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    VIM vimentin [ Homo sapiens (human) ]

    Gene ID: 7431, updated on 23-Apr-2017
    Official Symbol
    VIMprovided by HGNC
    Official Full Name
    vimentinprovided by HGNC
    Primary source
    HGNC:HGNC:12692
    See related
    Ensembl:ENSG00000026025 MIM:193060; Vega:OTTHUMG00000017744
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HEL113; CTRCT30
    Summary
    This gene encodes a member of the intermediate filament family. Intermediate filamentents, along with microtubules and actin microfilaments, make up the cytoskeleton. The protein encoded by this gene is responsible for maintaining cell shape, integrity of the cytoplasm, and stabilizing cytoskeletal interactions. It is also involved in the immune response, and controls the transport of low-density lipoprotein (LDL)-derived cholesterol from a lysosome to the site of esterification. It functions as an organizer of a number of critical proteins involved in attachment, migration, and cell signaling. Mutations in this gene causes a dominant, pulverulent cataract.[provided by RefSeq, Jun 2009]
    Orthologs
    Location:
    10p13
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 10 NC_000010.11 (17227935..17237593)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (17269934..17279592)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene cubilin Neighboring gene tRNA aspartic acid methyltransferase 1 Neighboring gene VIM antisense RNA 1 Neighboring gene ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6 Neighboring gene ST8SIA6 antisense RNA 1 Neighboring gene uncharacterized LOC105376436

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Cataract 30
    MedGen: C1861827 OMIM: 116300 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    Discovery and refinement of loci associated with lipid levels.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify vimentin (VIM), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    env The phosphorylation of the two major cytoskeletal proteins, vimentin and GFAP, which is normally stimulated by isoproterenol, is partially prevented by HIV-1 gp120 in astrocytes PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify vimentin (VIM), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify vimentin (VIM), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify vimentin (VIM), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Vif vif Vif has been reported to colocalize with vimentin filaments in the cytoplasm and cause the collapse of the intermediate filament network into a perinuclear aggregate, however in other reports this co-localization was not observed PubMed
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of vimentin (VIM) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
    vpr The proteomic assay from Vpr-expressing HTLV-1 transformed cells reveals apoptosis related protein changes, such as CASP3 activity indicator proteins (vimentin and Rho GDP-dissociation inhibitor 2) PubMed
    matrix gag Treatment of human stellate cells with HIV-1 MA upregulates the expression of CXCR2, syndecan-2, collagen-I, alpha-SMA, vimentin, and endothelin-1 PubMed
    retropepsin gag-pol HIV-1 protease cleaves three secondary sites of vimentin at positions 51-52, 60-61, and 92-93. PubMed
    gag-pol HIV-1 protease cleaves the intermediate filament proteins vimentin (both human and murine vimentin are cleaved between leucine-422 and arginine-423), desmin, and glial fibrillary acidic protein in vitro PubMed
    gag-pol Two regions of the vimentin head domain, residues 17-60 and 68-92, are released as a result of vimentin cleavage by HIV-1 protease, leading to altered chromatin distribution PubMed
    gag-pol Exposure of human skin fibroblasts to HIV-1 protease induces the degradation of the vimentin filament network and the disappearance of the tropomyosin isoforms microfilament network PubMed
    gag-pol Phosphorylation of human recombinant vimentin by PKC inhibits the cleavage of the vimentin head domain by HIV-1 protease PubMed

    Go to the HIV-1, Human Interaction Database

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      Caspase-mediated cleavage of cytoskeletal proteins, organism-specific biosystemCaspase-mediated cleavage of a number of proteins in the cortical actin network ( ) microfilament system and others involved in maintenance of the cytoskeletal architecture (vimentin, or Gas2 and ...
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    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ36605

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    double-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    glycoprotein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    keratin filament binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein C-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    scaffold protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    structural constituent of cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    structural constituent of eye lens IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    Bergmann glial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    SMAD protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    astrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    intermediate filament organization IEA
    Inferred from Electronic Annotation
    more info
     
    lens fiber cell development IEA
    Inferred from Electronic Annotation
    more info
     
    movement of cell or subcellular component TAS
    Traceable Author Statement
    more info
    PubMed 
    muscle filament sliding TAS
    Traceable Author Statement
    more info
     
    negative regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    viral process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cell leading edge IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoskeleton TAS
    Traceable Author Statement
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    intermediate filament IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuron projection IEA
    Inferred from Electronic Annotation
    more info
     
    peroxisome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    vimentin
    Names
    epididymis luminal protein 113

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012413.1 RefSeqGene

      Range
      5001..14335
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003380.3NP_003371.2  vimentin

      See identical proteins and their annotated locations for NP_003371.2

      Status: REVIEWED

      Source sequence(s)
      BC000163, BQ050765
      Consensus CDS
      CCDS7120.1
      UniProtKB/Swiss-Prot
      P08670
      UniProtKB/TrEMBL
      V9HWE1
      Related
      ENSP00000446007.1, ENST00000544301.6
      Conserved Domains (4) summary
      pfam00038
      Location:102410
      Filament; Intermediate filament protein
      pfam04732
      Location:14101
      Filament_head; Intermediate filament head (DNA binding) region
      pfam15112
      Location:153257
      DUF4559; Domain of unknown function (DUF4559)
      cl24005
      Location:290368
      DUF2570; Protein of unknown function (DUF2570)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p7 Primary Assembly

      Range
      17227935..17237593
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006717500.1XP_006717563.1  vimentin isoform X1

      See identical proteins and their annotated locations for XP_006717563.1

      UniProtKB/Swiss-Prot
      P08670
      UniProtKB/TrEMBL
      V9HWE1
      Related
      ENSP00000224237.5, OTTHUMP00000019224, ENST00000224237.9, OTTHUMT00000047015
      Conserved Domains (4) summary
      pfam00038
      Location:102410
      Filament; Intermediate filament protein
      pfam04732
      Location:14101
      Filament_head; Intermediate filament head (DNA binding) region
      pfam15112
      Location:153257
      DUF4559; Domain of unknown function (DUF4559)
      cl24005
      Location:290368
      DUF2570; Protein of unknown function (DUF2570)

    Alternate CHM1_1.1

    Genomic

    1. NC_018921.2 Alternate CHM1_1.1

      Range
      17270372..17279705
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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