U.S. flag

An official website of the United States government

Links from GEO Profiles

    • Showing Current items.

    Itga6 integrin alpha 6 [ Mus musculus (house mouse) ]

    Gene ID: 16403, updated on 10-Dec-2024

    Summary

    Official Symbol
    Itga6provided by MGI
    Official Full Name
    integrin alpha 6provided by MGI
    Primary source
    MGI:MGI:96605
    See related
    Ensembl:ENSMUSG00000027111 AllianceGenome:MGI:96605
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Cd49f; VLA-6; 5033401O05Rik
    Summary
    This gene encodes a protein that is a member of the integrin superfamily. Integrins are transmembrane receptors involved cell adhesion and signaling, and they are subdivided based on the heterodimer formation of alpha and beta chains. This protein has been shown to heterodimerize with beta 4 to bind laminin and to form the main component of hemidesmosomes, which mediate attachment of epithelia to basement membranes. In mouse, deficiency of this gene is associated with absence of hemidesmosomes, severe skin blistering, and early post-natal death. In humans mutations of this gene are associated with epidermolysis bullosa. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, May 2013]
    Expression
    Ubiquitous expression in subcutaneous fat pad adult (RPKM 14.9), large intestine adult (RPKM 14.4) and 27 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Itga6 in Genome Data Viewer
    Location:
    2 C2- C3; 2 42.79 cM
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (71617236..71688761)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (71786886..71858427)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_04804 Neighboring gene predicted gene, 17250 Neighboring gene ribosomal protein S7 pseudogene Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:71652164-71652396 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:71704749-71704932 Neighboring gene STARR-seq mESC enhancer starr_04811 Neighboring gene pyruvate dehydrogenase kinase, isoenzyme 1 Neighboring gene predicted gene, 46785

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables insulin-like growth factor I binding  
    enables insulin-like growth factor I binding  
    enables integrin binding  
    enables laminin binding  
    enables metal ion binding  
    enables neuregulin binding  
    enables neuregulin binding  
    enables protein binding PubMed 
    enables protein-containing complex binding  
    Items 1 - 25 of 27
    Process Evidence Code Pubs
    acts_upstream_of_or_within brown fat cell differentiation PubMed 
    involved_in cell adhesion mediated by integrin  
    involved_in cell-cell adhesion  
    involved_in cell-cell adhesion  
    involved_in cell-matrix adhesion  
    acts_upstream_of_or_within cell-matrix adhesion PubMed 
    involved_in cell-matrix adhesion  
    involved_in cell-substrate adhesion  
    acts_upstream_of_or_within filopodium assembly PubMed 
    involved_in integrin-mediated signaling pathway  
    involved_in integrin-mediated signaling pathway  
    involved_in leukocyte migration  
    acts_upstream_of_or_within leukocyte migration PubMed 
    acts_upstream_of_or_within leukocyte migration PubMed 
    acts_upstream_of_or_within lymphoid lineage cell migration PubMed 
    involved_in nail development  
    involved_in negative regulation of extrinsic apoptotic signaling pathway  
    acts_upstream_of_or_within odontogenesis of dentin-containing tooth PubMed 
    involved_in positive regulation of GTPase activity  
    acts_upstream_of_or_within positive regulation of apoptotic process  
    involved_in positive regulation of cell migration  
    acts_upstream_of_or_within positive regulation of cell-cell adhesion PubMed 
    involved_in positive regulation of cell-substrate adhesion  
    involved_in positive regulation of neuron projection development PubMed 
    involved_in positive regulation of phosphorylation  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in skin morphogenesis  
    Items 1 - 25 of 27
    Component Evidence Code Pubs
    located_in adherens junction  
    located_in basal part of cell PubMed 
    located_in basal plasma membrane PubMed 
    located_in basement membrane PubMed 
    located_in basolateral plasma membrane PubMed 
    located_in cell surface PubMed 
    located_in cell surface  
    is_active_in external side of plasma membrane  
    located_in external side of plasma membrane PubMed 
    located_in filopodium  
    located_in hemidesmosome PubMed 
    part_of integrin alpha6-beta1 complex  
    part_of integrin alpha6-beta4 complex  
    part_of integrin complex  
    part_of integrin complex PubMed 
    colocalizes_with plasma membrane PubMed 
    located_in plasma membrane PubMed 
    located_in plasma membrane  

    General protein information

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

    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.

    mRNA and Protein(s)

    1. NM_001277970.2NP_001264899.1  integrin alpha-6 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001264899.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate penultimate exon, compared to variant 1, resulting in a novel 3' coding region and shorter 3' UTR. It encodes isoform 2 which has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL928963
      Consensus CDS
      CCDS71074.1
      UniProtKB/Swiss-Prot
      A2AU04, Q61739
      UniProtKB/TrEMBL
      Q6PEE8
      Related
      ENSMUSP00000158895.2, ENSMUST00000238991.2
      Conserved Domains (2) summary
      smart00191
      Location:374425
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam08441
      Location:464939
      Integrin_alpha2; Integrin alpha
    2. NM_001406258.1NP_001393187.1  integrin alpha-6 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL928963
      UniProtKB/TrEMBL
      Q6PEE8, Q8CC06
    3. NM_008397.5NP_032423.2  integrin alpha-6 isoform 1 precursor

      See identical proteins and their annotated locations for NP_032423.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the shorter isoform (1).
      Source sequence(s)
      AL928963
      Consensus CDS
      CCDS16118.1
      UniProtKB/TrEMBL
      Q6PEE8, Q8CC06
      Related
      ENSMUSP00000028522.4, ENSMUST00000028522.10
      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

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      71617236..71688761
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011239308.2XP_011237610.1  integrin alpha-6 isoform X1

      See identical proteins and their annotated locations for XP_011237610.1

      UniProtKB/Swiss-Prot
      A2AU04, Q61739
      UniProtKB/TrEMBL
      Q6PEE8
      Related
      ENSMUSP00000107729.2, ENSMUST00000112101.8
      Conserved Domains (2) summary
      smart00191
      Location:374425
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam08441
      Location:464939
      Integrin_alpha2; Integrin alpha
    External link. Please review our privacy policy.