PLAZA 3.0 Dicots : Binding Sites

Binding sites with simlar sequences

Binding site: Motif_368
Name: CBF1 BS in cor15a
Description: Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs

Sequence: TGGCCGAC
Positional Weight Matrix

Minimum similarity percentage

Binding site	Name	Description	Similarity
Motif_99	DREB1A; DREB1C; DREB1B	Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems;Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression;Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit	75.00%
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	75.00%
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)	68.75%
Matrix_294	MEE35	Not Available	66.50%
Matrix_86	CRF5; CRF6; CRF4	Not Available	65.97%
Matrix_506	DRNL; ATERF-4	Not Available	65.72%
Matrix_426	CRF1; CRF2	Not Available	65.00%
Matrix_245	WRKY62; WRKY38	Not Available	64.97%
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	62.50%
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)	62.50%
Motif_457	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	62.50%
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	62.50%
Motif_189	CMSRE1IBSPOA	CMSRE-1 (Carbohydrate Metabolite Signal Responsive Element 1) found in the promoter of sweet potato sporamin A gene	62.50%
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	62.50%
Motif_545	SORLIP1AT	one of Sequences Over-Represented in Light-Induced Promoters (SORLIPs) in Arabidopsis; Computationally identified phyA-induced motifs; SORLIP 1 is most over-represented, and most statistically singnificant; Over-represented in light-induced cotyledon and root common genes and root-specific genes	62.50%
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	62.50%
Motif_543	TATCCACHVAL21	TATCCAC box is a part of the conserved cis-acting response complex (GARC) that most often contain three sequence motifs, the TAACAAA box, or GA-responsive element (GARE); the pyrimidine box, CCTTTT (see S000259); and the TATCCAC box, which are necessary for a full GA response	62.50%
Motif_510	LTRECOREATCOR15	Core of low temperature responsive element (LTRE) of cor15a gene in Arabidopsis; A portion of repeat-C (C-repeat), TGGCCGAC, which is repeated twice in cor15a promoter; ABA responsiveness; Involved in cold induction of BN115 gene from winter Brassica napus; LTRE; Light signaling mediated by phytochrome is necessary for cold- or drought- induced gene expression through the C/DRE in Arabidopsis	62.50%
Motif_525	CRTDREHVCBF2	Preferred sequence for AP2 transcriptional activator HvCBF2 of barley; Core CRT/DRE motif; HvCBF2 bound to a (G/a)(T/c)CGAC core motif; DNA binding is regulated by temperature	62.50%
Matrix_82	TCP17	Not Available	62.34%
Matrix_334	AT3G23230	Not Available	61.92%
Matrix_235	WRKY67; WRKY64; WRKY63; WRKY66	Not Available	60.33%
Matrix_281	TCP13	Not Available	60.31%
Matrix_275	ZAP1	Characterization of a zinc-dependent transcriptional activator from Arabidopsis	59.94%
Matrix_94	TCP5	Not Available	59.29%
Matrix_289	WRKY25	Not Available	59.28%
Matrix_368	ATWRKY56; WRKY45; WRKY75; WRKY24	Not Available	56.99%
Matrix_325	WRKY4; WRKY3; WRKY58; ATWRKY34; WRKY20; ATWRKY2	Not Available	56.70%
Matrix_242	AT2G25820; AT3G16280; AT4G32800; TINY2; tny	Not Available	56.62%
Motif_552	MRE1	MRE (metal responsive element); Consensus sequence of MRE; MRE; MEP-1; MBF-1; MTF-1	56.52%
Motif_307	TATCCAYMOTIFOSRAMY3D	TATCCAY motif found in rice RAmy3D alpha-amylase gene promoter; a GATA motif as its antisense sequence; TATCCAY motif and G motif are responsible for sugar repression	56.25%
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	56.25%
Motif_393	AUXREPSIAA4	AuxRE (Auxine responsive element ) of pea PS-IAA4/5 gene; Indoleacetic acid-inducible genes; domain A; TGA1a is preferentially expressed in root tip meristems; TGA1a may contribute to the expression of GST isoenzymes, especially in root tip meristems	56.25%
Matrix_484	ATERF13	Not Available	55.63%
Matrix_321	HRD	Not Available	55.63%
Motif_371	DRE-like promoter motif	The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses	55.28%
Matrix_146	ORA47	Not Available	55.08%
Matrix_73	DEAR3; RAP2.9; RAP2.10	Not Available	55.06%
Matrix_482	AT2G25650; AT4G00270	Not Available	53.88%
Matrix_243	RAP2.12; RAP2.2	Not Available	53.57%
