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    PCDHGA9 protocadherin gamma subfamily A, 9 [ Homo sapiens (human) ]

    Gene ID: 56107, updated on 12-Aug-2018

    Summary

    Official Symbol
    PCDHGA9provided by HGNC
    Official Full Name
    protocadherin gamma subfamily A, 9provided by HGNC
    Primary source
    HGNC:HGNC:8707
    See related
    Ensembl:ENSG00000261934 MIM:606296; Vega:OTTHUMG00000177473
    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-GAMMA-A9
    Summary
    This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
    Orthologs

    Genomic context

    See PCDHGA9 in Genome Data Viewer
    Location:
    5q31.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (141402953..141512979)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140782520..140892546)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 2 Neighboring gene protocadherin gamma subfamily A, 1 Neighboring gene TATA-box binding protein associated factor 7 Neighboring gene protocadherin gamma cluster Neighboring gene protocadherin gamma subfamily A, 2 Neighboring gene protocadherin gamma subfamily A, 3 Neighboring gene protocadherin gamma subfamily B, 1 Neighboring gene protocadherin gamma subfamily A, 4 Neighboring gene protocadherin gamma subfamily B, 2 Neighboring gene protocadherin gamma subfamily A, 5 Neighboring gene protocadherin gamma subfamily B, 3 Neighboring gene protocadherin gamma subfamily A, 6 Neighboring gene protocadherin gamma subfamily A, 7 Neighboring gene protocadherin gamma subfamily B, 4 Neighboring gene protocadherin gamma subfamily A, 8 Neighboring gene protocadherin gamma subfamily B, 5 Neighboring gene protocadherin gamma subfamily B, 6 Neighboring gene protocadherin gamma subfamily A, 10 Neighboring gene protocadherin gamma subfamily A, 11 Neighboring gene protocadherin gamma subfamily B, 7 Neighboring gene protocadherin gamma subfamily B, 8 pseudogene Neighboring gene protocadherin gamma subfamily A, 12 Neighboring gene protocadherin gamma subfamily B, 9 pseudogene Neighboring gene RNA, 7SL, cytoplasmic 68, pseudogene Neighboring gene protocadherin gamma subfamily C, 3 Neighboring gene protocadherin gamma subfamily C, 4 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene diaphanous related formin 1 Neighboring gene uncharacterized LOC100505658 Neighboring gene ribosomal protein S27a pseudogene 10

    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 Jun 15 11:32:44 2016

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding HDA PubMed 
    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 

    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_000012.2 

      Range
      113150..223176
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018921.2NP_061744.1  protocadherin gamma-A9 isoform 1 precursor

      See identical proteins and their annotated locations for NP_061744.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
      Source sequence(s)
      AF152329
      Consensus CDS
      CCDS58981.1
      UniProtKB/Swiss-Prot
      Q9Y5G4
      Related
      ENSP00000460274.1, OTTHUMP00000256753, ENST00000573521.1, OTTHUMT00000437105
      Conserved Domains (4) summary
      cd11304
      Location:246343
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30112
      Cadherin_2; Cadherin-like
      pfam15974
      Location:809905
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
      pfam16492
      Location:688772
      Cadherin_C_2; Cadherin cytoplasmic C-terminal
    2. NM_032089.1NP_114478.1  protocadherin gamma-A9 isoform 2 precursor

      See identical proteins and their annotated locations for NP_114478.1

      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 the shorter isoform (2).
      Source sequence(s)
      AF152516
      Consensus CDS
      CCDS75341.1
      UniProtKB/Swiss-Prot
      Q9Y5G4
      Related
      ENSP00000480862.1, OTTHUMP00000275827, ENST00000616887.1, OTTHUMT00000476697
      Conserved Domains (3) summary
      cd11304
      Location:246343
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30112
      Cadherin_2; Cadherin-like
      pfam16492
      Location:688772
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

      Range
      141402953..141512979
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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