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

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; 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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Poor Prognosis of Oral Squamous Cell Carcinoma Correlates With ITGA6.
Title: Poor Prognosis of Oral Squamous Cell Carcinoma Correlates With ITGA6.
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.
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.
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.
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.
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.
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

Associated conditions

Description	Tests
Epidermolysis bullosa, junctional 6, with pyloric atresia MedGen: C5676957 OMIM: 619817 GeneReviews: Epidermolysis Bullosa with Pyloric Atresia	not available

EBI GWAS Catalog

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

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH69051 (e-PCR)
- UniSTS:11018

G62018 (e-PCR)
- UniSTS:139097

RH48692 (e-PCR)
- UniSTS:3447

RH98245 (e-PCR)
- UniSTS:91524

G13288 (e-PCR)
- UniSTS:71089

SHGC-84040 (e-PCR)
- UniSTS:104640

SHGC-12676 (e-PCR)
- UniSTS:43727

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cadherin binding	HDA more info	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 more info	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 more info	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

NG_008853.1 RefSeqGene

Range

5001..83874

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

172427336..172506459

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
XM_047444221.1 → XP_047300177.1 integrin alpha-6 isoform X3
XM_047444222.1 → XP_047300178.1 integrin alpha-6 isoform X4