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

    Gene ID: 3655, updated on 10-Dec-2024

    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; AllianceGenome:HGNC:6142
    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
    JEB6; CD49f; VLA-6; ITGA6A; 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
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    Genomic context

    See ITGA6 in Genome Data Viewer
    Location:
    2q31.1
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (172427336..172506459)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (172913095..172992707)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (173292064..173371187)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906157 Neighboring gene Sharpr-MPRA regulatory region 4152 Neighboring gene uncharacterized LOC107985960 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:173117619-173118818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:173134675-173135248 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:173179610-173180254 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:173180255-173180898 Neighboring gene uncharacterized LOC105373742 Neighboring gene Sharpr-MPRA regulatory region 14975 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:173245777-173246288 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_55951 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:173245267-173245776 Neighboring gene NANOG hESC enhancer GRCh37_chr2:173280388-173280889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12110 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:173293126-173293626 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:173295051-173296250 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:173299510-173300010 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:173318135-173318864 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56026 Neighboring gene ITGA6 and PDK1 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56072 Neighboring gene PDK1 and ITGA6 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 994 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:173399678-173400178 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:173413559-173414301 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:173414302-173415043 Neighboring gene Sharpr-MPRA regulatory region 4236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16763 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12111 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:173456666-173456873 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56189 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56221 Neighboring gene pyruvate dehydrogenase kinase 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56231 Neighboring gene Sharpr-MPRA regulatory region 7042 Neighboring gene small nucleolar RNA U13 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56260 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56279 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:173577807-173578364 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:173590766-173591266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:173591267-173591767 Neighboring gene RAPGEF4 antisense RNA 1 Neighboring gene Rap guanine nucleotide exchange factor 4

    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

    BioGRID CRISPR Screen Phenotypes (25 hits/1274 screens)

    Associated conditions

    EBI GWAS Catalog

    Description
    Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
    EBI GWAS Catalog

    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

    General gene information

    Clone Names

    • FLJ18737, DKFZp686J01244

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cadherin binding PubMed 
    enables insulin-like growth factor I binding PubMed 
    enables integrin binding  
    enables laminin binding  
    enables metal ion binding  
    enables neuregulin binding PubMed 
    enables protein binding PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion mediated by integrin  
    involved_in cell-cell adhesion  
    involved_in cell-matrix adhesion  
    involved_in cell-matrix adhesion PubMed 
    involved_in cell-substrate adhesion PubMed 
    involved_in cell-substrate junction assembly PubMed 
    involved_in cellular response to organic cyclic compound  
    involved_in ectodermal cell differentiation PubMed 
    involved_in integrin-mediated signaling pathway  
    involved_in integrin-mediated signaling pathway PubMed 
    involved_in leukocyte migration  
    involved_in nail development PubMed 
    involved_in negative regulation of extrinsic apoptotic signaling pathway PubMed 
    involved_in positive regulation of GTPase activity PubMed 
    acts_upstream_of_or_within positive regulation of apoptotic process PubMed 
    involved_in positive regulation of cell migration PubMed 
    involved_in positive regulation of cell-substrate adhesion  
    involved_in positive regulation of neuron projection development  
    involved_in positive regulation of phosphorylation PubMed 
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    involved_in skin morphogenesis PubMed 
    Component Evidence Code Pubs
    located_in adherens junction  
    located_in cell surface PubMed 
    located_in cell surface PubMed 
    is_active_in external side of plasma membrane  
    located_in filopodium  
    located_in focal adhesion PubMed 
    part_of integrin alpha6-beta1 complex PubMed 
    part_of integrin alpha6-beta4 complex  
    part_of integrin complex  
    located_in plasma membrane PubMed 
    located_in plasma membrane  

    General protein information

    Preferred Names
    integrin alpha-6
    Names
    CD49 antigen-like family member F
    integrin alpha6B
    integrin, alpha 6
    very late activation protein 6

    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.

    Genomic

    1. NG_008853.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_000210.4 → NP_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
      ENSP00000508249.1, ENST00000684293.1
      Conserved Domains (3) summary
      smart00191
      Location:374 → 425
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam00357
      Location:1038 → 1052
      Integrin_alpha; Integrin alpha cytoplasmic region
      pfam08441
      Location:464 → 939
      Integrin_alpha2; Integrin alpha
    2. NM_001079818.3 → NP_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:374 → 425
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam08441
      Location:464 → 939
      Integrin_alpha2; Integrin alpha
    3. NM_001316306.2 → NP_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:255 → 306
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam00357
      Location:919 → 933
      Integrin_alpha; Integrin alpha cytoplasmic region
      pfam08441
      Location:345 → 820
      Integrin_alpha2; Integrin alpha
    4. NM_001365529.2 → NP_001352458.1  integrin alpha-6 isoform d precursor

      Status: REVIEWED

      Source sequence(s)
      AC078883
      Conserved Domains (2) summary
      smart00191
      Location:374 → 425
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam08441
      Location:464 → 924
      Integrin_alpha2; Integrin alpha
    5. NM_001365530.2 → NP_001352459.1  integrin alpha-6 isoform e precursor

      Status: REVIEWED

      Source sequence(s)
      AC078883
      Consensus CDS
      CCDS92898.1
      UniProtKB/TrEMBL
      A0A8C8KBL6
      Related
      ENSP00000264107.8, ENST00000264107.12
      Conserved Domains (3) summary
      smart00191
      Location:374 → 425
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam00357
      Location:1023 → 1037
      Integrin_alpha; Integrin alpha cytoplasmic region
      pfam08441
      Location:464 → 924
      Integrin_alpha2; Integrin alpha
    6. NM_001394928.1 → NP_001381857.1  integrin alpha-6 isoform 6 precursor

      Status: REVIEWED

      Source sequence(s)
      AC078883
      Consensus CDS
      CCDS92897.1
      UniProtKB/Swiss-Prot
      B2RMU9, B4DG69, B4DKB8, C4AM96, G5E9H1, P23229, Q08443, Q0MRC7, Q14646, Q16508, Q53RX7, Q59HB7, Q86VL6, Q9UCT1, Q9UN03
      Related
      ENSP00000406694.1, ENST00000442250.6
      Conserved Domains (2) summary
      smart00191
      Location:413 → 464
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam08441
      Location:503 → 978
      Integrin_alpha2; Integrin alpha

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

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

      UniProtKB/TrEMBL
      A0AAQ5BID9
      Related
      ENSP00000520448.1, ENST00000715295.1
      Conserved Domains (2) summary
      smart00191
      Location:260 → 311
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam08441
      Location:350 → 825
      Integrin_alpha2; Integrin alpha
    2. XM_017004006.2 → XP_016859495.1  integrin alpha-6 isoform X2

      Conserved Domains (2) summary
      smart00191
      Location:260 → 311
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam08441
      Location:350 → 810
      Integrin_alpha2; Integrin alpha
    3. XM_047444221.1 → XP_047300177.1  integrin alpha-6 isoform X3

    4. XM_047444222.1 → XP_047300178.1  integrin alpha-6 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      172913095..172992707
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341874.1 → XP_054197849.1  integrin alpha-6 isoform X5

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