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    Pcdha4 protocadherin alpha 4 [ Mus musculus (house mouse) ]

    Gene ID: 12936, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Pcdha4provided by MGI
    Official Full Name
    protocadherin alpha 4provided by MGI
    Primary source
    MGI:MGI:1298406
    See related
    Ensembl:ENSMUSG00000104252 AllianceGenome:MGI:1298406
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Cnr1; Crnr1
    Summary
    Enables calcium ion binding activity and identical protein binding activity. Predicted to be involved in cell adhesion. Located in endoplasmic reticulum; membrane; and synapse. Is expressed in brain. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in CNS E18 (RPKM 20.9), cortex adult (RPKM 12.7) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Pcdha4 in Genome Data Viewer
    Location:
    18 B2- B3; 18 19.46 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (37085742..37320710)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (36952689..37187657)

    Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer mm9_chr18:36962302-36962603 Neighboring gene STARR-positive B cell enhancer ABC_E1207 Neighboring gene STARR-seq mESC enhancer starr_44299 Neighboring gene STARR-seq mESC enhancer starr_44300 Neighboring gene vault RNA component 5 Neighboring gene STARR-seq mESC enhancer starr_44301 Neighboring gene STARR-seq mESC enhancer starr_44302 Neighboring gene STARR-seq mESC enhancer starr_44303 Neighboring gene STARR-seq mESC enhancer starr_44304 Neighboring gene STARR-seq mESC enhancer starr_44305 Neighboring gene 3-phosphoglycerate dehydrogenase pseudogene Neighboring gene protocadherin alpha 1 Neighboring gene protocadherin alpha 2 Neighboring gene protocadherin alpha 4B Neighboring gene protocadherin alpha 3 Neighboring gene predicted gene, 38666 Neighboring gene predicted gene, 38667 Neighboring gene predicted gene, 36858 Neighboring gene protocadherin alpha 5 Neighboring gene protocadherin alpha 6 Neighboring gene protocadherin alpha 7 Neighboring gene protocadherin alpha 10 Neighboring gene protocadherin alpha 8 Neighboring gene predicted gene 10545 Neighboring gene protocadherin alpha 11 Neighboring gene protocadherin alpha 9 Neighboring gene protocadherin alpha 5 pseudogene Neighboring gene protocadherin alpha 12 Neighboring gene heat shock transcription factor 2 binding protein pseudogene Neighboring gene protocadherin alpha subfamily C, 1 Neighboring gene protocadherin alpha subfamily C, 2 Neighboring gene predicted gene 10544 Neighboring gene STARR-seq mESC enhancer starr_44309 Neighboring gene protocadherin beta 1 Neighboring gene protocadherin beta 2

    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
    • 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. 1H, 13C and 15N resonance assignments of the first cadherin domain of Cadherin-related neuronal receptor (CNR)/protocadherin alpha. Umitsu M, et al. J Biomol NMR, 2005 Apr. PMID 15929006
    2. Combinatorial expression of alpha- and gamma-protocadherins alters their presenilin-dependent processing. Bonn S, et al. Mol Cell Biol, 2007 Jun. PMID 17403907, Free PMC Article
    3. Cadherin-related neuronal receptor 1 (CNR1) has cell adhesion activity with beta1 integrin mediated through the RGD site of CNR1. Mutoh T, et al. Exp Cell Res, 2004 Apr 1. PMID 15023537
    4. Proteolytic processing of protocadherin proteins requires endocytosis. Buchanan SM, et al. Proc Natl Acad Sci U S A, 2010 Oct 12. PMID 20876099, Free PMC Article
    5. Phosphorylation of protocadherin proteins by the receptor tyrosine kinase Ret. Schalm SS, et al. Proc Natl Acad Sci U S A, 2010 Aug 3. PMID 20616001, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Shedding of the Pcdhalpha extracellular domain and subsequent processing by gamma-secretase require endocytosis.
      Title: Proteolytic processing of protocadherin proteins requires endocytosis.
    2. show that protocadherins (Pcdhs) form a heteromeric signaling complex(es), consisting of multiple Pcdh isoforms, receptor tyrosine kinases, phosphatases, and cell adhesion molecules.
      Title: Phosphorylation of protocadherin proteins by the receptor tyrosine kinase Ret.
    3. CNR1 has a heterophilic, calcium-dependent cell adhesion activity with the beta1 integrin subfamily, suggesting the possibility of CNR-beta1 integrin association in synaptogenesis.
      Title: Cadherin-related neuronal receptor 1 (CNR1) has cell adhesion activity with beta1 integrin mediated through the RGD site of CNR1.
    4. This pattern of Pcdha4 expression suggests its involvement in the development of neocortical connectivity.
      Title: CNR/Pcdhalpha family in subplate neurons, and developing cortical connectivity.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough Pcdha4b

    Readthrough gene: Pcdha4b, Included gene: Pcdhga9

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables calcium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IC
    Inferred by Curator
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protocadherin alpha-4
    Names
    PCDH-alpha-4
    cadherin-related neuronal receptor 1

    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_007766.3 → NP_031792.1  protocadherin alpha-4 precursor

      See identical proteins and their annotated locations for NP_031792.1

      Status: VALIDATED

      Source sequence(s)
      AC020968, AC020972, AC020973
      Consensus CDS
      CCDS37776.1
      UniProtKB/Swiss-Prot
      O88689, Q3UEX3, Q6PAM9, Q8K487, Q8K489
      Related
      ENSMUSP00000141408.2, ENSMUST00000192512.6
      Conserved Domains (3) summary
      cd11304
      Location:247 → 346
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30 → 111
      Cadherin_2; Cadherin-like
      pfam15974
      Location:796 → 939
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    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_000084.7 Reference GRCm39 C57BL/6J

      Range
      37085742..37320710
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O88689.1 GenPept UniProtKB/Swiss-Prot:O88689

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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