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    VIM vimentin [ Homo sapiens (human) ]

    Gene ID: 7431, updated on 9-Jun-2024

    Summary

    Official Symbol
    VIMprovided by HGNC
    Official Full Name
    vimentinprovided by HGNC
    Primary source
    HGNC:HGNC:12692
    See related
    Ensembl:ENSG00000026025 MIM:193060; AllianceGenome:HGNC:12692
    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
    Summary
    This gene encodes a type III intermediate filament protein. Intermediate filaments, along with microtubules and actin microfilaments, make up the cytoskeleton. The encoded protein is responsible for maintaining cell shape and integrity of the cytoplasm, and stabilizing cytoskeletal interactions. This protein is involved in neuritogenesis and cholesterol transport and functions as an organizer of a number of other critical proteins involved in cell attachment, migration, and signaling. Bacterial and viral pathogens have been shown to attach to this protein on the host cell surface. Mutations in this gene are associated with congenital cataracts in human patients. [provided by RefSeq, Aug 2017]
    Expression
    Ubiquitous expression in ovary (RPKM 1051.1), fat (RPKM 720.1) and 22 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See VIM in Genome Data Viewer
    Location:
    10p13
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (17228241..17237593)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (17246786..17256137)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (17270240..17279592)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak881 silencer Neighboring gene MPRA-validated peak882 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:16933270-16934469 Neighboring gene cubilin Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:16942960-16943677 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:16970960-16971553 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:17010389-17010952 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:17026880-17027039 Neighboring gene GATA motif-containing MPRA enhancer 283 Neighboring gene Sharpr-MPRA regulatory region 1431 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:17104252-17105451 Neighboring gene MPRA-validated peak883 silencer Neighboring gene MPRA-validated peak884 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:17157167-17158366 Neighboring gene tRNA aspartic acid methyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2181 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:17268719-17268933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2182 Neighboring gene Sharpr-MPRA regulatory region 14556 Neighboring gene VIM antisense RNA 1 Neighboring gene MPRA-validated peak886 silencer Neighboring gene ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6 Neighboring gene ST8SIA6 antisense RNA 1 Neighboring gene uncharacterized LOC105376436

    Genomic regions, transcripts, and products

    Expression

    • 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Cataract 30
    MedGen: C3805411 OMIM: 116300 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog

    HIV-1 interactions

    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 HIV-1 Gag trafficking to the plasma membrane is inhibited by LGALS3BP (M2BP) and the inhibition by LGALS3BP is dependent upon vimentin PubMed
    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ36605

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables double-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables keratin filament binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables molecular adaptor activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables scaffold protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables structural constituent of cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables structural constituent of cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables structural constituent of eye lens IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in Bergmann glial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in astrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to lipopolysaccharide IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to muramyl dipeptide IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to type II interferon IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intermediate filament organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in intermediate filament organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in lens fiber cell development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron projection development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of collagen biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of mRNA stability IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cell leading edge IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoskeleton TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in focal adhesion HDA PubMed 
    is_active_in intermediate filament IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in intermediate filament IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in intermediate filament cytoskeleton IDA
    Inferred from Direct Assay
    more info
     
    located_in microtubule organizing center TAS
    Traceable Author Statement
    more info
     
    located_in nuclear matrix IEA
    Inferred from Electronic Annotation
    more info
     
    located_in peroxisome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in phagocytic vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    vimentin
    Names
    epididymis secretory sperm binding protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      4983..14335
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003380.5NP_003371.2  vimentin

      See identical proteins and their annotated locations for NP_003371.2

      Status: REVIEWED

      Source sequence(s)
      BC000163, BQ050765, DA980400
      Consensus CDS
      CCDS7120.1
      UniProtKB/Swiss-Prot
      B0YJC2, D3DRU4, P08670, Q15867, Q15868, Q15869, Q548L2, Q6LER9, Q8N850, Q96ML2, Q9NTM3
      UniProtKB/TrEMBL
      Q53HU8, V9HWE1
      Related
      ENSP00000446007.1, ENST00000544301.7
      Conserved Domains (2) summary
      pfam00038
      Location:102410
      Filament; Intermediate filament protein
      pfam04732
      Location:14101
      Filament_head; Intermediate filament head (DNA binding) region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      17228241..17237593
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      17246786..17256137
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)