| Matrix_109 | GBF3 | Not available | Upstream | -544 |
| Matrix_113 | ABI5 | Not available | Upstream | -544 |
| Matrix_122 | ABF1;AREB2 | Not available | Upstream | -543 |
| Matrix_130 | TCP16 | Not available | Upstream | -1971 |
| Matrix_134 | ABF1 | Not available | Upstream | -543 |
| Matrix_145 | GBF4;AT5G44080 | Not available | Upstream | -542 |
| Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -547 |
| Matrix_151 | ASIL1 | Not available | Upstream | -388 |
| Matrix_155 | RAP2.6;ERF110;ABR1 | Not available | Upstream | -424 |
| Matrix_156 | POC1 | Not available | Upstream | -544 |
| Matrix_164 | AT1G02030;AT2G45120;AZF2;AT3G60580 | Not available | Upstream | -513 |
| Matrix_176 | MYB98 | Not available | Upstream | -136 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -546 |
| Matrix_198 | STZ;C2H2;AZF3 | Not available | Upstream | -513 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -546 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -507 |
| | | Downstream | 3503 |
| Matrix_296 | GBF2 | Not available | Upstream | -543 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -543 |
| Matrix_301 | PIL5 | Not available | Upstream | -542 |
| Matrix_331 | GBF1 | Not available | Upstream | -544 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -543 |
| Matrix_334 | AT3G23230 | Not available | Upstream | -424 |
| Matrix_345 | POC1 | Not available | Upstream | -1993 |
| Matrix_379 | RHL41 | Not available | Upstream | -513 |
| Matrix_401 | MYB55 | Not available | Upstream | -428 |
| Matrix_406 | ATERF-7 | Not available | Upstream | -423 |
| Matrix_426 | CRF1;CRF2 | Not available | Upstream | -424 |
| Matrix_436 | AT3G49930;AZF1 | Not available | Upstream | -513 |
| Matrix_480 | BES1 | Not available | Upstream | -544 |
| Matrix_488 | ABF1 | Not available | Upstream | -551 |
| Matrix_506 | DRNL;ATERF-4 | Not available | Upstream | -424 |
| Matrix_510 | AtMYB84 | More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -432 |
| Matrix_55 | PIF3 | Not available | Upstream | -544 |
| Matrix_60 | AT1G01260;AT5G57150 | Not available | Upstream | -542 |
| Matrix_65 | POC1;PIL1 | Not available | Upstream | -542 |
| Matrix_7 | PIF4 | Not available | Upstream | -543 |
| Matrix_86 | CRF5;CRF6;CRF4 | Not available | Upstream | -424 |
| Motif_116 | INRNTPSADB | Inr (initiator) elements found in the tobacco psaDb gene promoter without TATA boxes; Light-responsive transcription of psaDb depends on Inr, but not TATA box | Upstream | -496 |
| Motif_153 | MARABOX1 | A-box found in SAR(scaffold attachment region; or matrix attachment region, MAR) | Upstream | -714 |
| | | Upstream | -710 |
| Motif_16 | -300ELEMENT | Present upstream of the promoter from the B-hordein gene of barley and the alpha-gliadin, gamma-gliadin, and low molecular weight glutenin genes of wheat; See S000001 -300CORE; See S000002 -300MOTIF | Downstream | 3596 |
| 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 | -541 |
| 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 | -487 |
| 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 | -541 |
| 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 | -543 |
| 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 | -542 |
| | | Upstream | -541 |
| 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 | -559 |
| | | Upstream | -487 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -543 |
| 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 | -541 |
| Motif_27 | MYB98 | MYB98 positively regulates a battery of synergid-expressed genes encoding filiform apparatus localized proteins | Downstream | 3480 |
| 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 | -543 |
| Motif_321 | TATABOX5 | TATA box; TATA box found in the 5'upstream region of pea (Pisum sativum) glutamine synthetase gene; a functional TATA element by in vivo analysis | Upstream | -711 |
| | | Upstream | -707 |
| | | Upstream | -703 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -487 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -541 |
| Motif_342 | POLASIG1 | PolyA signal; poly A signal found in legA gene of pea, rice alpha-amylase; -10 to -30 in the case of animal genes. Near upstream elements (NUE) in Arabidopsis | Upstream | -714 |
| | | Upstream | -710 |
| | | Upstream | -706 |
| Motif_371 | DRE-like promoter motif | The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses | Upstream | -557 |
| Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -542 |
| Motif_454 | DRECRTCOREAT | Core motif of DRE/CRT (dehydration-responsive element/C-repeat) cis-acting element found in many genes in Arabidopsis and in rice; Os DREB1A bound to GCCGAC more preferentially than to ACCGAC whereas At DREB1A bound to both GCCGAC and ACCGAC efficiently; Maize ZmDREB1A bound to DRE; HaDREB2 in Helianthus annuus (sunflower) | Upstream | -557 |
| 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 | -543 |
| Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Downstream | 3505 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -543 |
| 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 | Downstream | 3596 |
| Motif_570 | POLASIG2 | PolyA signal; poly A signal found in rice alpha-amylase; -10 to -30 in the case of animal genes | Upstream | -1362 |
| Motif_575 | TATABOX3 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene | Upstream | -481 |
| Motif_591 | CBFHV | Binding site of barley CBF1, and also of barley CBF2; CBF = C-repeat (CRT) binding factors; CBFs are also known as dehydration-responsive element (DRE) binding proteins (DREBs) | Upstream | -557 |
| 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 | -543 |
| Motif_638 | ABRE binding site motif | Not available | Upstream | -543 |
| Motif_641 | LRENPCABE | LRE; A positive light regulatory element in tobacco CAB (cab-E) gene; Located at -241 | Upstream | -544 |
| Motif_643 | DRE2COREZMRAB17 | DRE2 core found in maize rab17 gene promoter; DBF1 and DBF2 bound to DRE2; rab17 is expressed during late embryogenesis, and is induced by ABA | Upstream | -557 |
| 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 | -493 |
| | | Upstream | -492 |
| 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 | -540 |
| 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 | -556 |
| Motif_92 | ABREATRD22 | ABRE (ABA responsive element) in Arabidopsis dehydration-responsive gene rd22 | Upstream | -544 |
| Motif_98 | SEF3MOTIFGM | SEF3 binding site; Soybean consensus sequence found in the 5' upstream region of beta-conglycinin (7S globulin) gene; AACCCA(-27bp-)AACCCA; SEF=soybean embryo factor; SEF2; SEF3; SEF4 | Downstream | 3582 |
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