Format

Send to:

Choose Destination
    • Showing Current items.

    ITGB6 integrin subunit beta 6 [ Homo sapiens (human) ]

    Gene ID: 3694, updated on 13-Mar-2020

    Summary

    Official Symbol
    ITGB6provided by HGNC
    Official Full Name
    integrin subunit beta 6provided by HGNC
    Primary source
    HGNC:HGNC:6161
    See related
    Ensembl:ENSG00000115221 MIM:147558
    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
    AI1H
    Summary
    This gene encodes a protein that is a member of the integrin superfamily. Members of this family are adhesion receptors that function in signaling from the extracellular matrix to the cell. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. The encoded protein forms a dimer with an alpha v chain and this heterodimer can bind to ligands like fibronectin and transforming growth factor beta 1. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
    Expression
    Biased expression in lung (RPKM 25.8), urinary bladder (RPKM 17.2) and 12 other tissues See more
    Orthologs

    Genomic context

    See ITGB6 in Genome Data Viewer
    Location:
    2q24.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    109.20200228 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (160099666..160200313, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (160956182..161110349, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene LY75-CD302 readthrough Neighboring gene lymphocyte antigen 75 Neighboring gene phospholipase A2 receptor 1 Neighboring gene uncharacterized LOC105373717 Neighboring gene ITGB6-RBMS1 intergenic CAGE-defined low expression enhancer Neighboring gene long intergenic non-protein coding RNA 2478

    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
    Amelogenesis imperfecta, type IH
    MedGen: C4015557 OMIM: 616221 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    Genetic variants at 2q24 are associated with susceptibility to type 2 diabetes.
    NHGRI GWA Catalog
    Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy.
    NHGRI GWA Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Alpha 5 integrin antibody 17E6 and alpha 5/beta 6 integrins inhibitor EMD 409849 inhibit HIV-1 infection of primary macrophages at an early stage of the virus cycle, suggesting the interaction of HIV-1 gp120 with alpha 5/beta 6 integrins 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
    integrin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    virus receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    cell adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    cell adhesion mediated by integrin IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell adhesion mediated by integrin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-matrix adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    integrin-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    regulation of transforming growth factor beta activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transforming growth factor-beta secretion IEA
    Inferred from Electronic Annotation
    more info
     
    viral entry into host cell IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cell junction IDA
    Inferred from Direct Assay
    more info
     
    cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    centrosome IDA
    Inferred from Direct Assay
    more info
     
    external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    focal adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integrin alphav-beta6 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    integrin alphav-beta6 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integrin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    integrin complex TAS
    Traceable Author Statement
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    receptor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    integrin beta-6
    Names
    integrin, beta 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_042041.1 RefSeqGene

      Range
      5042..105643
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000888.5NP_000879.2  integrin beta-6 isoform a precursor

      See identical proteins and their annotated locations for NP_000879.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC080166, AC092153, AI264144, AL831998, BC121178, DB222211
      Consensus CDS
      CCDS2212.1
      UniProtKB/Swiss-Prot
      P18564
      Related
      ENSP00000283249.2, ENST00000283249.7
      Conserved Domains (4) summary
      pfam00362
      Location:30454
      Integrin_beta; Integrin, beta chain
      pfam07965
      Location:624706
      Integrin_B_tail; Integrin beta tail domain
      pfam07974
      Location:546574
      EGF_2; EGF-like domain
      pfam08725
      Location:733775
      Integrin_b_cyt; Integrin beta cytoplasmic domain
    2. NM_001282353.2NP_001269282.1  integrin beta-6 isoform a precursor

