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    PCDH9 protocadherin 9 [ Homo sapiens (human) ]

    Gene ID: 5101, updated on 4-Jul-2021

    Summary

    Official Symbol
    PCDH9provided by HGNC
    Official Full Name
    protocadherin 9provided by HGNC
    Primary source
    HGNC:HGNC:8661
    See related
    Ensembl:ENSG00000184226 MIM:603581
    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
    Summary
    This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Nov 2012]
    Expression
    Biased expression in brain (RPKM 8.9), fat (RPKM 0.9) and 2 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PCDH9 in Genome Data Viewer
    Location:
    13q21.32
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (66302834..67230336, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (66876966..67804468, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene microRNA 4704 Neighboring gene tripartite motif containing 60 pseudogene 19 Neighboring gene uncharacterized LOC105370247 Neighboring gene RNA, U7 small nuclear 87 pseudogene Neighboring gene PCDH9 antisense RNA 2 Neighboring gene PCDH9 antisense RNA 3 Neighboring gene PCDH9 antisense RNA 4 Neighboring gene uncharacterized LOC105370246 Neighboring gene ribosomal protein SA pseudogene 53 Neighboring gene long intergenic non-protein coding RNA 364

    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

    Associated conditions

    Description Tests
    A genome-wide association study on obesity and obesity-related traits.
    GeneReviews: Not available
    Genome-wide association study identifies candidate genes for male fertility traits in humans.
    GeneReviews: Not available
    Genome-wide association study of lung function decline in adults with and without asthma.
    GeneReviews: Not available
    Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations
    GeneReviews: Not available
    GWAS of dental caries patterns in the permanent dentition.
    GeneReviews: Not available

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-06-07)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-06-07)

    ClinGen Genome Curation Page

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of PCDH9 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in forebrain development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cell-cell contact zone IEA
    Inferred from Electronic Annotation
    more info
     
    located_in growth cone IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    protocadherin-9
    Names
    cadherin superfamily protein VR4-11

    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_011876.2 RefSeqGene

      Range
      5001..932503
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001318372.2NP_001305301.1  protocadherin-9 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, as compared to variant 1. It encodes a shorter isoform (3) which is missing an internal segment, as compared to isoform 1.
      Source sequence(s)
      AI300218, AL834258, BC144321, DA496130, DA497692
      Consensus CDS
      CCDS81770.1
      UniProtKB/Swiss-Prot
      Q9HC56
      UniProtKB/TrEMBL
      B7ZM79
      Related
      ENSP00000401699.2, ENST00000456367.5
      Conserved Domains (3) summary
      cd11304
      Location:576671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777997
      Protocadherin; Protocadherin
      cl09101
      Location:28117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    2. NM_001318373.2NP_001305302.1  protocadherin-9 isoform 4 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two in-frame exons in the coding region, as compared to variant 1. It encodes a shorter isoform (4) which is missing an internal segment, as compared to isoform 1.
      Source sequence(s)
      AI300218, AL834258, BC144321, DA353918, DA496130, DA497692
      UniProtKB/Swiss-Prot
      Q9HC56
      UniProtKB/TrEMBL
      B7ZM79
      Conserved Domains (3) summary
      cd11304
      Location:576671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777997
      Protocadherin; Protocadherin
      cl09101
      Location:28117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    3. NM_001318374.2NP_001305303.1  protocadherin-9 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes a shorter isoform (5) which has a distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      AL160254, AL603863, BC144321, BC150296, DA496130, DA497692
      Consensus CDS
      CCDS81769.1
      UniProtKB/TrEMBL
      A7E2D9, B7ZM79, Q5VT82
      Related
      ENSP00000367092.3, ENST00000377861.4
      Conserved Domains (3) summary
      cd11304
      Location:576671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777997
      Protocadherin; Protocadherin
      cl09101
      Location:28117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    4. NM_020403.5NP_065136.1  protocadherin-9 isoform 2 precursor

      See identical proteins and their annotated locations for NP_065136.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, as compared to variant 1. It encodes a shorter isoform (2) which is missing an internal segment, as compared to isoform 1.
      Source sequence(s)
      AI300218, AK054661, AL603863, AL834258, BC136627, BX537422
      Consensus CDS
      CCDS9443.1
      UniProtKB/Swiss-Prot
      Q9HC56
      Related
      ENSP00000442186.2, ENST00000544246.5
      Conserved Domains (3) summary
      cd11304
      Location:576671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777997
      Protocadherin; Protocadherin
      cl09101
      Location:28117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    5. NM_203487.3NP_982354.1  protocadherin-9 isoform 1 precursor

      See identical proteins and their annotated locations for NP_982354.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AI300218, AK054661, AL834258, BX537422, DA278856
      Consensus CDS
      CCDS9444.1
      UniProtKB/Swiss-Prot
      Q9HC56
      UniProtKB/TrEMBL
      X5D7N0
      Related
      ENSP00000367096.2, ENST00000377865.7
      Conserved Domains (2) summary
      cd11304
      Location:576671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777997
      Protocadherin; Protocadherin

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

      Range
      66302834..67230336 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020619.2XP_016876108.1  protocadherin-9 isoform X1

      UniProtKB/Swiss-Prot
      Q9HC56
      UniProtKB/TrEMBL
      X5D7N0
      Conserved Domains (2) summary
      cd11304
      Location:576671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777997
      Protocadherin; Protocadherin
    2. XM_017020620.2XP_016876109.1  protocadherin-9 isoform X2

    3. XM_011535099.2XP_011533401.1  protocadherin-9 isoform X3

      Conserved Domains (3) summary
      cd11304
      Location:576671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777997
      Protocadherin; Protocadherin
      cl09101
      Location:28117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    4. XM_005266408.4XP_005266465.1  protocadherin-9 isoform X4

      Conserved Domains (3) summary
      cd11304
      Location:576671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777997
      Protocadherin; Protocadherin
      cl09101
      Location:28117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    5. XM_017020621.2XP_016876110.1  protocadherin-9 isoform X4

      Conserved Domains (3) summary
      cd11304
      Location:576671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777997
      Protocadherin; Protocadherin
      cl09101
      Location:28117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
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