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VIM vimentin [ Homo sapiens (human) ]

Gene ID: 7431, updated on 5-Jul-2020

Summary

Official Symbol
VIMprovided by HGNC
Official Full Name
vimentinprovided by HGNC
Primary source
HGNC:HGNC:12692
See related
Ensembl:ENSG00000026025 MIM:193060
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

Genomic context

See VIM in Genome Data Viewer
Location:
10p13
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (17228241..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 GATA motif-containing MPRA enhancer 283 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

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

NHGRI GWAS Catalog

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

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 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
keratin filament binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific 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
 
cellular response to interferon-gamma IEA
Inferred from Electronic Annotation
more info
 
cellular response to lipopolysaccharide IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to muramyl dipeptide IMP
Inferred from Mutant Phenotype
more info
PubMed 
cytokine-mediated signaling pathway TAS
Traceable Author Statement
more info
 
intermediate filament organization ISS
Inferred from Sequence or Structural Similarity
more info
 
lens fiber cell development IEA
Inferred from Electronic Annotation
more info
 
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 collagen biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of translation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of mRNA stability IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 HDA PubMed 
focal adhesion HDA PubMed 
intermediate filament IDA
Inferred from Direct Assay
more info
PubMed 
intermediate filament cytoskeleton IDA
Inferred from Direct Assay
more info
 
neuron projection IEA
Inferred from Electronic Annotation
more info
 
nuclear matrix IEA
Inferred from Electronic Annotation
more info
 
peroxisome IDA
Inferred from Direct Assay
more info
PubMed 
phagocytic vesicle IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
polysome IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
vimentin
Names
epididymis secretory sperm binding protein

NCBI Reference Sequences (RefSeq)

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
    P08670
    UniProtKB/TrEMBL
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_006717500.2XP_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, ENST00000224237.9
    Conserved Domains (2) summary
    pfam00038
    Location:102410
    Filament; Intermediate filament protein
    pfam04732
    Location:14101
    Filament_head; Intermediate filament head (DNA binding) region
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