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

Gene ID: 3694, updated on 1-Jun-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
109.20200522 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)
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