View conserved binding sites


Gene
PPE_005G05250
Description
Regulator of nonsense transcripts 1
Alias
ppa000334m.g;ppa000334m;PAC:17640540;ppa000334m
Binding siteNameDescriptionLocationPosition
Matrix_26ATMYB3;MYB24Not availableDownstream12589
Matrix_330MYC2;TT8Not availableUpstream-371
Matrix_369AT2G18300Not availableUpstream-343
Matrix_407AP1Not availableIntron5148
Intron7673
Matrix_465MYC4Not availableUpstream-371
Matrix_480BES1Not availableUpstream-342
Matrix_77PRR5Not availableUpstream-372
Matrix_80BIM1Not availableUpstream-342
Motif_116INRNTPSADBInr (initiator) elements found in the tobacco psaDb gene promoter without TATA boxes; Light-responsive transcription of psaDb depends on Inr, but not TATA boxUpstream-133
Motif_136SEF4MOTIFGM7SSEF4 binding site; Soybean consensus sequence found in 5'upstream region (-199) of beta-conglycinin (7S globulin) gene (Gmg17.1); Binding with SEF4 (soybean embryo factor 4)Downstream12458
Downstream12561
Motif_139RHERPATEXPA7Right 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 patternsUpstream-370
Upstream-340
Motif_155NODCON1GMOne of two putative nodulin consensus sequences; See also NODCON2GM; One of the consensus sequence motifs of organ-specific elements (OSE) characteristic of the promoters activated in infected cells of root nodulesDownstream12201
Motif_165AP3SV40AP-3 binding site consensus sequence in enhancer regions of SV40, MMTV, MLV, IL2Downstream12246
Downstream12553
Motif_171TCP binding consensusfound enriched in peaks in chip-seq data for SEP3Downstream12351
Motif_174SREATMSDsugar-repressive element (SRE) found in 272 of the 1592 down-regulated genes after main stem decapitation in ArabidopsisDownstream12251
Downstream12370
Motif_193GLK1GLK transcription factors coordinate expression of the photosynthetic apparatus in ArabidopsisUpstream-299
Downstream12388
Motif_194EBOXBNNAPAE-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; ICE1Upstream-970
Motif_195TATABOX4TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiationDownstream12711
Motif_207MAMMALENHANCore sequence in enhancers from polyoma virus and from the IgM heavy chain geneIntron8728
Intron10795
Intron10956
Motif_249DPBF1&2 binding site motifA 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 systemUpstream-971
Downstream12190
Motif_254MYB46;MYB83MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genesUpstream-121
Motif_26GRF7Arabidopsis GROWTH-REGULATING FACTOR7 Functions as a Transcriptional Repressor of Abscisic Acid- and Osmotic Stress-Responsive Genes, Including DREB2ADownstream12606
Motif_279POLASIG3Plant polyA signal; Consensus sequence for plant polyadenylation signalDownstream12135
Downstream12289
Downstream12533
Downstream12629
Motif_292MYBPZMCore of consensus maize P (myb homolog) binding site; 6 bp core; Maize P gene specifies red pigmentation of kernel pericarp, cob, and other floral organs; P binds to A1 gene, but not Bz1 gene; Maize C1 (myb homolog) activates both A1 and Bz1 genesUpstream-53
Downstream12472
Motif_318CGCGBOXATCGCG 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 AtSRsUpstream-287
Motif_33ACGTCBOXC-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 siteUpstream-197
Motif_346SND1;VND6;VND7;NST1;NST2Global analysis of direct targets of secondary wall NAC master switches in ArabidopsisUpstream-129
Downstream12189
Motif_383UPRE-III(bZIP60)The plant-specific transcription factor NAC103 is induced by bZIP60 through a new cis-regulatory element to modulate the unfolded protein response in ArabidopsisDownstream12646
Motif_391REALPHALGLHCB21REalpha found in Lemna gibba Lhcb21 gene promoter; Located at -134 to -129; Binding site of proteins of whole-cell extracts; The DNA binding activity is high in etiolated plants but much lower in green plants; Required for phytochrome regulationDownstream12728
Motif_419MYB4 binding site motifNot availableUpstream-121
Motif_423MYB2Evidence for a role for AtMYB2 in the induction of the Arabidopsis alcohol dehydrogenase gene (ADH1) by low oxygenDownstream12728
Motif_441GAGA8HVBKN3GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBRIntron5837
Motif_453HEXMOTIFTAH3H4hexamer 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 siteUpstream-198
Motif_49TATAPVTRNALEUTATA-like motif; A TATA-like sequence found in Phaseolus vulgaris tRNALeu gene promoter; Frequently observed upstream of plant tRNA genes; Found in maize glycolytic glyceraldehyde-3-phospate dehydrogenase 4 (GapC4) gene promoter; Binding site of TATA binding protein (TBP)Downstream12711
Motif_490PROLAMINBOXOSGLUB1Prolamine box found in the rice GluB-1 gene promoter; Involved in quantitative regulation of the GluB-1 geneDownstream12160
Motif_503EECCRCAH1EEC; Consensus motif of the two enhancer elements, EE-1 and EE-2, both found in the promoter region of the Chlamydomonas Cah1 (encoding a periplasmic carbonic anhydrase); Binding site of Myb transcription factor LCR1Downstream12582
Motif_51MYB46Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesisUpstream-122
Motif_563PYRIMIDINEBOXOSRAMY1APyrimidine 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 siteDownstream12366
Motif_576TGACGTVMAMYTGACGT 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 seedsUpstream-198
Motif_584UPRE-III(bZIP60)The plant-specific transcription factor NAC103 is induced by bZIP60 through a new cis-regulatory element to modulate the unfolded protein response in ArabidopsisDownstream12646
Motif_618MYB1ATMYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in ArabidopsisDownstream12248
Downstream12456
Downstream12729
Motif_645BES1A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thalianaUpstream-970
Motif_6492SSEEDPROTBANAPAConserved in many storage-protein gene promoters; May be important for high activity of the napA promoterUpstream-119
Motif_658GT1CONSENSUSConsensus 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 expressionDownstream12417
Downstream12521
Downstream12522
Downstream12552
Motif_666MYB binding site promoterA flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genesUpstream-122
Motif_69CTRMCAMV35SCT-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 GAGAUpstream-210
Intron5837
Intron5839
Intron5841
Intron5843
Motif_70CANBNNAPACore of (CA)n element in storage protein genes in Brasica napus; embryo- and endosperm-specific transcription of napin (storage protein) gene, napA; seed specificity; activator and repressorUpstream-119
Motif_83CIACADIANLELHCRegion necessary for circadian expression of tomato Lhc geneDownstream12200
Motif_98SEF3MOTIFGMSEF3 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; SEF4Downstream12149