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

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; AllianceGenome:HGNC:6161
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: mouse all
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Genomic context

Location:: 2q24.2

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (160099671..160200272, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (160557539..160657754, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (160956182..161056783, complement)

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
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?

ITGB6 promotes pancreatic fibrosis and aggravates the malignant process of pancreatic cancer via JAK2/STAT3 signaling pathway.
Title: ITGB6 promotes pancreatic fibrosis and aggravates the malignant process of pancreatic cancer via JAK2/STAT3 signaling pathway.
CRISPR/Cas9-mediated knock out of ITGB6 in human OSCC cells reduced migration and proliferation ability.
Title: CRISPR/Cas9-mediated knock out of ITGB6 in human OSCC cells reduced migration and proliferation ability.
Acidity-induced ITGB6 promote migration and invasion of lung cancer cells by epithelial-mesenchymal transition and focal adhesion.
Title: Acidity-induced ITGB6 promote migration and invasion of lung cancer cells by epithelial-mesenchymal transition and focal adhesion.
Extracellular vesicles rich in HAX1 promote angiogenesis by modulating ITGB6 translation.
Title: Extracellular vesicles rich in HAX1 promote angiogenesis by modulating ITGB6 translation.
Integrin alphavbeta6 contributes to the development of intestinal fibrosis via the FAK/AKT signaling pathway.
Title: Integrin αvβ6 contributes to the development of intestinal fibrosis via the FAK/AKT signaling pathway.
The ITGB6 gene: its role in experimental and clinical biology.
Title: The ITGB6 gene: its role in experimental and clinical biology.
Transgenic overexpression of ITGB6 in intestinal epithelial cells exacerbates dextran sulfate sodium-induced colitis in mice.
Title: Transgenic overexpression of ITGB6 in intestinal epithelial cells exacerbates dextran sulfate sodium-induced colitis in mice.
Expression of integrin alphanubeta6 differentiates perihilar cholangiocarcinoma (PHC) from benign disease mimicking PHC.
Title: Expression of integrin ανβ6 differentiates perihilar cholangiocarcinoma (PHC) from benign disease mimicking PHC.
ITGB6-Knockout Suppresses Cholangiocarcinoma Cell Migration and Invasion with Declining PODXL2 Expression.
Title: ITGB6-Knockout Suppresses Cholangiocarcinoma Cell Migration and Invasion with Declining PODXL2 Expression.
The relationship between integrin avss6 and HBV infection in patients with liver cirrhosis and hepatocellular carcinoma: a preliminary report.
Title: The relationship between integrin avß6 and HBV infection in patients with liver cirrhosis and hepatocellular carcinoma: a preliminary report.

Submit: New GeneRIF Correction See all GeneRIFs (90)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Amelogenesis imperfecta type 1H MedGen: C4015557 OMIM: 616221 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Genetic variants at 2q24 are associated with susceptibility to type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy. 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
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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-86148 (e-PCR)
- UniSTS:104796

RH94144 (e-PCR)
- UniSTS:93035

SHGC-54614 (e-PCR)
- UniSTS:60344

RH120622 (e-PCR)
- UniSTS:132563

Itgb6 (e-PCR), detects polymorphism
- UniSTS:507377

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables integrin binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables virus receptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Langerhans cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in bone development	IEA Inferred from Electronic Annotation more info
involved_in bronchiole development	IEA Inferred from Electronic Annotation more info
involved_in cell adhesion	TAS Traceable Author Statement more info	PubMed
involved_in cell adhesion mediated by integrin	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell adhesion mediated by integrin	IDA Inferred from Direct Assay more info	PubMed
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell morphogenesis	IEA Inferred from Electronic Annotation 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	NAS Non-traceable Author Statement more info	PubMed
involved_in cellular response to ionizing radiation	IEA Inferred from Electronic Annotation more info
involved_in enamel mineralization	IEA Inferred from Electronic Annotation more info
involved_in hard palate development	IEA Inferred from Electronic Annotation more info
involved_in immune response	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
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 lung alveolus development	IEA Inferred from Electronic Annotation more info
involved_in phospholipid homeostasis	IEA Inferred from Electronic Annotation more info
involved_in response to virus	IEA Inferred from Electronic Annotation more info
involved_in skin development	IEA Inferred from Electronic Annotation more info
involved_in surfactant homeostasis	IEA Inferred from Electronic Annotation more info
involved_in symbiont entry into host cell	IEA Inferred from Electronic Annotation more info
involved_in transforming growth factor beta production	IEA Inferred from Electronic Annotation more info
involved_in transforming growth factor beta receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in wound healing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell junction	IDA Inferred from Direct Assay more info
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in centrosome	IDA Inferred from Direct Assay more info
located_in external side of plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in focal adhesion	IBA Inferred from Biological aspect of Ancestor more info
located_in focal adhesion	IDA Inferred from Direct Assay more info	PubMed
part_of integrin alphav-beta6 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of integrin alphav-beta6 complex	IDA Inferred from Direct Assay more info	PubMed
part_of integrin alphav-beta6 complex	IPI Inferred from Physical Interaction more info	PubMed
part_of integrin complex	TAS Traceable Author Statement more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in plasma membrane	TAS Traceable Author Statement more info
part_of receptor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: integrin beta-6

