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VIM vimentin [ Homo sapiens (human) ]

Gene ID: 7431, updated on 21-Mar-2015
Official Symbol
VIMprovided by HGNC
Official Full Name
vimentinprovided by HGNC
Primary source
HGNC:HGNC:12692
See related
Ensembl:ENSG00000026025; HPRD:01899; 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
See VIM in MapViewer
Location:
10p13
Exon count:
9
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 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 (intrinsic factor-cobalamin receptor) 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Cataract, nuclear diffuse nonprogressive
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

  • Alpha6-Beta4 Integrin Signaling Pathway, organism-specific biosystem (from WikiPathways)
    Alpha6-Beta4 Integrin Signaling Pathway, organism-specific biosystem"Integrins are cell surface heterodimeric protein complex consisting of one alpha and one beta chain. Integrins act as cell adhesion molecules as well as participate in cellular signaling. The ligand...
  • Apoptosis, organism-specific biosystem (from REACTOME)
    Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
  • Apoptotic cleavage of cellular proteins, organism-specific biosystem (from REACTOME)
    Apoptotic cleavage of cellular proteins, organism-specific biosystemApoptotic cell death is achieved by the caspase-mediatedcleavage of various vital proteins. Among caspase targets are proteins such as E-cadherin, Beta-catenin, alpha fodrin, GAS2, FADK, alpha adduc...
  • Apoptotic execution phase, organism-specific biosystem (from REACTOME)
    Apoptotic execution phase, organism-specific biosystemIn the execution phase of apoptosis, effector caspases cleave vital cellular proteins leading to the morphological changes that characterize apoptosis. These changes include destruction of the nucle...
  • Aurora B signaling, organism-specific biosystem (from Pathway Interaction Database)
    Aurora B signaling, organism-specific biosystem
    Aurora B signaling
  • Caspase cascade in apoptosis, organism-specific biosystem (from Pathway Interaction Database)
    Caspase cascade in apoptosis, organism-specific biosystem
    Caspase cascade in apoptosis
  • Caspase-mediated cleavage of cytoskeletal proteins, organism-specific biosystem (from REACTOME)
    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 ...
  • Epstein-Barr virus infection, organism-specific biosystem (from KEGG)
    Epstein-Barr virus infection, organism-specific biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
  • Epstein-Barr virus infection, conserved biosystem (from KEGG)
    Epstein-Barr virus infection, conserved biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
  • MicroRNAs in cancer, organism-specific biosystem (from KEGG)
    MicroRNAs in cancer, organism-specific biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • MicroRNAs in cancer, conserved biosystem (from KEGG)
    MicroRNAs in cancer, conserved biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • Muscle contraction, organism-specific biosystem (from REACTOME)
    Muscle contraction, organism-specific biosystemIn this module, the processes by which calcium binding triggers actin - myosin interactions and force generation in smooth and striated muscle tissues are annotated.
  • Programmed Cell Death, organism-specific biosystem (from REACTOME)
    Programmed Cell Death, organism-specific biosystemCell death is a fundamental cellular response that has a crucial role in shaping our bodies during development and in regulating tissue homeostasis by eliminating unwanted cells. There are a number o...
  • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
    Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multistep process that...
  • Striated Muscle Contraction, organism-specific biosystem (from WikiPathways)
    Striated Muscle Contraction, organism-specific biosystemMuscle contraction is the process where muscle tissue is activated by a signal from the nervous system. In case of voluntary action the nervous signals are initiated from the brain by so called actio...
  • Striated Muscle Contraction, organism-specific biosystem (from REACTOME)
    Striated Muscle Contraction, organism-specific biosystemStriated muscle contraction is a process whereby force is generated within striated muscle tissue, resulting in a change in muscle geometry, or in short, increased force being exerted on the tendons....
  • TCR Signaling Pathway, organism-specific biosystem (from WikiPathways)
    TCR Signaling Pathway, organism-specific biosystemThe T-cell antigen receptor (TCR) complex is composed of a ligand-binding subunit, the ? and ? chains, and a signaling subunit, namely the CD3?, ? and ? chains and the TCR? chain. This complex partic...
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
 
apoptotic process TAS
Traceable Author Statement
more info
 
astrocyte development IEA
Inferred from Electronic Annotation
more info
 
cellular component disassembly involved in execution phase of apoptosis TAS
Traceable Author Statement
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 
focal adhesion IDA
Inferred from Direct Assay
more info
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
 
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
vimentin
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 proteins identical to NP_003371.2

    Status: REVIEWED

    Source sequence(s)
    BC000163, BQ050765
    Consensus CDS
    CCDS7120.1
    UniProtKB/Swiss-Prot
    P08670
    UniProtKB/TrEMBL
    V9HWE1
    Related
    ENSP00000446007, ENST00000544301
    Conserved Domains (3) summary
    pfam00038
    Location:102410
    Filament; Intermediate filament protein
    pfam04732
    Location:14101
    Filament_head; Intermediate filament head (DNA binding) region
    TIGR03495
    Location:290368
    Probable_spanin_inner_membrane_subunit; phage lysis regulatory protein, LysB family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p2 Primary Assembly

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

mRNA and Protein(s)

  1. XM_006717500.1XP_006717563.1  

    See proteins identical to XP_006717563.1

    UniProtKB/Swiss-Prot
    P08670
    UniProtKB/TrEMBL
    V9HWE1
    Conserved Domains (3) summary
    pfam00038
    Location:102410
    Filament; Intermediate filament protein
    pfam04732
    Location:14101
    Filament_head; Intermediate filament head (DNA binding) region
    TIGR03495
    Location:290368
    Probable_spanin_inner_membrane_subunit; phage lysis regulatory protein, LysB family
  2. XM_011519649.1XP_011517951.1  

    See proteins identical to XP_011517951.1

    Conserved Domains (3) summary
    pfam00038
    Location:102410
    Filament; Intermediate filament protein
    pfam04732
    Location:14101
    Filament_head; Intermediate filament head (DNA binding) region
    TIGR03495
    Location:290368
    Probable_spanin_inner_membrane_subunit; phage lysis regulatory protein, LysB family

Alternate CHM1_1.1

Genomic

  1. NC_018921.2 Alternate CHM1_1.1

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