Matrix_478	AT1G01250	Not Available	53.44%
Matrix_390	GT-1	Not Available	53.22%
Matrix_61	ATCBF3	Not Available	53.03%
Matrix_360	ORA59	Not Available	52.17%
Motif_372	E2FAT	E2F-binding site found in many potential E2F target genes; most potential E2F targets identified in silico show a cell cycle-regulated expression	51.67%
Motif_443	KN1; BP	The knotted1-like homeobox gene BREVIPEDICELLUS regulates cell differentiation by modulating metabolic pathways. Selective interaction of plant homeodomain proteins mediates high DNA-binding affinity	51.67%
Matrix_147	ERF3; AT1G80580	Not Available	51.06%
Matrix_295	ERF1	Not Available	50.97%
Matrix_504	WRKY40	Not Available	50.80%
Matrix_42	AT2G45680	Not Available	50.72%
Matrix_232	TCP23	Not Available	50.57%
Matrix_344	ATERF15; AT4G18450	Not Available	50.22%
Matrix_261	ATERF-1	Not Available	50.18%
Matrix_297	TCP15	Not Available	50.12%
Motif_310	ANAERO3CONSENSUS	One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1); Arbitrary named ANAERO3CONSENSUS by the PLACEdb curator	50.00%
Motif_351	GARE1OSREP1	Gibberellin-responsive element (GARE) found in the promoter region of a cystein proteinase (REP-1) gene in rice	50.00%
Motif_312	OCTAMERMOTIFTAH3H4	Octamer motif found in promoter of wheat histone genes H3 and H4, and corn histone genes H3 and H4; Arabidopsis histone H4; histone-specific octamer; About half of the Oct motifs are present together with another element, HexA, TCA or CCAAT-box, forming OCES (Oct-containing composite elements); Nucleotide sequences of two corn histone H3 genes. Genomic organization of the corn histone H3 and H4 genes	50.00%
Motif_219	E2Fa	The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants	50.00%
Motif_144	DREB2A; DREB1A	Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems;Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses	50.00%
Motif_163	BOXCPSAS1	Box C in pea (P.s.) asparagine synthetase (AS1) gene; Found at -45; AS1 is negatively regulated by light; Box C binds with nuclear proteins, which was competed by a putative repressor element RE1	50.00%
Motif_132	PIATGAPB	PI found in the Arabidopsis thaliana GAPB gene promoter; Located between -157 and -150; Mutations in the PI resulted in reductions of light-activated gene transcription; GAPB encodes the B subunit of chloroplast glyceraldehyde-3-phosphate dehydrogenase(GADPH) of A.T.; Promoter analysis of the nuclear gene encoding the chloroplast glyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsis thaliana	50.00%
Motif_122	TGTCACACMCUCUMISIN	TGTCACA motif found in the region (from -254 to -215) of cucumisin (a subtilisin-like serine protease) in the fruit of melon; A novel enhancer element necessary for fruit-specific expression of the cucumisin gene	50.00%
Motif_118	CAATBOX2	CAAT box found in the 5' upstream region (-80) of many eukaryotic genes; GGC(or T)CAATCT	50.00%
Motif_199	GCN4OSGLUB1	GCN4 motif found in GluB-1 gene in rice; Required for endosperm-specific expression; AACA and ACGT motifs was found sufficient to confer a detectable level of endosperm expression; This motif is the recognition site for a basic leucine zipper transcription factor that belongs to the group of maize Opaque-2 (O2)-like proteins; Although all the RISBZ proteins are able to interact with the GCN4 motif, only RISBZ1 is capable of activating the gene expression	50.00%
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	50.00%
Motif_293	NONAMERATH4	Nonamer motif of Arabidopsis thaliana histone H4 promoter;Identification of cis-elements regulating the expression of an Arabidopsis histone H4 gene	50.00%
Motif_286	SEBFCONSSTPR10A	Binding site of the potato silencing element binding factor (SEBF) gene found in promoter of pathogenesis-related gene (PR-10a); Located between -45 and -39; Similar to the auxin response element	50.00%
Motif_287	BIHD1OS	Binding site of OsBIHD1, a rice BELL homeodomain transcription factor	50.00%
Motif_270	ELRECOREPCRP1	ElRE (Elicitor Responsive Element) core of parsley PR1 genes; consensus sequence of elements W1 and W2 of parsley PR1-1 and PR1-2 promoters; Box W1 and W2 are the binding site of WRKY1 and WRKY2, respectively; ERE; WA box; One of the W boxes found in the Parsley WRKY1 gene promoter; Required for elicitor responsiveness; WC box WB box and WC box constitute a palindrome; WRKY1 protein binding site; W-box found in thioredoxin h5 gene in Arabidopsis	50.00%
