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 DCAR_032078
Organism
Daucus carota
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: 262aa    MW: 29503.3 Da    PI: 9.9586
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
DCAR_032078genomeARS-USDAView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2156.9e-05175197323
                  ET..TTTEEESSHHHHHHHHHHT CS
      zf-C2H2   3 Cp..dCgksFsrksnLkrHirtH 23 
                  C+   Cgk F ++ +L +H+++H
  DCAR_032078 175 CSvkGCGKKFASHKYLIHHQKVH 197
                  77779****************99 PP
2zf-C2H210.70.0017204227223
                  EET..TTTEEESSHHHHHHHHHHT CS
      zf-C2H2   2 kCp..dCgksFsrksnLkrHirtH 23 
                  +C+   C+k+F+     + Hir+H
  DCAR_032078 204 QCTweGCTKTFKWAWARTEHIRVH 227
                  79999*****************99 PP
3zf-C2H216.62.3e-05233259123
                  EEET..TTTEEESSHHHHHHHHHH..T CS
      zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt..H 23 
                  y+C    Cgk+F+  s++ rH r+  H
  DCAR_032078 233 YTCAetGCGKTFRFVSDFSRHRRKtgH 259
                  99*********************9777 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM00355100152172IPR015880Zinc finger, C2H2-like
SMARTSM003550.011173197IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.487173202IPR007087Zinc finger, C2H2
SuperFamilySSF576672.19E-6174210No hitNo description
PROSITE patternPS000280175197IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.1E-5175196IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
Gene3DG3DSA:3.30.160.602.1E-6197209IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0026203227IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.03203232IPR007087Zinc finger, C2H2
PROSITE patternPS000280205227IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.0E-6210225IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576676.05E-11213255No hitNo description
Gene3DG3DSA:3.30.160.608.7E-11226256IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.27233259IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.279233261IPR007087Zinc finger, C2H2
PROSITE patternPS000280235259IPR007087Zinc 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: 262 aa     Download sequence    Send to blast
MDDLEPAQRS KFPRVEESTE ATDQEQVRVS ENLPKPPEPD VVPGNLYRTT DLASGSRKDK  60
CIIQYKRTYK NKSKVKPIQE ETPHDQGTDI LEGGPSTRLR PRKLNQPPKD PEHVSHKVVA  120
KDELKTSSNR GKSASGIQAS AGSSSKKAEA KYSCEVCMMN FGSKKELGLH EKNICSVKGC  180
GKKFASHKYL IHHQKVHRED RPLQCTWEGC TKTFKWAWAR TEHIRVHTGD RPYTCAETGC  240
GKTFRFVSDF SRHRRKTGHS G*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A2e-5515026021133Lysine-specific demethylase REF6
6a58_A2e-5515026021133Lysine-specific demethylase REF6
6a59_A2e-5515026021133Lysine-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_017217467.10.0PREDICTED: lysine-specific demethylase JMJ705-like
RefseqXP_017217471.10.0PREDICTED: lysine-specific demethylase REF6-like
RefseqXP_017217476.10.0PREDICTED: lysine-specific demethylase REF6-like
SwissprotQ9STM32e-52REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A175Y9Q80.0A0A175Y9Q8_DAUCS; Uncharacterized protein
STRINGPOPTR_0015s10040.12e-63(Populus trichocarpa)
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
AT3G48430.14e-53relative 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]