U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Protein

    • Showing Current items.

    VIM5 zinc finger (C3HC4-type RING finger) family protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 842155, updated on 18-Sep-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    VIM5
    Official Full Name
    zinc finger (C3HC4-type RING finger) family protein
    Primary source
    TAIR:AT1G57800
    Locus tag
    AT1G57800
    See related
    Araport:AT1G57800
    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
    F12K22.15; F12K22_15; ORTH3; ORTHRUS 3; VARIANT IN METHYLATION 5
    Summary
    predicted to encode a protein with an N-terminal PHD domain and two RING domains surrounding an SRA domain. Attempts to isolate ORTH3/VIM5 cDNA through RT-PCR were unsuccessful and only one Arabidopsis EST is associated with this locus. A paternally expressed imprinted gene.
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See VIM5 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    9
    Sequence:
    Chromosome: 1; NC_003070.9 (21408623..21412283, complement)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene F-box family protein Neighboring gene ncRNA Neighboring gene pseudo Neighboring gene Zinc finger (C3HC4-type RING finger) family protein

    Genomic regions, transcripts, and products

    Go to the top of the page Help
    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. DNA Geminivirus Infection Induces an Imprinted E3 Ligase Gene to Epigenetically Activate Viral Gene Transcription. Chen ZQ, et al. Plant Cell, 2020 Oct. PMID 32769133, Free PMC Article
    2. 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. DNA Geminivirus Infection Induces an Imprinted E3 Ligase Gene to Epigenetically Activate Viral Gene Transcription.
      Title: DNA Geminivirus Infection Induces an Imprinted E3 Ligase Gene to Epigenetically Activate Viral Gene Transcription.
    Submit: New GeneRIF Correction

    General gene information

    Go to the top of the page Help
    NM_001333805.1
    NM_104575.3

    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    zinc finger (C3HC4-type RING finger) family protein
    NP_176091.2
    • VARIANT IN METHYLATION 5 (VIM5); FUNCTIONS IN: zinc ion binding; LOCATED IN: cellular_component unknown; CONTAINS InterPro DOMAIN/s: SRA-YDG (InterPro:IPR003105), Zinc finger, RING-type, conserved site (InterPro:IPR017907), Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Zinc finger, FYVE/PHD-type (InterPro:IPR011011); BEST Arabidopsis thaliana protein match is: Zinc finger (C3HC4-type RING finger) family protein (TAIR:AT1G57820.1); Has 5254 Blast hits to 5127 proteins in 1563 species: Archae - 0; Bacteria - 14; Metazoa - 4362; Fungi - 258; Plants - 447; Viruses - 0; Other Eukaryotes - 173 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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
      21408623..21412283 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_104575.3 → NP_176091.2  zinc finger (C3HC4-type RING finger) family protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_176091.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9FVS2
      UniProtKB/TrEMBL
      A0A654EPA5
      Conserved Domains (3) summary
      smart00249
      Location:14 → 60
      PHD; PHD zinc finger
      cd00162
      Location:140 → 200
      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:274 → 433
      SAD_SRA; SAD/SRA domain

    2. NM_001333805.1 → NP_001321213.1  zinc finger (C3HC4-type RING finger) family protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8AQ73, A0A654EPA5
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9FVS2.2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.