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    ITGA9 integrin subunit alpha 9 [ Homo sapiens (human) ]

    Gene ID: 3680, updated on 9-Dec-2024

    Summary

    Official Symbol
    ITGA9provided by HGNC
    Official Full Name
    integrin subunit alpha 9provided by HGNC
    Primary source
    HGNC:HGNC:6145
    See related
    Ensembl:ENSG00000144668 MIM:603963; AllianceGenome:HGNC:6145
    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
    RLC; ITGA4L; ALPHA-RLC
    Summary
    This gene encodes an alpha integrin. Integrins are heterodimeric integral membrane glycoproteins composed of an alpha chain and a beta chain that mediate cell-cell and cell-matrix adhesion. The protein encoded by this gene, when bound to the beta 1 chain, forms an integrin that is a receptor for VCAM1, cytotactin and osteopontin. Expression of this gene has been found to be upregulated in small cell lung cancers. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 11.9), spleen (RPKM 11.4) and 24 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See ITGA9 in Genome Data Viewer
    Location:
    3p22.2
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (37452141..37823507)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (37453682..37827665)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (37493632..37864998)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene golgin A4 Neighboring gene RNA, 5S ribosomal pseudogene 129 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:37485219-37485403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14199 Neighboring gene APRG1 tumor suppressor candidate Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37516063-37516575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37516576-37517087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37539704-37540204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37579429-37579930 Neighboring gene RNA, U7 small nuclear 73 pseudogene Neighboring gene MPRA-validated peak4612 silencer Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:37734983-37735674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37783057-37783865 Neighboring gene NANOG hESC enhancer GRCh37_chr3:37784268-37784945 Neighboring gene VISTA enhancer hs1961 Neighboring gene ribosomal protein L21 pseudogene 135 Neighboring gene ITGA9 antisense RNA 1 Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 4 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37904633-37905134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37905135-37905634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:37945100-37945826 Neighboring gene Sharpr-MPRA regulatory region 2528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19674 Neighboring gene CTD small phosphatase like Neighboring gene HNF1 motif-containing MPRA enhancer 248 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:38003356-38003967 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38010565-38011128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38011129-38011690 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:38028477-38028654 Neighboring gene Sharpr-MPRA regulatory region 12639 Neighboring gene Sharpr-MPRA regulatory region 7921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38035775-38036392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38039104-38039674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38047479-38047979 Neighboring gene microRNA 26a-1 Neighboring gene villin like

    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

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies ITGA9 conferring risk of nasopharyngeal carcinoma.
    EBI GWAS Catalog
    A genome-wide association study of behavioral disinhibition.
    EBI GWAS Catalog
    Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
    EBI GWAS Catalog
    Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
    EBI GWAS Catalog
    Novel loci associated with PR interval in a genome-wide association study of 10 African American cohorts.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables integrin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables integrin binding involved in cell-matrix adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell adhesion IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    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 NAS
    Non-traceable Author Statement
    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 negative regulation of vasoconstriction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neutrophil chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in basal plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of integrin alpha9-beta1 complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of integrin alpha9-beta1 complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of integrin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    integrin alpha-9
    Names
    integrin alpha-RLC

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_016166.1 RefSeqGene

      Range
      5001..372469
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_002207.3NP_002198.2  integrin alpha-9 precursor

      See identical proteins and their annotated locations for NP_002198.2

      Status: REVIEWED

      Source sequence(s)
      AC092055, AC093415, BC030198, BX647350, D25303, L24158
      Consensus CDS
      CCDS2669.1
      UniProtKB/Swiss-Prot
      Q13797, Q14638
      Related
      ENSP00000264741.5, ENST00000264741.10
      Conserved Domains (2) summary
      smart00191
      Location:361414
      Int_alpha; Integrin alpha (beta-propellor repeats)
      pfam08441
      Location:459903
      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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      37452141..37823507
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791771.1 Reference GRCh38.p14 PATCHES

      Range
      21980..396164
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      37453682..37827665
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)