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Pcdh9 protocadherin 9 [ Mus musculus (house mouse) ]

Gene ID: 211712, updated on 2-Nov-2024

Summary

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Official Symbol
Pcdh9provided by MGI
Official Full Name
protocadherin 9provided by MGI
Primary source
MGI:MGI:1306801
See related
Ensembl:ENSMUSG00000055421 AllianceGenome:MGI:1306801
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
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 multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]
Expression
Biased expression in cerebellum adult (RPKM 14.4), cortex adult (RPKM 12.5) and 6 other tissues See more
Orthologs
human all
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Genomic context

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See Pcdh9 in Genome Data Viewer
Location:
14 E2.1; 14 45.8 cM
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (93251136..94132619, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (93013700..93892834, complement)

Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_37386 Neighboring gene STARR-seq mESC enhancer starr_37387 Neighboring gene predicted gene, 24127 Neighboring gene heat shock protein 8 pseudogene Neighboring gene STARR-seq mESC enhancer starr_37389 Neighboring gene STARR-seq mESC enhancer starr_37390 Neighboring gene STARR-seq mESC enhancer starr_37392 Neighboring gene STARR-seq mESC enhancer starr_37394 Neighboring gene predicted gene, 23509 Neighboring gene nucleophosmin 1 pseudogene Neighboring gene L-lactate dehydrogenase A pseudogene Neighboring gene STARR-seq mESC enhancer starr_37395 Neighboring gene STARR-seq mESC enhancer starr_37396 Neighboring gene predicted gene, 23324 Neighboring gene predicted gene, 18074

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Deficiency of protocadherin 9 leads to reduction in positive emotional behaviour. Uemura M, et al. Sci Rep, 2022 Jul 13. PMID 35831353, Free PMC Article
  2. Cadherin expression in the somatosensory cortex: evidence for a combinatorial molecular code at the single-cell level. Krishna-K K, et al. Neuroscience, 2011 Feb 23. PMID 21129452
  3. Genetic Mapping in Mice Reveals the Involvement of Pcdh9 in Long-Term Social and Object Recognition and Sensorimotor Development. Bruining H, et al. Biol Psychiatry, 2015 Oct 1. PMID 25802080
  4. Characterization of two novel protocadherins (PCDH8 and PCDH9) localized on human chromosome 13 and mouse chromosome 14. Strehl S, et al. Genomics, 1998 Oct 1. PMID 9787079
  5. Single-Cell Transcriptomics Reveals Regulators of Neuronal Migration and Maturation During Brain Development. Pensold D, et al. J Exp Neurosci, 2018. PMID 29551912, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Deficiency of protocadherin 9 leads to reduction in positive emotional behaviour.
    Title: Deficiency of protocadherin 9 leads to reduction in positive emotional behaviour.
  2. Quantitative analysis of basic mouse behavior uncovered a role for Pcdh9 in specific cognitive functions required for long-term recognition, involvement of Pcdh9 in sensory cortex development and showed effect of its deletion on sensorimotor behaviors
    Title: Genetic Mapping in Mice Reveals the Involvement of Pcdh9 in Long-Term Social and Object Recognition and Sensorimotor Development.
  3. The results of this study demonistrated that the distribution of Pcdh9 protein in the olfactory bulb, retina, spinal cord, and dorsal root ganglion
    Title: Distribution of protocadherin 9 protein in the developing mouse nervous system.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Targeted (3)  1 citation

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cell-cell contact zone IDA
Inferred from Direct Assay
more info
 PubMed 
located_in growth cone IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
protocadherin-9

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001081377.3 → NP_001074846.1  protocadherin-9 isoform a precursor

    See identical proteins and their annotated locations for NP_001074846.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a, also known as 3).
    Source sequence(s)
    AC122355, AC123919, AC125095, AC132470, CF745283
    Consensus CDS
    CCDS36992.1
    UniProtKB/TrEMBL
    B2RY69, F8VPK8
    Related
    ENSMUSP00000141396.2, ENSMUST00000195826.6
    Conserved Domains (3) summary
    cd11304
    Location:576 → 671
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:777 → 997
    Protocadherin; Protocadherin
    cl09101
    Location:28 → 117
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  2. NM_001271798.1 → NP_001258727.1  protocadherin-9 isoform b precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an in-frame exon, compared to variant 1. The encoded isoform (b, also known as 2) is shorter than isoform a.
    Source sequence(s)
    AC123919, AC125095, AC132470
    Consensus CDS
    CCDS79350.1
    UniProtKB/TrEMBL
    A0A0A6YWY8, B2RY66
    Related
    ENSMUSP00000141759.2, ENSMUST00000193901.6
    Conserved Domains (3) summary
    cd11304
    Location:576 → 671
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:777 → 997
    Protocadherin; Protocadherin
    cl09101
    Location:28 → 117
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  3. NM_001271799.1 → NP_001258728.1  protocadherin-9 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains multiple differences in the 5' UTR and coding region, compared to variant 1. It initiates translation at an alternate start codon. The encoded isoform (c) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC123919, BC060736, CJ107832
    Consensus CDS
    CCDS79352.1
    UniProtKB/TrEMBL
    A0A0A6YY37, B2RXR7
    Related
    ENSMUSP00000142260.2, ENSMUST00000192221.6
    Conserved Domains (2) summary
    cd11304
    Location:453 → 548
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:654 → 874
    Protocadherin; Protocadherin

  4. NM_001271800.2 → NP_001258729.1  protocadherin-9 isoform d precursor

    See identical proteins and their annotated locations for NP_001258729.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon and uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (d, also known as 4) is shorter than isoform a.
    Source sequence(s)
    AC123919, AC125095, AC132470, CF745283
    UniProtKB/TrEMBL
    B2RXR7
    Conserved Domains (3) summary
    cd11304
    Location:576 → 671
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:777 → 997
    Protocadherin; Protocadherin
    cl09101
    Location:28 → 117
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  5. NM_001346722.1 → NP_001333651.1  protocadherin-9 isoform e precursor

    Status: REVIEWED

    Source sequence(s)
    AC122355, AC123919, AC125095, AC132470
    Consensus CDS
    CCDS84156.1
    UniProtKB/TrEMBL
    A0A0A6YY09, B2RXR7
    Related
    ENSMUSP00000142224.2, ENSMUST00000195376.6

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000080.7 Reference GRCm39 C57BL/6J

    Range
    93251136..94132619 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006518777.5 → XP_006518840.1  protocadherin-9 isoform X2

    UniProtKB/TrEMBL
    B2RXR7
    Conserved Domains (2) summary
    cd11304
    Location:576 → 671
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:777 → 1000
    Protocadherin

  2. XM_036158532.1 → XP_036014425.1  protocadherin-9 isoform X1

    UniProtKB/TrEMBL
    B2RY69
    Conserved Domains (2) summary
    cd11304
    Location:576 → 671
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:777 → 1000
    Protocadherin

RNA

  1. XR_003950833.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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