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VIM2 Zinc finger (C3HC4-type RING finger) family protein [ Arabidopsis thaliana (thale cress) ]

Gene ID: 842919, updated on 18-Sep-2024

Summary

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Official Symbol
VIM2
Official Full Name
Zinc finger (C3HC4-type RING finger) family protein
Primary source
TAIR:AT1G66050
Locus tag
AT1G66050
See related
Araport:AT1G66050
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Arabidopsis thaliana (ecotype: Columbia)
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as
F15E12.5; F15E12_5; ORTH5; ORTHRUS 5; VARIANT IN METHYLATION 2
Summary
Encodes a protein that is similar to VIM1 but is not involved in cytosine methylation. This protein has an N-terminal PHD domain and two RING domains surrounding an SRA domain. ORTH5/VIM2 has E3 ubiquitin ligase activity in vitro.
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Genomic context

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See VIM2 in Genome Data Viewer
Location:
chromosome: 1
Exon count:
9
Sequence:
Chromosome: 1; NC_003070.9 (24589343..24592780)

Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene Zinc finger (C3HC4-type RING finger) family protein Neighboring gene reverse transcriptase-like protein Neighboring gene hypothetical protein (DUF577) Neighboring gene Translation initiation factor eIF3 subunit

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003070.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis. Woo HR, et al. PLoS Genet, 2008 Aug 15. PMID 18704160, Free PMC Article
  2. VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway. Shook MS, et al. Epigenetics, 2014 Jul. PMID 24762702, Free PMC Article
  3. ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases. Kraft E, et al. Plant J, 2008 Dec. PMID 18643997, Free PMC Article
  4. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Theologis A, et al. Nature, 2000 Dec 14. PMID 11130712

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. VIM proteins function in transcriptional regulation via their roles in the MET1 DNA methylation pathway.
    Title: VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway.
  2. VIM1, VIM2, and VIM3 have overlapping functions in maintenance of global CpG methylation and epigenetic transcriptional silencing.
    Title: Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.
Submit: New GeneRIF Correction

General gene information

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NM_105276.4

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables histone binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables methyl-CpG binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables methyl-CpNpG binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables methyl-CpNpN binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of gene expression via chromosomal CpG island methylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISM
Inferred from Sequence Model
more info
  

General protein information

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Preferred Names
Zinc finger (C3HC4-type RING finger) family protein
NP_176779.2
  • VARIANT IN METHYLATION 2 (VIM2); CONTAINS InterPro DOMAIN/s: Zinc finger, RING-type, conserved site (InterPro:IPR017907), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, PHD-type (InterPro:IPR001965), SRA-YDG (InterPro:IPR003105), Zinc finger, C3HC4 RING-type (InterPro:IPR018957), Zinc finger, FYVE/PHD-type (InterPro:IPR011011); BEST Arabidopsis thaliana protein match is: Zinc finger (C3HC4-type RING finger) family protein (TAIR:AT1G66040.1); Has 6271 Blast hits to 5010 proteins in 428 species: Archae - 0; Bacteria - 14; Metazoa - 4526; Fungi - 407; Plants - 903; Viruses - 19; Other Eukaryotes - 402 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_003070.9 Reference assembly

    Range
    24589343..24592780
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_105276.4 → NP_176779.2  Zinc finger (C3HC4-type RING finger) family protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_176779.2

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q680I0, Q6NQ90, Q9C8E0
    UniProtKB/TrEMBL
    A0A178W2T8
    Conserved Domains (3) summary
    smart00249
    Location:14 → 59
    PHD; PHD zinc finger
    cd00162
    Location:129 → 172
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam02182
    Location:247 → 409
    SAD_SRA; SAD/SRA domain
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q680I0.1

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