PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID DCAR_023885
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Apiales; Apiineae; Apiaceae; Apioideae; Scandiceae; Daucinae; Daucus
Family C2H2
Protein Properties Length: 105aa    MW: 12149.9 Da    PI: 10.4381
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
DCAR_023885genomeARS-USDAView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.21.4e-051840323
                 ET..TTTEEESSHHHHHHHHHHT CS
      zf-C2H2  3 Cp..dCgksFsrksnLkrHirtH 23
                 C+   Cgk F ++ +L +H+++H
  DCAR_023885 18 CSvkGCGKKFASHKYLIHHQKVH 40
                 77779****************99 PP

2zf-C2H212.60.000414770223
                 EET..TTTEEESSHHHHHHHHHHT CS
      zf-C2H2  2 kCp..dCgksFsrksnLkrHirtH 23
                 +C+   C+k+F+     + Hir+H
  DCAR_023885 47 QCTweGCTKTFKWAWARTEHIRVH 70
                 79999*****************99 PP

3zf-C2H216.23.1e-0576102123
                  EEET..TTTEEESSHHHHHHHHHH..T CS
      zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt..H 23 
                  y+C    C+k+F+  s++ rH r+  H
  DCAR_023885  76 YTCAetGCSKTFRFVSDFSRHRRKtgH 102
                  99*********************9777 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003550.0111640IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.4871645IPR007087Zinc finger, C2H2
PROSITE patternPS0002801840IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.3E-61844IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576677.31E-153082No hitNo description
Gene3DG3DSA:3.30.160.603.1E-114570IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00264670IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.034675IPR007087Zinc finger, C2H2
PROSITE patternPS0002804870IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.607.8E-117199IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.876102IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.55276104IPR007087Zinc finger, C2H2
PROSITE patternPS00028078102IPR007087Zinc 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: 105 aa     Download sequence    Send to blast
MMNFGSKKEL GLHEKNICSV KGCGKKFASH KYLIHHQKVH REDRPLQCTW EGCTKTFKWA  60
WARTEHIRVH TGDRPYTCAE TGCSKTFRFV SDFSRHRRKT GHSG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A2e-53210332133Lysine-specific demethylase REF6
6a58_A2e-53210332133Lysine-specific demethylase REF6
6a59_A2e-53210332133Lysine-specific demethylase REF6
Search in ModeBase
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_017217471.11e-73PREDICTED: lysine-specific demethylase REF6-like
RefseqXP_017217475.15e-73PREDICTED: lysine-specific demethylase REF6-like
RefseqXP_017217476.11e-73PREDICTED: lysine-specific demethylase REF6-like
SwissprotQ9STM33e-50REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A175Y9Q83e-72A0A175Y9Q8_DAUCS; Uncharacterized protein
STRINGVIT_17s0000g09980.t016e-52(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA49882331
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.11e-52relative 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]