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

Gene ID: 3655, updated on 27-Nov-2024

Summary

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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

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Integrin alpha6 cleavage: a novel modification to modulate cell migration. Pawar SC, et al. Exp Cell Res, 2007 Apr 1. PMID 17303120, Free PMC Article
  2. Extracellular engagement of alpha6 integrin inhibited urokinase-type plasminogen activator-mediated cleavage and delayed human prostate bone metastasis. Ports MO, et al. Cancer Res, 2009 Jun 15. PMID 19491258, Free PMC Article
  3. Use of integrin alpha 6 transcripts in a stool mRNA assay for the detection of colorectal cancers at curable stages. Beaulieu JF, et al. Oncotarget, 2016 Mar 22. PMID 26895101, Free PMC Article
  4. Differential expression of the integrins alpha6Abeta4 and alpha6Bbeta4 along the crypt-villus axis in the human small intestine. Dydensborg AB, et al. Histochem Cell Biol, 2009 Apr. PMID 19107504
  5. The role of alpha 6 integrin in prostate cancer migration and bone pain in a novel xenograft model. King TE, et al. PLoS One, 2008. PMID 18958175, Free PMC Article

See all (359) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RAC1-mediated integrin alpha-6 expression in E-cadherin-deficient gastric cancer cells promotes interactions with the stroma and peritoneal dissemination.
    Title: RAC1-mediated integrin alpha-6 expression in E-cadherin-deficient gastric cancer cells promotes interactions with the stroma and peritoneal dissemination.
  2. Long noncoding RNA SNHG3 interacts with microRNA-502-3p to mediate ITGA6 expression in liver hepatocellular carcinoma.
    Title: Long noncoding RNA SNHG3 interacts with microRNA-502-3p to mediate ITGA6 expression in liver hepatocellular carcinoma.
  3. m6A/HOXA10-AS/ITGA6 axis aggravates oxidative resistance and malignant progression of laryngeal squamous cell carcinoma through regulating Notch and Keap1/Nrf2 pathways.
    Title: m6A/HOXA10-AS/ITGA6 axis aggravates oxidative resistance and malignant progression of laryngeal squamous cell carcinoma through regulating Notch and Keap1/Nrf2 pathways.
  4. Poor Prognosis of Oral Squamous Cell Carcinoma Correlates With ITGA6.
    Title: Poor Prognosis of Oral Squamous Cell Carcinoma Correlates With ITGA6.
  5. Integrin alpha 6 is upregulated and drives hepatocellular carcinoma progression through integrin alpha6beta4 complex.
    Title: Integrin alpha 6 is upregulated and drives hepatocellular carcinoma progression through integrin α6β4 complex.
  6. TM4SF1 promotes esophageal squamous cell carcinoma metastasis by interacting with integrin alpha6.
    Title: TM4SF1 promotes esophageal squamous cell carcinoma metastasis by interacting with integrin α6.
  7. Pancreatic ductal adenocarcinoma cells employ integrin alpha6beta4 to form hemidesmosomes and regulate cell proliferation.
    Title: Pancreatic ductal adenocarcinoma cells employ integrin α6β4 to form hemidesmosomes and regulate cell proliferation.
  8. Extracellular vesicle-mediated delivery of miR-127-3p inhibits the proliferation and invasion of choriocarcinoma cells by targeting ITGA6.
    Title: Extracellular vesicle-mediated delivery of miR-127-3p inhibits the proliferation and invasion of choriocarcinoma cells by targeting ITGA6.
  9. ID1/ID3 mediate the contribution of skin fibroblasts to local nerve regeneration through Itga6 in wound repair.
    Title: ID1/ID3 mediate the contribution of skin fibroblasts to local nerve regeneration through Itga6 in wound repair.
  10. Integrin alpha6A (ITGA6A)-type Splice Variant in Extracellular Vesicles Has a Potential as a Novel Marker of the Early Recurrence of Pancreatic Cancer.
    Title: Integrin α6A (ITGA6A)-type Splice Variant in Extracellular Vesicles Has a Potential as a Novel Marker of the Early Recurrence of Pancreatic Cancer.
Submit: New GeneRIF Correction See all GeneRIFs (215)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ18737, DKFZp686J01244

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cadherin binding HDA PubMed 
enables insulin-like growth factor I binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables integrin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables laminin binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables neuregulin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell adhesion mediated by integrin IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell-matrix adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell-matrix adhesion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cell-substrate adhesion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cell-substrate junction assembly TAS
Traceable Author Statement
more info
 PubMed 
involved_in cellular response to organic cyclic compound IEA
Inferred from Electronic Annotation
more info
  
involved_in ectodermal cell differentiation IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in integrin-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in integrin-mediated signaling pathway NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in leukocyte migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nail development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of extrinsic apoptotic signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within positive regulation of apoptotic process IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell-substrate adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of phosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in skin morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in adherens junction IEA
Inferred from Electronic Annotation
more info
  
located_in cell surface HDA PubMed 
located_in cell surface IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in filopodium IEA
Inferred from Electronic Annotation
more info
  
located_in focal adhesion HDA PubMed 
part_of integrin alpha6-beta1 complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of integrin alpha6-beta4 complex IEA
Inferred from Electronic Annotation
more info
  
part_of integrin complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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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)

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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

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P23229.5 GenPept UniProtKB/Swiss-Prot:P23229

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