Names: integrin, beta 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_042041.1 RefSeqGene

Range

5042..105643

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000888.5 → NP_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

B2R9W5, C9JA97, P18564, Q0VA95, Q16500, Q53RG5, Q53RR6

UniProtKB/TrEMBL

A8K2N5

Related

ENSP00000283249.2, ENST00000283249.7

Conserved Domains (4) summary

pfam00362
Location:30 → 454

Integrin_beta; Integrin, beta chain

pfam07965
Location:624 → 706

Integrin_B_tail; Integrin beta tail domain

pfam07974
Location:546 → 574

EGF_2; EGF-like domain

pfam08725
Location:733 → 775

Integrin_b_cyt; Integrin beta cytoplasmic domain
NM_001282353.2 → NP_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

B2R9W5, C9JA97, P18564, Q0VA95, Q16500, Q53RG5, Q53RR6

UniProtKB/TrEMBL

A8K2N5

Related

ENSP00000386367.1, ENST00000409872.1

Conserved Domains (4) summary

pfam00362
Location:30 → 454

Integrin_beta; Integrin, beta chain

pfam07965
Location:624 → 706

Integrin_B_tail; Integrin beta tail domain

pfam07974
Location:546 → 574

EGF_2; EGF-like domain

pfam08725
Location:733 → 775

Integrin_b_cyt; Integrin beta cytoplasmic domain
NM_001282354.2 → NP_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, A8K2N5

Related

ENSP00000481183.1, ENST00000620391.4

Conserved Domains (4) summary

pfam00362
Location:21 → 359

Integrin_beta; Integrin, beta chain

pfam07965
Location:529 → 611

Integrin_B_tail; Integrin beta tail domain

pfam07974
Location:451 → 479

EGF_2; EGF-like domain

pfam08725
Location:638 → 680

Integrin_b_cyt; Integrin beta cytoplasmic domain
NM_001282355.2 → NP_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/TrEMBL

A8K2N5

Related

ENSP00000386828.2, ENST00000409967.6

Conserved Domains (3) summary

pfam00362
Location:30 → 454

Integrin_beta; Integrin, beta chain

pfam07965
Location:554 → 599

Integrin_B_tail; Integrin beta tail domain

pfam08725
Location:626 → 668

Integrin_b_cyt; Integrin beta cytoplasmic domain
NM_001282388.2 → NP_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/TrEMBL

B4E2B8, E9PEE8

Related

ENSP00000408024.2, ENST00000428609.6

Conserved Domains (4) summary

pfam00362
Location:5 → 412

Integrin_beta; Integrin, beta chain

pfam07965
Location:582 → 664

Integrin_B_tail; Integrin beta tail domain

pfam07974
Location:504 → 532

EGF_2; EGF-like domain

pfam08725
Location:691 → 733

Integrin_b_cyt; Integrin beta cytoplasmic domain
NM_001282389.2 → NP_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

UniProtKB/TrEMBL

B4E2B8

Conserved Domains (4) summary

pfam00362
Location:36 → 381

Integrin_beta; Integrin, beta chain

pfam07965
Location:551 → 633

Integrin_B_tail; Integrin beta tail domain

pfam07974
Location:473 → 501

EGF_2; EGF-like domain

pfam08725
Location:660 → 702

Integrin_b_cyt; Integrin beta cytoplasmic domain
NM_001282390.2 → NP_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

UniProtKB/TrEMBL

B4E2B8

Conserved Domains (4) summary

pfam00362
Location:1 → 316

Integrin_beta; Integrin, beta chain

pfam07965
Location:486 → 568

Integrin_B_tail; Integrin beta tail domain

pfam07974
Location:408 → 436

EGF_2; EGF-like domain

pfam08725
Location:595 → 637

Integrin_b_cyt; Integrin beta cytoplasmic domain