Motif_305	SP1SV40	SP-1 binding site (GC box) in enhancer regions of SV40 and human metallothionein IIA (hMT IIA)	50.00%
Motif_469	QELEMENTZMZM13	Q(quantitative)-element in maize ZM13 gene promoter; Found at -107 to -102; Involved in expression enhancing activity; ZM13 is a maize homolog of tomato LAT52 gene; ZM13 is a pollen-specific maize gene	50.00%
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	50.00%
Motif_632	EREGCC	GCC box in ERE (ethylene responsive element); Ethylene-responsive region of tobacco (N.t.) chitinase gene contains two copies of the GCC-box; ERF2 and ERF4 enhanced the GCC box-mediated transcription; ERF3 reduced the transcription of the reporter gene in tobacco protoplasts; Binding site of AtEBP; Pti4/5/6 proteins from tomato which belong to the ERF family activate the expression of GCC box-containing PR genes; ERF3 was found to interact with NtUBC2, a ubiquitin-conjugating enzyme; Identification of an ethylene-responsive region in the promoter of a tobacco class I chitinase gene	50.00%
Motif_625	AtERF-4; AtERF-3	Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression	50.00%
Motif_622	SORLIP2AT	one of Sequences Over-Represented in Light-Induced Promoters (SORLIPs) in Arabidopsis; Computationally identified phyA-induced motifs; See also all SORLIPs and also all SORLREPs; Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data	50.00%
Motif_602	E2Fc; E2Fd	The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants	50.00%
Motif_620	DREB1&2 BS in rd29a	Related to responsiveness to drought, low-temperature or high-salt stress; Binding site of DREB1 and DREB2: Binding site of Arabidopsis CBF1(C-repeat/DRE binding factor); Overexpression of DREB1A activated the expression of stress tolerance genes; CBF1 overexpression induces COR genes and enhances freezing tolerance; Heterologous CBF1 expression enhances oxidative stresses tolerance; DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A in Arabidopsis;Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor	50.00%
Motif_639	WRKY18	Identification of genes encoding receptor-like protein kinases as possible targets of pathogen- and salicylic acid-induced WRKY DNA-binding proteins in Arabidopsis	50.00%
Motif_650	SITEIIAOSPCNA	Site IIa of rice PCNA (proliferating cell nuclear antigen) gene; Found at -197 to -188; 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; See AUXREPSIAA4	50.00%
Motif_663	E2F binding site motif; E2F/DP BS in AtCDC6	Not Available	50.00%
Motif_685	PALINDROMICCBOXGM	Palindromic C-box in soybean;bZIP factors, STGA1 and STFs (STF1 and STF2) found in soybean apical hypocotyl, bind to this sequence	50.00%
Motif_661	WBOXATNPR1	W-box found in promoter of Arabidopsis thaliana NPR1 gene; Located between +70 and +79 in tandem; They were recognized specifically by salicylic acid (SA)-induced WRKY DNA binding proteins; A cluster of WRKY binding sites act as negative regulatory elements for the inducible expression of AtWRKY18; Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expression	50.00%
Motif_653	INTRONLOWER	3' intron-exon splice junctions; Plant intron lower sequence; Consensus sequence for plant introns	50.00%
Motif_652	AUXRETGA2GMGH3	TGA-box #2 in putative auxin-resonsive element (AUXRE) E1 of soybean GH3 promoter; Strong binding site for proteins in plant nuclear extracts; Hex-like element; E1 element=-249 to -203; E2 element=-241 to -224	50.00%
Motif_590	MYB3 binding site motif	Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses	50.00%
Motif_586	ASF1MOTIFCAMV	ASF-1 binding site in CaMV 35S promoter; ASF-1 binds to two TGACG motifs; Found in HBP-1 binding site of wheat histone H3 gene; TGACG motifs are found in many promoters and are involved in transcriptional activation of several genes by auxin and/or salicylic acid; May be relevant to light regulation; Binding site of tobacco TGA1a; TGA1a and b show homology to CREB; TGA6 is a new member of the TGA family; Abiotic and biotic stress differentially stimulate as-1 element activity	50.00%
Motif_461	MYB80	The MYB80 transcription factor is required for pollen development and the regulation of tapetal programmed cell death in Arabidopsis thaliana	50.00%
