrix_356 | PRR5 | Not available | Upstream | -559 |
| Matrix_403 | BZR1 | Not available | Upstream | -558 |
| Matrix_42 | AT2G45680 | Not available | Upstream | -495 |
| Matrix_438 | AtbZIP63 | Not available | Upstream | -556 |
| Matrix_449 | BIM2 | Not available | Upstream | -556 |
| Matrix_45 | DRN | Not available | Upstream | -586 |
| Matrix_488 | ABF1 | Not available | Upstream | -564 |
| Matrix_496 | ATMYB15 | Not available | Upstream | -473 |
| Matrix_514 | DYT1 | Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development | Upstream | -558 |
| Matrix_518 | AT2G21230 | Not available | Upstream | -452 |
| | | Upstream | -450 |
| Matrix_53 | MYC3 | Not available | Upstream | -558 |
| Matrix_55 | PIF3 | Not available | Upstream | -557 |
| Matrix_64 | PIF5 | Not available | Upstream | -555 |
| Matrix_7 | PIF4 | Not available | Upstream | -556 |
| 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 | -553 |
| 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 | -554 |
| Motif_182 | MYB2CONSENSUSAT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; see MYB2 and MYBATRD22 | Upstream | -449 |
| Motif_190 | WUSATAg | Target sequence of WUS in the intron of AGAMOUS gene in Arabidopsis | Upstream | -1463 |
| 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 | -554 |
| | | Upstream | -504 |
| | | Upstream | -449 |
| | | Upstream | -214 |
| | | Downstream | 1088 |
| 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 | -555 |
| 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 | Upstream | -449 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -556 |
| | | Upstream | -520 |
| 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 | -214 |
| Motif_258 | -10PEHVPSBD | -10 promoter element found in the barley (H.v.) chloroplast psbD gene promoter; Involved in the expression of the plastid gene psbD which encodes a photosystem II reaction center chlorophyll-binding protein that is activated by blue, white or UV-A light | Downstream | 1095 |
| 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 | -252 |
| 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 | -556 |
| Motif_317 | GAREAT | GARE (GA-responsive element); Occurrence of GARE in GA-inducible, GA-responsible, and GA-nonresponsive genes found in Arabidopsis seed germination was 20, 18, and 12%, respectively | Upstream | -525 |
| | | Upstream | -221 |
| | | Downstream | 1090 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -449 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -554 |
| | | Upstream | -518 |
| 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 | -534 |
| Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -555 |
| Motif_453 | HEXMOTIFTAH3H4 | hexamer motif found in promoter of wheat histone genes H3 and H4; CaMV35S; NOS; Binding with HBP-1A and HBP-1B; Binding site of wheat nuclear protein HBP-1 (histone DNA binding protein-1); HBP-1 has a leucine zipper motif; hexamer motif in type 1 element may play important roles in regulation of replication- dependent but not of replication-independent expression of the wheat histone H3 gene;Rice OBF1-homodimer-binding site | Upstream | -517 |
| 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 | -557 |
| Motif_520 | AMYBOX1 | amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barley | Upstream | -525 |
| | | Upstream | -221 |
| | | Downstream | 1090 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -556 |
| Motif_576 | TGACGTVMAMY | TGACGT motif found in the Vigna mungo alpha-Amylase (Amy) gene promoter; Located between -128 and -123; Required for high level expression of alpha-Amylase in the cotyledons of the germinated seeds | Upstream | -517 |
| Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -525 |
| | | Upstream | -221 |
| | | Downstream | 1090 |
| Motif_614 | MYBGAHV | Central element of gibberellin (GA) response complex (GARC) in high-pI alpha-amylase gene in barley; Similar to c-myb and v-myb consensus binding site; GAmyb binds specifically to the TAACAAA box in vitro; GAmyb is the sole GA-regulated transcriptional factor required for transcriptional activation of the high-pI alpha-amylase; GARC consist of the pyrimidine, TAACAAA and TATCCAC boxes; GARE in RAmy1A gene; GARE and pyrimidine box in RAmy1A are partially involved in sugar repression | Upstream | -525 |
| | | Upstream | -221 |
| | | Downstream | 1090 |
| 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 | -556 |
| Motif_638 | ABRE binding site motif | Not available | Upstream | -556 |
| Motif_645 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -214 |
| 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 | -250 |
| Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -525 |
| | | Upstream | -221 |
| | | Downstream | 1090 |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Upstream | -382 |
| | | Upstream | -214 |
| Motif_85 | SORLIP5AT | one of Sequences Over-Represented in Light-Induced Promoters (SORLIPs) in Arabidopsis; Computationally identified phyA-induced motifs; Over-represented in both light-induced cotyledon-specific and root-specific genes; Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | Upstream | -499 |
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