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    ITGA6 integrin subunit alpha 6 [ Homo sapiens (human) ]

    Gene ID: 3655, updated on 29-Mar-2020

    Summary

    Official Symbol
    ITGA6provided by HGNC
    Official Full Name
    integrin subunit alpha 6provided by HGNC
    Primary source
    HGNC:HGNC:6142
    See related
    Ensembl:ENSG00000091409 MIM:147556
    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
    CD49f; VLA-6; ITGA6B
    Summary
    The gene encodes a member of the integrin alpha chain family of proteins. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain that function in cell surface adhesion and signaling. The encoded preproprotein is proteolytically processed to generate light and heavy chains that comprise the alpha 6 subunit. This subunit may associate with a beta 1 or beta 4 subunit to form an integrin that interacts with extracellular matrix proteins including members of the laminin family. The alpha 6 beta 4 integrin may promote tumorigenesis, while the alpha 6 beta 1 integrin may negatively regulate erbB2/HER2 signaling. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]
    Expression
    Ubiquitous expression in colon (RPKM 44.7), placenta (RPKM 40.9) and 24 other tissues See more
    Orthologs

    Genomic context

    See ITGA6 in Genome Data Viewer
    Location:
    2q31.1
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    109.20200228 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (172427336..172506459)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (173291954..173371181)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985960 Neighboring gene uncharacterized LOC105376738 Neighboring gene uncharacterized LOC105373742 Neighboring gene ITGA6 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 4236 Neighboring gene pyruvate dehydrogenase kinase 1

    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?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif downregulates the expression of integrin, alpha 6 (ITGA6) in Vif-expression T cells PubMed
    Vpr vpr HIV-1 Vpr-expressing Jurkat T cell clones showed upregulated expression of integrin alpha 6, suggesting a role of Vpr in modulating the cell adhesion process 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

    • FLJ18737, DKFZp686J01244

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    cadherin binding HDA PubMed 
    insulin-like growth factor I binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    laminin binding IEA
    Inferred from Electronic Annotation
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    neuregulin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein-containing complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    brown fat cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    cell-matrix adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    cell-substrate adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell-substrate junction assembly TAS
    Traceable Author Statement
    more info
    PubMed 
    cellular response to extracellular stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to organic cyclic compound IEA
    Inferred from Electronic Annotation
    more info
     
    ectodermal cell differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    filopodium assembly IEA
    Inferred from Electronic Annotation
    more info
     
    hemidesmosome assembly TAS
    Traceable Author Statement
    more info
     
    integrin-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    leukocyte migration TAS
    Traceable Author Statement
    more info
     
    nail development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of extrinsic apoptotic signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    odontogenesis of dentin-containing tooth IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of GTPase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of cell-substrate adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    skin morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    basal plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    basement membrane IEA
    Inferred from Electronic Annotation
    more info
     
    cell surface HDA PubMed 
    cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    filopodium IEA
    Inferred from Electronic Annotation
    more info
     
    focal adhesion HDA PubMed 
    hemidesmosome IEA
    Inferred from Electronic Annotation
    more info
     
    integrin alpha6-beta4 complex IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    integrin alpha-6
    Names
    CD49 antigen-like family member F
    integrin alpha6B
    integrin, alpha 6

    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_008853.1 RefSeqGene

      Range
      5001..83874
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000210.4NP_000201.2  integrin alpha-6 isoform b preproprotein

      See identical proteins and their annotated locations for NP_000201.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate coding exon compared to variant 1, which results in a frameshift. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
      Source sequence(s)
      AB208842, AC078883, BG180469, DB457895, X53586, X59512
      Consensus CDS
      CCDS2249.1
      UniProtKB/Swiss-Prot
      P23229
      Related
      ENSP00000264107.7, ENST00000264107.11
      Conserved Domains (3) summary
      smart00191
      Location:374425
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam00357
      Location:10381052
      Integrin_alpha; Integrin alpha cytoplasmic region
      pfam08441
      Location:464939
      Integrin_alpha2; Integrin alpha
    2. NM_001079818.3NP_001073286.1  integrin alpha-6 isoform a preproprotein

      See identical proteins and their annotated locations for NP_001073286.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (a).
      Source sequence(s)
      AB208842, AC078883, BG180469, DB457895, X53586, X59512
      Consensus CDS
      CCDS46451.1
      UniProtKB/Swiss-Prot
      P23229
      Related
      ENSP00000386896.1, ENST00000409080.6
      Conserved Domains (2) summary
      smart00191
      Location:374425
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam08441
      Location:464939
      Integrin_alpha2; Integrin alpha
    3. NM_001316306.2NP_001303235.1  integrin alpha-6 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences compared to variant 1. The encoded isoform (c) is shorter and has a distinct C-terminus compared to isoform a, and lacks the predicted signal peptide present in isoforms a and b. It is not known whether this isoform (c) is proteolytically processed in the same manner as isoforms a and b.
      Source sequence(s)
      AB208842, AC078883, AK294436, AK296496, AK311695, BG180469
      Consensus CDS
      CCDS82534.1
      UniProtKB/Swiss-Prot
      P23229
      Related
      ENSP00000386614.1, ENST00000409532.5
      Conserved Domains (3) summary
      smart00191
      Location:255306
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam00357
      Location:919933
      Integrin_alpha; Integrin alpha cytoplasmic region
      pfam08441
      Location:345820
      Integrin_alpha2; Integrin alpha
    4. NM_001365529.2NP_001352458.1  integrin alpha-6 isoform d precursor

      Status: REVIEWED

      Source sequence(s)
      AC078883
      Conserved Domains (2) summary
      smart00191
      Location:374425
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam08441
      Location:464924
      Integrin_alpha2; Integrin alpha
    5. NM_001365530.2NP_001352459.1  integrin alpha-6 isoform e precursor

      Status: REVIEWED

      Source sequence(s)
      AC078883
      Conserved Domains (3) summary
      smart00191
      Location:374425
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam00357
      Location:10231037
      Integrin_alpha; Integrin alpha cytoplasmic region
      pfam08441
      Location:464924
      Integrin_alpha2; Integrin alpha

    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_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      172427336..172506459
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004007.1XP_016859496.1  integrin alpha-6 isoform X3

    2. XM_017004005.1XP_016859494.1  integrin alpha-6 isoform X1

    3. XM_017004008.1XP_016859497.1  integrin alpha-6 isoform X4

    4. XM_017004006.1XP_016859495.1  integrin alpha-6 isoform X2

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