PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Vang11g07510.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
Family C2H2
Protein Properties Length: 1532aa    MW: 174773 Da    PI: 8.7176
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Vang11g07510.1genomeSNUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.40.0004914161441123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                      y+C    C++sF +k +L +H r+ +
  Vang11g07510.1 1416 YQCDieGCTMSFGSKQELLQHKRNiC 1441
                      99********************9877 PP

2zf-C2H212.90.0003414411463323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk F ++ +L++H r+H
  Vang11g07510.1 1441 CPvkGCGKKFFSHKYLVQHRRVH 1463
                      9999*****************99 PP

3zf-C2H211.80.0007514991525123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C    Cg++F+  s++ rH r+  H
  Vang11g07510.1 1499 YVCAepGCGQTFRFVSDFSRHKRKtgH 1525
                      899999****************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.0E-171657IPR003349JmjN domain
PROSITE profilePS5118314.0631758IPR003349JmjN domain
PfamPF023754.1E-141851IPR003349JmjN domain
SuperFamilySSF511976.59E-2694341No hitNo description
PROSITE profilePS5118434.656166335IPR003347JmjC domain
SMARTSM005581.2E-47166335IPR003347JmjC domain
PfamPF023733.6E-36199318IPR003347JmjC domain
Gene3DG3DSA:3.30.160.605.8E-514031438IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003556.614161438IPR015880Zinc finger, C2H2-like
SuperFamilySSF576677.59E-614391475No hitNo description
SMARTSM003550.004514391463IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.50814391468IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.5E-514411467IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014411463IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.7E-814681493IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.82414691498IPR007087Zinc finger, C2H2
SMARTSM003550.001614691493IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014711493IPR007087Zinc finger, C2H2
SuperFamilySSF576672.73E-914791523No hitNo description
Gene3DG3DSA:3.30.160.602.4E-914941522IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.6214991525IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.84514991530IPR007087Zinc finger, C2H2
PROSITE patternPS00028015011525IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1532 aa     Download sequence    Send to blast
MAASEEVLPW LKSLPVAPEY RPTEAEFQNP IAYIFKIEKE ASQYGICKII PPLPPSPKKT  60
ATANLTRSQP TFTTRQQQIG FCPRRVQPVR RRVWYSGHHY SLREFEAKAK AFHKTYLKKS  120
KPKPSPLELE TLYWKATLDK PFSVEYANDI PGSAFSPLRA LRDVDHVGDT PWNMRTVSRG  180
SDSLLRFMKE EIPGVTSPMV YVAMLFSWFA WHVEDHDLHS LNYLHFGAPK TWYGVPKDAA  240
VAFEEVVRVH GYGGEINPLV TFAILGEKTT VMSPEVFVGA GVPCCRLVQN AGEFIVTFPR  300
AYHTGFSHGF NCGEAANIAT PEWLRFAKDA AIRRASINYP PMVSHFQLLY DLGLALCSRY  360
DILSDLGGMS FYWCFENHSV RPENSELVGI PGGIRAEPRS SRLKYKRNGE GETVIKELFV  420
QDVVENNDLL HTLSKGSDIV LLPRSSSDFS VCSKLRVGSR QLKVNPDFSL NVYNYEGMDS  480
SDFISNDLMF NRNHGIKQVK SFYSVKEKFV TLCERNRVLP LSSNGNIYTS SSKTLQRDSE  540
KETDQGDGLS DHRLFSCVTC GILSFSCVAI VQPREPAATY LMSADCSFFN DWIVGSGVTS  600
NKFSIAHEDA RWSKQNAQHD SNGVPIQSVK HHAQIADQNY EEALNSGREK GNTALALLAS  660
AYGNSSDSEE DRGGLDIALD DDELNAVNHS TSNGSQEMSS MPSHFQDPHT SPMVRVIRLN  720
KGDDIHSRRK DNYEYYMHKR LEQIMTPFDY SVKSEDHDNT SGVAFRNTRA VPHPTLNCSQ  780
DTHTDEDSSR MHIFYYPKIE AEAKFVAEEL GIGYTWKNTV YRQANREDEE RIQSALDSEE  840
AIPGNGDWAV KLGINLFYSA NLSRSALYSK QIPYNSVIYK AFGQSSPGSS PTEPKVYQRR  900
TIKQKKLVAG KWCGKVWMSN QVHPLLAKRD SEDVEDETSL HGWPLPDEKI ERSESNHKSN  960
TSTRKSGKKW KKSVEKGGIW EESFVERGWL SDNSIEDKSN KYQRRIIGGK RSRHIERDDT  1020
ASEGDYSPLP LHRKPITKHS ESSEDDAMSD DFLDDDSCIQ HRGRANTNKA KLIDSDVFSD  1080
DTMDYGSDWL RRGELSNEQD AISDDSLSAG SLQLHGKTPK GKYDKYITEE DVISDDQREV  1140
CLWKQRGKIS KGRQRSLSAK NEDGLKHHRQ KQQQRNLRSR QDKHFAVENI TSDDQMEGRF  1200
FKCQRRIPKN KQVKLIEEED VMSDDQLKDD FQKPQRSTRR SRQNKYNDKD VMDDLAENNF  1260
HILYRTRKRK QVKGMDEDNI DSDDQMDDIL HQQHKRTLQS KQSKAQILQQ TKQTNPRHAR  1320
NKTSHPAKQK QGVHTQMKSK AARQTKNQSG NSKDLTLHVE EEEDGGPRTR LRKRVLEKES  1380
EGKLKEKRTK REKEKNTTAA KVLVGHAKTK DEESEYQCDI EGCTMSFGSK QELLQHKRNI  1440
CPVKGCGKKF FSHKYLVQHR RVHEDDRPLK CPWKGCKMSF KWAWARTEHI RVHTGARPYV  1500
CAEPGCGQTF RFVSDFSRHK RKTGHATKKN C*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A6e-8183496346Transcription factor jumonji (Jmj) family protein
6ip4_A6e-8183496346Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
112651270TRKRKQ
Functional Description ? help Back to Top
Source Description
UniProtHistone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034). {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:20711170, ECO:0000269|PubMed:21642989, ECO:0000269|PubMed:25105952, ECO:0000269|PubMed:27111034, ECO:0000269|PubMed:27111035}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapVang11g07510.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0150340.0AP015034.1 Vigna angularis var. angularis DNA, chromosome 1, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_017438995.10.0PREDICTED: lysine-specific demethylase REF6-like
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A0S3R6760.0A0A0S3R676_PHAAN; Uncharacterized protein
STRINGXP_007155510.10.0(Phaseolus vulgaris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF56483250
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.10.0relative of early flowering 6
Publications ? help Back to Top
  1. Li C, et al.
    Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 687-93
    [PMID:27111034]
  2. Cui X, et al.
    REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 694-9
    [PMID:27111035]
  3. Hyun Y, et al.
    Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem.
    Dev. Cell, 2016. 37(3): p. 254-66
    [PMID:27134142]
  4. Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE
    Research progress on the autonomous flowering time pathway in Arabidopsis.
    Physiol Mol Biol Plants, 2017. 23(3): p. 477-485
    [PMID:28878488]
  5. Li C, et al.
    Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis.
    Plant Biotechnol. J., 2018. 16(8): p. 1446-1451
    [PMID:29331085]
  6. Wang X, et al.
    The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis.
    PLoS Genet., 2019. 15(4): p. e1008068
    [PMID:30969965]
  7. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]