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

Gene ID: 3694, updated on 21-Apr-2019

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:
16
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 FunctionsWhat'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 BioSystems

  • Arrhythmogenic Right Ventricular Cardiomyopathy, organism-specific biosystem (from WikiPathways)
    Arrhythmogenic Right Ventricular Cardiomyopathy, organism-specific biosystemAdapted from KEGG: http://www.genome.jp/kegg/pathway/hsa/hsa05412.html
  • Arrhythmogenic right ventricular cardiomyopathy (ARVC), organism-specific biosystem (from KEGG)
    Arrhythmogenic right ventricular cardiomyopathy (ARVC), organism-specific biosystemArrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disease that may result in arrhythmia, heart failure, and sudden death. The hallmark pathological findings are prog...
  • Arrhythmogenic right ventricular cardiomyopathy (ARVC), conserved biosystem (from KEGG)
    Arrhythmogenic right ventricular cardiomyopathy (ARVC), conserved biosystemArrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disease that may result in arrhythmia, heart failure, and sudden death. The hallmark pathological findings are prog...
  • Dilated cardiomyopathy, organism-specific biosystem (from KEGG)
    Dilated cardiomyopathy, organism-specific biosystemDilated cardiomyopathy (DCM) is a heart muscle disease characterised by dilation and impaired contraction of the left or both ventricles that results in progressive heart failure and sudden cardiac d...
  • Dilated cardiomyopathy, conserved biosystem (from KEGG)
    Dilated cardiomyopathy, conserved biosystemDilated cardiomyopathy (DCM) is a heart muscle disease characterised by dilation and impaired contraction of the left or both ventricles that results in progressive heart failure and sudden cardiac d...
  • ECM proteoglycans, organism-specific biosystem (from REACTOME)
    ECM proteoglycans, organism-specific biosystemProteoglycans are major components of the extracellular matrix. In cartilage the matrix constitutes more than 90% of tissue dry weight. Proteoglycans are proteins substituted with glycosaminoglycans ...
  • ECM-receptor interaction, organism-specific biosystem (from KEGG)
    ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • ECM-receptor interaction, conserved biosystem (from KEGG)
    ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • Elastic fibre formation, organism-specific biosystem (from REACTOME)
    Elastic fibre formation, organism-specific biosystemElastic fibres (EF) are a major structural constituent of dynamic connective tissues such as large arteries and lung parenchyma, where they provide essential properties of elastic recoil and resilien...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Focal Adhesion, organism-specific biosystem (from WikiPathways)
    Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, organism-specific biosystem (from KEGG)
    Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, conserved biosystem (from KEGG)
    Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Hypertrophic cardiomyopathy (HCM), organism-specific biosystem (from KEGG)
    Hypertrophic cardiomyopathy (HCM), organism-specific biosystemHypertrophic cardiomyopathy (HCM) is a primary myocardial disorder with an autosomal dominant pattern of inheritance that is characterized by hypertrophy of the left ventricles with histological feat...
  • Hypertrophic cardiomyopathy (HCM), conserved biosystem (from KEGG)
    Hypertrophic cardiomyopathy (HCM), conserved biosystemHypertrophic cardiomyopathy (HCM) is a primary myocardial disorder with an autosomal dominant pattern of inheritance that is characterized by hypertrophy of the left ventricles with histological feat...
  • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
    Integrin cell surface interactions, organism-specific biosystemThe extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength...
  • Integrin-mediated Cell Adhesion, organism-specific biosystem (from WikiPathways)
    Integrin-mediated Cell Adhesion, organism-specific biosystemIntegrins are receptors that mediate attachment between a cell and the tissues surrounding it, which may be other cells or the extracellular matrix (ECM). They also play a role in cell signaling and ...
  • Molecules associated with elastic fibres, organism-specific biosystem (from REACTOME)
    Molecules associated with elastic fibres, organism-specific biosystemProteins found associated with microfibrils include vitronectin (Dahlback et al. 1990), latent transforming growth factor beta-binding proteins (Kielty et al. 2002, Munger & Sheppard 2011), emilin (B...
  • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
    PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
    PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • Regulation of actin cytoskeleton, organism-specific biosystem (from KEGG)
    Regulation of actin cytoskeleton, organism-specific biosystem
    Regulation of actin cytoskeleton
  • Regulation of actin cytoskeleton, conserved biosystem (from KEGG)
    Regulation of actin cytoskeleton, conserved biosystem
    Regulation of actin cytoskeleton
  • TGF-beta Receptor Signaling, organism-specific biosystem (from WikiPathways)
    TGF-beta Receptor Signaling, organism-specific biosystemThe Transforming growth factor beta (TGFβ) signaling pathway is involved in many cellular processes in both the adult organism and the developing embryo including cell growth, cell differentiat...
  • miRNA targets in ECM and membrane receptors, organism-specific biosystem (from WikiPathways)
    miRNA targets in ECM and membrane receptors, organism-specific biosystemBased on the KEGG ECM-receptor interactions pathway (hsa04512), a depiction a plausible mechanism, where miRNAs regulate components of both extracellular matrix (top panel) and transmembrane receptor...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 IDA
Inferred from Direct Assay
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
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
 
centrosome IDA
Inferred from Direct Assay
more info
 
external side of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
focal adhesion IDA
Inferred from Direct Assay
more info
PubMed 
integrin alphav-beta6 complex IDA
Inferred from Direct Assay
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
    5001..105648
    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_001282353.1NP_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, DB222211
    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_001282355.1NP_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_001282388.1NP_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_001282389.1NP_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_001282390.1NP_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 Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

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