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

Gene ID: 3655, updated on 5-Jan-2020

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
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
CD49f; VLA-6; 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

Genomic context

See ITGA6 in Genome Data Viewer
Location:
2q31.1
Exon count:
28
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (172427336..172506459)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (173291954..173371181)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985960 Neighboring gene uncharacterized LOC105376738 Neighboring gene uncharacterized LOC105373742 Neighboring gene ITGA6 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 4236 Neighboring gene pyruvate dehydrogenase kinase 1

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?

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ18737, DKFZp686J01244

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cadherin binding HDA PubMed 
insulin-like growth factor I binding IDA
Inferred from Direct Assay
more info
PubMed 
laminin binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
neuregulin binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
amelogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
brown fat cell differentiation IEA
Inferred from Electronic Annotation
more info
 
cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
 
cell-matrix adhesion IEA
Inferred from Electronic Annotation
more info
 
cell-substrate adhesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell-substrate junction assembly TAS
Traceable Author Statement
more info
PubMed 
cellular response to extracellular stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to organic cyclic compound IEA
Inferred from Electronic Annotation
more info
 
digestive tract development IMP
Inferred from Mutant Phenotype
more info
PubMed 
ectodermal cell differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
filopodium assembly IEA
Inferred from Electronic Annotation
more info
 
hemidesmosome assembly TAS
Traceable Author Statement
more info
 
integrin-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
leukocyte migration TAS
Traceable Author Statement
more info
 
nail development IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of extrinsic apoptotic signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of apoptotic process IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell-substrate adhesion IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
renal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
skin development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
basal plasma membrane IEA
Inferred from Electronic Annotation
more info
 
basement membrane IEA
Inferred from Electronic Annotation
more info
 
cell surface HDA PubMed 
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
cell-cell adherens junction IEA
Inferred from Electronic Annotation
more info
 
external side of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
filopodium IEA
Inferred from Electronic Annotation
more info
 
focal adhesion HDA PubMed 
hemidesmosome IEA
Inferred from Electronic Annotation
more info
 
integrin alpha6-beta4 complex IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
integrin alpha-6
Names
CD49 antigen-like family member F
integrin alpha6B
integrin, alpha 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_008853.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_000210.4NP_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
    ENSP00000264107.7, ENST00000264107.11
    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
  2. NM_001079818.3NP_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:374425
    Int_alpha; Integrin alpha (beta-propellor repeats)
    pfam08441
    Location:464939
    Integrin_alpha2; Integrin alpha
  3. NM_001316306.2NP_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:255306
    Int_alpha; Integrin alpha (beta-propellor repeats)
    pfam00357
    Location:919933
    Integrin_alpha; Integrin alpha cytoplasmic region
    pfam08441
    Location:345820
    Integrin_alpha2; Integrin alpha
  4. NM_001365529.2NP_001352458.1  integrin alpha-6 isoform d precursor

    Status: REVIEWED

    Source sequence(s)
    AC078883
    Conserved Domains (2) summary
    smart00191
    Location:374425
    Int_alpha; Integrin alpha (beta-propellor repeats)
    pfam08441
    Location:464924
    Integrin_alpha2; Integrin alpha
  5. NM_001365530.2NP_001352459.1  integrin alpha-6 isoform e precursor

    Status: REVIEWED

    Source sequence(s)
    AC078883
    Conserved Domains (3) summary
    smart00191
    Location:374425
    Int_alpha; Integrin alpha (beta-propellor repeats)
    pfam00357
    Location:10231037
    Integrin_alpha; Integrin alpha cytoplasmic region
    pfam08441
    Location:464924
    Integrin_alpha2; Integrin alpha

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

mRNA and Protein(s)

  1. XM_017004007.1XP_016859496.1  integrin alpha-6 isoform X3

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

  3. XM_017004008.1XP_016859497.1  integrin alpha-6 isoform X4

  4. XM_017004006.1XP_016859495.1  integrin alpha-6 isoform X2

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