PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Vun001530
Organism
Vigna unguiculata
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: 361aa    MW: 42009.7 Da    PI: 10.5608
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
gnl|UG|Vun#S45847455PU_unrefUnigeneView CDS
PUT-167a-Vigna_unguiculata-23963PU_refplantGDBView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2130.00031245270123
                EEET..TTTEEESSHHHHHHHHHH.T CS
    zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                y+C    C++sF +k +L +H ++ +
  Vun001530 245 YQCDidGCSMSFGSKQELLHHKKNiC 270
                99*******************99866 PP
2zf-C2H215.16.4e-05270292323
                ET..TTTEEESSHHHHHHHHHHT CS
    zf-C2H2   3 Cp..dCgksFsrksnLkrHirtH 23 
                Cp   Cgk F ++ +L++H r+H
  Vun001530 270 CPvkGCGKKFFSHKYLVQHRRVH 292
                9999*****************99 PP
3zf-C2H214.10.00014328354123
                EEET..TTTEEESSHHHHHHHHHH..T CS
    zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt..H 23 
                y+C    Cg++F+  s++ rH r+  H
  Vun001530 328 YVCAepGCGQTFRFVSDFSRHKRKtgH 354
                899999*****************9777 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.609.1E-4239266IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003556.5245267IPR015880Zinc finger, C2H2-like
SMARTSM003550.0045268292IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.944268297IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.9E-7269296IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280270292IPR007087Zinc finger, C2H2
SuperFamilySSF576673.25E-10284326No hitNo description
Gene3DG3DSA:3.30.160.602.1E-9297322IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.741298327IPR007087Zinc finger, C2H2
SMARTSM003550.0014298322IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280300322IPR007087Zinc finger, C2H2
SuperFamilySSF576675.29E-9316350No hitNo description
Gene3DG3DSA:3.30.160.604.2E-10323351IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.62328354IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.468328359IPR007087Zinc finger, C2H2
PROSITE patternPS000280330354IPR007087Zinc 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: 361 aa     Download sequence    Send to blast
RRNPKGRQAK CVAEEDEMSG DQLEDHCQKL QTSFSRKKQN KGIDREVKYV MSDDQLEDHF  60
PKQQRRIPKS RQNKYPDKEV MDDSAENNSR LLHRTPKRKQ AKCMDEDDLN SDDEMEDDQK  120
LRRTLRSKQS KPKTLQQMKQ ANSVHAKSQA SRSIKRVSRV LVKSKTPQQI KPRNKQSTNS  180
REFSLLMEDE EEGGPSTRLR KRATKAQGTE GKLKEKQTKR KKMKNDSTAK VSVGHVKGKD  240
EEADYQCDID GCSMSFGSKQ ELLHHKKNIC PVKGCGKKFF SHKYLVQHRR VHEDERPLKC  300
PWKGCKMTFK WAWARTEHIR VHTGARPYVC AEPGCGQTFR FVSDFSRHKR KTGHSAKKSR  360
Q
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A6e-7324335921137Lysine-specific demethylase REF6
6a58_A6e-7324335921137Lysine-specific demethylase REF6
6a59_A6e-7324335921137Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1199221RKRATKAQGTEGKLKEKQTKRKK
2199223RKRATKAQGTEGKLKEKQTKRKKMK
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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_027904450.10.0lysine-specific demethylase REF6-like
SwissprotQ9STM32e-70REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A4D6NT530.0A0A4D6NT53_VIGUN; Histone demethylase JARID1
STRINGXP_007137965.10.0(Phaseolus vulgaris)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.12e-72relative 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]