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    VCL vinculin [ Homo sapiens (human) ]

    Gene ID: 7414, updated on 4-Oct-2020

    Summary

    Official Symbol
    VCLprovided by HGNC
    Official Full Name
    vinculinprovided by HGNC
    Primary source
    HGNC:HGNC:12665
    See related
    Ensembl:ENSG00000035403 MIM:193065
    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
    MV; MVCL; CMD1W; CMH15; HEL114
    Summary
    Vinculin is a cytoskeletal protein associated with cell-cell and cell-matrix junctions, where it is thought to function as one of several interacting proteins involved in anchoring F-actin to the membrane. Defects in VCL are the cause of cardiomyopathy dilated type 1W. Dilated cardiomyopathy is a disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in endometrium (RPKM 87.7), prostate (RPKM 70.2) and 25 other tissues See more
    Orthologs

    Genomic context

    See VCL in Genome Data Viewer
    Location:
    10q22.2
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    109.20200815 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (73998116..74121363)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (75757836..75879918)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr10.2661 Neighboring gene CRISPRi-validated cis-regulatory element chr10.2662 Neighboring gene uncharacterized LOC107984244 Neighboring gene adaptor related protein complex 3 subunit mu 1 Neighboring gene adenosine kinase Neighboring gene TIMM9 pseudogene 1 Neighboring gene ribosomal protein SA pseudogene 6

    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
    Dilated cardiomyopathy 1W
    MedGen: C1969639 OMIM: 611407
    Compare labs
    Familial hypertrophic cardiomyopathy 15
    MedGen: C2750459 OMIM: 613255 GeneReviews: Not available
    Compare labs
    Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances.
    GeneReviews: Not available
    Primary dilated cardiomyopathy
    MedGen: C0007193
    Compare labs

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef HIV-1 Nef co-localizes with vinvulin inside podosomes in human monocyte-derived macrophages PubMed
    nef HIV-1 Nef induces polarization of vinculin, a molecule important for dendritic cell (DC) adhesion, motility, and maturation, at one pole of DCs corresponding to the substrate-adhering portion or leading edge of the cell PubMed
    matrix gag HIV-1 MA co-localizes with beta2 integrin, alphaM and alphaX integrins in the intracellular thick electron-dense membrane compartments, which contain talin, vinculin and paxillin that connect the integrin complexes to the actin cytoskeleton 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    actin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT actin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    alpha-catenin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    beta-catenin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    cadherin binding HDA PubMed 
    cadherin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    dystroglycan binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    structural molecule activity IEA
    Inferred from Electronic Annotation
    more info
     
    ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    adherens junction assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    apical junction assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    axon extension IEA
    Inferred from Electronic Annotation
    more info
     
    cell adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    cell-matrix adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    epithelial cell-cell adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    lamellipodium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    maintenance of permeability of blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    morphogenesis of an epithelium IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    muscle contraction TAS
    Traceable Author Statement
    more info
     
    negative regulation of cell migration TAS
    Traceable Author Statement
    more info
    PubMed 
    neutrophil degranulation TAS
    Traceable Author Statement
    more info
     
    platelet aggregation HMP PubMed 
    platelet degranulation TAS
    Traceable Author Statement
    more info
     
    protein localization to cell surface IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of establishment of endothelial barrier IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of focal adhesion assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of protein localization to cell-cell adherens junction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    adherens junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    adherens junction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cell-cell contact zone IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell-cell junction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell-cell junction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cell-substrate junction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    costamere IDA
    Inferred from Direct Assay
    more info
    PubMed 
    costamere ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytoskeleton TAS
    Traceable Author Statement
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    extracellular exosome HDA PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     
    extracellular vesicle HDA PubMed 
    fascia adherens IEA
    Inferred from Electronic Annotation
    more info
     
    ficolin-1-rich granule lumen TAS
    Traceable Author Statement
    more info
     
    focal adhesion HDA PubMed 
    focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    focal adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    focal adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    podosome IEA
    Inferred from Electronic Annotation
    more info
     
    protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    sarcolemma ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    secretory granule lumen TAS
    Traceable Author Statement
    more info
     
    specific granule lumen TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    vinculin
    Names
    epididymis luminal protein 114
    epididymis secretory sperm binding protein
    meta-vinculin
    metavinculin

    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_008868.1 RefSeqGene

      Range
      5001..127047
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_383

    mRNA and Protein(s)

    1. NM_003373.4NP_003364.1  vinculin isoform VCL

      See identical proteins and their annotated locations for NP_003364.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a 3' coding exon, as compared to variant 1. It encodes a shorter isoform (VCL), which is the major talin-binding protein in platelets.
      Source sequence(s)
      AI290052, AK126978, AL708715, AL731576, AL832130, BC013847, BC039174, BX537994
      Consensus CDS
      CCDS7340.1
      UniProtKB/Swiss-Prot
      P18206
      UniProtKB/TrEMBL
      A0A024QZN4, B3KXA2
      Related
      ENSP00000361841.3, ENST00000372755.7
      Conserved Domains (1) summary
      pfam01044
      Location:31066
      Vinculin; Vinculin family
    2. NM_014000.3NP_054706.1  vinculin isoform meta-VCL

      See identical proteins and their annotated locations for NP_054706.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs from variant 2 in having an additional exon in the 3' coding region. It thus encodes a longer isoform (meta-VCL).
      Source sequence(s)
      AA368699, AI290052, AK126978, AL700886, AL708715, AL731576, AL832130, BC013847, BC039174
      Consensus CDS
      CCDS7341.1
      UniProtKB/Swiss-Prot
      P18206
      UniProtKB/TrEMBL
      B3KXA2, V9HWK2
      Related
      ENSP00000211998.4, ENST00000211998.9
      Conserved Domains (1) summary
      pfam01044
      Location:31134
      Vinculin; Vinculin family

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

    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
      73998116..74121363
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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