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 GSVIVT01007564001
Common NameVIT_17s0000g09980
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis
Family C2H2
Protein Properties Length: 950aa    MW: 105704 Da    PI: 8.3751
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSVIVT01007564001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.50.00045833858123
                        EEET..TTTEEESSHHHHHHHHHH.T CS
            zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                        y+C    C++sFs+k +L  H ++ +
  GSVIVT01007564001 833 YQCDmeGCTMSFSSKPELALHKKNiC 858
                        99*******************99866 PP

2zf-C2H213.60.00019858880323
                        ET..TTTEEESSHHHHHHHHHHT CS
            zf-C2H2   3 Cp..dCgksFsrksnLkrHirtH 23 
                        Cp   Cgk F ++ +L++H r+H
  GSVIVT01007564001 858 CPvkGCGKKFFSHKYLVQHRRVH 880
                        9999*****************99 PP

3zf-C2H211.90.00069916942123
                        EEET..TTTEEESSHHHHHHHHHH..T CS
            zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt..H 23 
                        y C+   Cg++F+  s++ rH r+  H
  GSVIVT01007564001 916 YICTeaGCGQTFRFVSDFSRHKRKtgH 942
                        899999****************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005582.1E-441162IPR003347JmjC domain
PROSITE profilePS5118433.6331162IPR003347JmjC domain
SuperFamilySSF511971.92E-268176No hitNo description
PfamPF023732.0E-3726145IPR003347JmjC domain
SMARTSM003557.7833855IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.383856885IPR007087Zinc finger, C2H2
SMARTSM003550.0045856880IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.1E-5857879IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280858880IPR007087Zinc finger, C2H2
SuperFamilySSF576671.56E-9872914No hitNo description
Gene3DG3DSA:3.30.160.601.0E-9880908IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.741886915IPR007087Zinc finger, C2H2
SMARTSM003550.0014886910IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280888910IPR007087Zinc finger, C2H2
SuperFamilySSF576677.62E-8904938No hitNo description
Gene3DG3DSA:3.30.160.603.5E-9909939IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.24916942IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.489916947IPR007087Zinc finger, C2H2
PROSITE patternPS000280918942IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009741Biological Processresponse to brassinosteroid
GO:0009826Biological Processunidimensional cell growth
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0033169Biological Processhistone H3-K9 demethylation
GO:0035067Biological Processnegative regulation of histone acetylation
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 950 aa     Download sequence    Send to blast
MRGISRAKGS LLRFMKEEIP GVTSPMVYVA MMFSWFAWHV EDHDLHSLNY LHMGAGKTWY  60
GVPREAAVAF EEVVRVHGYG GEINPLVTFA VLGEKTTVMS PEVFVSAGIP CCRLVQNPGE  120
FVVTFPRAYH SGFSHGFNCG EAANIATPEW LRVAKDAAIR RASINYPPMV SHFQLLYDLA  180
LALCSRIPMS ISVEPRSSRL KDKKRGEGET VVKELFVQNI MQNNDLLHIL GKGSSIVLLP  240
KRSSDISVCP NLRVGSSSRV KPRLSLGLCN LEEAMKTSKS ILHLSHGNDN GSALTSQTQN  300
METKIESISH GDGLSDQALF SCVTCGILSF ACVALIQPRE AAARYLMSAD CSFFNDWIVG  360
SGPSGVANED FTGVSGDVHN SELNSCSGWM RKRVPNALFD VPIQSANYQI QTVDQNNEVV  420
SNTGTQKNTS ALGLLALTYA NSSDSEEDQL EPDIPLEADN LASTESNSSE GIFRDPLAIS  480
WATSKYSPVG HDAERAKFSN AIVPVENTNM SFAPRSDEDY SRIHVFCLEH AVEVEQQLRP  540
IGGVNMLLLC HPDYPKVEAE AKLVAEDLGI DYLWNDFVYR DATKEDGEMI QSALDSEECI  600
PGNGDWAVKL GVNLYYSANL SRSPLYIKQM PYNSVIYNVF GRSSANSPTA PDVYGRGPGK  660
QKKIVVAGKW CGKVWMSNQV HPLLAQKDPE EQEEDRNFHV WVKKPDEKPE RKSESSRKAE  720
TSSAPRKSGR KRKMMVENGS TKKANRPERE DPTPRRRNSC EQSAREFDSY VEDELEGGPS  780
TRLRRRNPKP PKELEAKPVV KKQTARKKAK KAPAAKAPGN HNNAKIQDEE EEYQCDMEGC  840
TMSFSSKPEL ALHKKNICPV KGCGKKFFSH KYLVQHRRVH IDDRPLKCPW KGCKMTFKWA  900
WARTEHIRVH TGARPYICTE AGCGQTFRFV SDFSRHKRKT GHSAKKARG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A9e-6883394723137Lysine-specific demethylase REF6
6a58_A9e-6883394723137Lysine-specific demethylase REF6
6a59_A9e-6883394723137Lysine-specific demethylase REF6
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Vvi.295250.0inflorescence
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}.
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00608ChIP-seqTransfer from AT3G48430Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4668320.0AM466832.1 Vitis vinifera, whole genome shotgun sequence, contig VV78X011128.17, clone ENTAV 115.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_028116352.10.0LOW QUALITY PROTEIN: lysine-specific demethylase REF6-like
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLF6GTM20.0F6GTM2_VITVI; Uncharacterized protein
STRINGVIT_17s0000g09980.t010.0(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP44011217
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]