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    PCDHA9 protocadherin alpha 9 [ Homo sapiens (human) ]

    Gene ID: 9752, updated on 17-Jun-2019

    Summary

    Official Symbol
    PCDHA9provided by HGNC
    Official Full Name
    protocadherin alpha 9provided by HGNC
    Primary source
    HGNC:HGNC:8675
    See related
    Ensembl:ENSG00000204961 MIM:606315
    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
    PCDH-ALPHA9
    Summary
    This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]
    Orthologs

    Genomic context

    See PCDHA9 in Genome Data Viewer
    Location:
    5q31.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (140847772..141012344)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140227357..140391929)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378198 Neighboring gene Sharpr-MPRA regulatory region 6103 Neighboring gene vault RNA 1-3 Neighboring gene ZFP14 zinc finger protein pseudogene Neighboring gene protocadherin alpha cluster, complex locus Neighboring gene protocadherin alpha 1 Neighboring gene protocadherin alpha 2 Neighboring gene protocadherin alpha 3 Neighboring gene protocadherin alpha 4 Neighboring gene uncharacterized LOC112267934 Neighboring gene protocadherin alpha 5 Neighboring gene protocadherin alpha 6 Neighboring gene protocadherin alpha 7 Neighboring gene protocadherin alpha 8 Neighboring gene protocadherin alpha 10 Neighboring gene protocadherin alpha 14 pseudogene Neighboring gene protocadherin alpha 11 Neighboring gene protocadherin alpha 12 Neighboring gene protocadherin alpha 13 Neighboring gene protocadherin alpha subfamily C, 1 Neighboring gene protocadherin alpha subfamily C, 2 Neighboring gene protocadherin alpha constant Neighboring gene uncharacterized LOC101926905 Neighboring gene protocadherin beta 1 Neighboring gene protocadherin beta cluster Neighboring gene protocadherin beta 2

    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

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    NHGRI GWA Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0345

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    protocadherin alpha-9
    Names
    KIAA0345-like 5
    PCDH-alpha-9

    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_000016.2 

      Range
      113645..278218
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014005.4NP_054724.1  protocadherin alpha-9 isoform 2 precursor

      See identical proteins and their annotated locations for NP_054724.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) utilizes the large, first exon then continues into the downstream intron 1 sequence before terminating. This one-exon transcript encodes a shorter isoform (2), compared to isoform 1. This short variant is represented based on data in PMID:10380929.
      Source sequence(s)
      AB002343, AC005609, AF152487, KF458020, KF458022
      UniProtKB/Swiss-Prot
      Q9Y5H5
      Related
      ENSP00000367362.3, ENST00000378122.4
      Conserved Domains (2) summary
      cd11304
      Location:247346
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30111
      Cadherin_2; Cadherin-like
    2. NM_031857.1NP_114063.1  protocadherin alpha-9 isoform 1 precursor

      See identical proteins and their annotated locations for NP_114063.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
      Source sequence(s)
      AB002343, AF152317
      Consensus CDS
      CCDS54920.1
      UniProtKB/Swiss-Prot
      Q9Y5H5
      Related
      ENSP00000436042.1, ENST00000532602.1
      Conserved Domains (3) summary
      cd11304
      Location:247346
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30111
      Cadherin_2; Cadherin-like
      pfam15974
      Location:800942
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

      Range
      140847772..141012344
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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