      See identical proteins and their annotated locations for NP_001269282.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein (isoform a).
      Source sequence(s)
      AC080166, AI264144, AK313944
      Consensus CDS
      CCDS2212.1
      UniProtKB/Swiss-Prot
      P18564
      Related
      ENSP00000386367.1, ENST00000409872.1
      Conserved Domains (4) summary
      pfam00362
      Location:30454
      Integrin_beta; Integrin, beta chain
      pfam07965
      Location:624706
      Integrin_B_tail; Integrin beta tail domain
      pfam07974
      Location:546574
      EGF_2; EGF-like domain
      pfam08725
      Location:733775
      Integrin_b_cyt; Integrin beta cytoplasmic domain
    3. NM_001282354.1NP_001269283.1  integrin beta-6 isoform b precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two in-frame exons in the 5' coding region compared to variant 1. The encoded isoform (b) is shorter compared to isoform a.
      Source sequence(s)
      AC080166, AI264144, BC143656, CD013946, DB222211
      Consensus CDS
      CCDS74597.1
      UniProtKB/TrEMBL
      A0A087WXP3
      Related
      ENSP00000481183.1, ENST00000620391.4
      Conserved Domains (4) summary
      pfam00362
      Location:21359
      Integrin_beta; Integrin, beta chain
      pfam07965
      Location:529611
      Integrin_B_tail; Integrin beta tail domain
      pfam07974
      Location:451479
      EGF_2; EGF-like domain
      pfam08725
      Location:638680
      Integrin_b_cyt; Integrin beta cytoplasmic domain
    4. NM_001282355.2NP_001269284.1  integrin beta-6 isoform c precursor

      See identical proteins and their annotated locations for NP_001269284.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two in-frame exons in the 3' coding region compared to variant 1. The encoded isoform (c) is shorter compared to isoform a.
      Source sequence(s)
      AC080166, AI264144, BC121178, BC143656, CD013945, DB222211
      Consensus CDS
      CCDS63040.1
      UniProtKB/Swiss-Prot
      P18564
      Related
      ENSP00000386828.2, ENST00000409967.6
      Conserved Domains (3) summary
      pfam00362
      Location:30454
      Integrin_beta; Integrin, beta chain
      pfam07965
      Location:554599
      Integrin_B_tail; Integrin beta tail domain
      pfam08725
      Location:626668
      Integrin_b_cyt; Integrin beta cytoplasmic domain
    5. NM_001282388.2NP_001269317.1  integrin beta-6 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate 5' exon, compared to variant 1. This variant represents translation initiation at a downstream AUG compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream AUG resulting in a shorter isoform (d) with a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC080166, AI264144, AK304203, AK313944, DB222211
      Consensus CDS
      CCDS74596.1
      UniProtKB/Swiss-Prot
      P18564
      UniProtKB/TrEMBL
      B4E2B8, E9PEE8
      Related
      ENSP00000408024.2, ENST00000428609.6
      Conserved Domains (4) summary
      pfam00362
      Location:5412
      Integrin_beta; Integrin, beta chain
      pfam07965
      Location:582664
      Integrin_B_tail; Integrin beta tail domain
      pfam07974
      Location:504532
      EGF_2; EGF-like domain
      pfam08725
      Location:691733
      Integrin_b_cyt; Integrin beta cytoplasmic domain
    6. NM_001282389.2NP_001269318.1  integrin beta-6 isoform e

      See identical proteins and their annotated locations for NP_001269318.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate 5' splice site, compared to variant 1. This variant represents translation initiation at a downstream AUG compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream AUG resulting in a shorter isoform (e) with a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC080166, AI264144, BC143656, CD013947, DB222211
      Conserved Domains (4) summary
      pfam00362
      Location:36381
      Integrin_beta; Integrin, beta chain
      pfam07965
      Location:551633
      Integrin_B_tail; Integrin beta tail domain
      pfam07974
      Location:473501
      EGF_2; EGF-like domain
      pfam08725
      Location:660702
      Integrin_b_cyt; Integrin beta cytoplasmic domain
    7. NM_001282390.2NP_001269319.1  integrin beta-6 isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an alternate 5' exon and uses an alternate 5' splice site, compared to variant 1. This variant represents translation initiation at a downstream AUG compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream AUG resulting in a shorter isoform (f) compared to isoform a.
      Source sequence(s)
      AC080166, AI264144, BC143656, CD013944, DB222211
      Conserved Domains (4) summary
      pfam00362
      Location:1316
      Integrin_beta; Integrin, beta chain
      pfam07965
      Location:486568
      Integrin_B_tail; Integrin beta tail domain
      pfam07974
      Location:408436
      EGF_2; EGF-like domain
      pfam08725
      Location:595637
      Integrin_b_cyt; Integrin beta cytoplasmic domain

    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
      160099666..160200313 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center