Format

Send to:

Choose Destination

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
Support Center