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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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