Motif_462	TE2F2NTPCNA	te2f-2 found in the promoter of tobacco PCNA gene; Located between -84 and -77; Binding site of OsE2F1 and OsE2F2; Involved in transcriptional activation in actively dividing cells and tissue	50.00%
Motif_437	ANAERO2CONSENSUS	One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1)	50.00%
Motif_412	SORLREP5AT	one of Sequences Over-Represented in Light-Repressed Promoters (SORLREPs) in Arabidopsis; Computationally identified phyA-repressed motifs; See also all SORLREPs and all SORLIPs; Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data	50.00%
Motif_402	AtTINY2	Molecular cloning, phylogenetic analysis, expressional profiling and in vitro studies of TINY2 from Arabidopsis thaliana	50.00%
Motif_405	DREB2A; DREB1A	Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems. Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses	50.00%
Motif_485	NRRBNEXTA	NRR (negative regulatory region) in promoter region of Brassica napus extA extensin gene; Removal of this region leads to expression in all tissues within the stem internode, petiole and root	50.00%
Motif_490	PROLAMINBOXOSGLUB1	Prolamine box found in the rice GluB-1 gene promoter; Involved in quantitative regulation of the GluB-1 gene	50.00%
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	50.00%
Motif_577	GRAZMRAB28	GRA; GC-rich rab activator; Found in the promoter of ABA responsive rab28 gene from maize; Similar (seven of 12 bases) to the GRA element from the maize rab17 promoter (GRAZMRAB17); Found at -138 to -130	50.00%
Motif_522	E2Fa	The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants	50.00%
Motif_513	WRKY71OS	A core of TGAC-containing W-box of, e.g., Amy32b promoter; Binding site of rice WRKY71, a transcriptional repressor of the gibberellin signaling pathway; Parsley WRKY proteins bind specifically to TGAC-containing W box elements within the Pathogenesis-Related Class10 (PR-10) genes	50.00%
Motif_509	AtTINY2	Molecular cloning, phylogenetic analysis, expressional profiling and in vitro studies of TINY2 from Arabidopsis thaliana	50.00%
Motif_385	GGTCCCATGMSAUR	Sequence found in NDE element in Soybean SAUR (Small Auxin-Up RNA) 15A gene promoter; Involved in auxin responsiveness	50.00%
Motif_369	SURECOREATSULTR11	Core of sulfur-responsive element (SURE) found in the promoter of SULTR1;1 high-affinity sulfate transporter gene in Arabidopsis; SURE contains auxin response factor (ARF) binding sequence (GAGACA)(see S000270 ARF:TGTCTC; its complementary seq is GAGACA), and this core sequence is a part of it; this core seq is involved in -S response; Beware of other SURE (sucrose responsive element)	50.00%
Motif_26	GRF7	Arabidopsis GROWTH-REGULATING FACTOR7 Functions as a Transcriptional Repressor of Abscisic Acid- and Osmotic Stress-Responsive Genes, Including DREB2A	50.00%
Motif_17	AUXRETGA1GMGH3	TGA-box #1 in putative auxin-resonsive element (AUXRE) of soybean GH3 promoter; Strong binding site for proteins in plant nuclear extracts	50.00%
Motif_15	AMYBOX2	amylase box; amylase element; Conserved sequence found in 5'upstream region of alpha-amylase gene of rice, wheat, barley	50.00%
Motif_33	ACGTCBOX	C-box according to the nomenclature of ACGT elements; One of ACGT elements; Factors groups 1, 2 and 3 have affinity for C-box;RITA-1 binding site	50.00%
Motif_60	AtERF-4; AtERF-3	Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression	50.00%
Motif_54	LTREATLTI78	Putative low temperature responsive element (LTRE); Found in Arabidopsis thaliana low-temperature-induced (lti) genes, lti78 and lti65; Repeated four times in lti78 which is also known as cor78 and rd29A; Found also in barley low temperature responsive genes, blt4.2, blt4.6, blt4.9 (lipid transfer genes); cold inducible; See LTRECORE; Also present in rab18, kin1, and kin2; Differential expression of two related, low-temperature-induced genes in Arabidopsis thaliana	50.00%
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	50.00%
Motif_13	E2F-varient binding site motif	A genome-wide identification of E2F-regulated genes in Arabidopsis	50.00%
Motif_80	AP1SV40	AP-1 binding site in enhancer regions of SV40 and human metallothionein IIA (hMT IIA)	50.00%