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    Pcdha5 protocadherin alpha 5 [ Mus musculus (house mouse) ]

    Gene ID: 12941, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Pcdha5provided by MGI
    Official Full Name
    protocadherin alpha 5provided by MGI
    Primary source
    MGI:MGI:1298371
    See related
    Ensembl:ENSMUSG00000103092 AllianceGenome:MGI:1298371
    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
    Cnr6; Crnr6
    Summary
    Predicted to be involved in cell adhesion. Located in membrane. Is expressed in brain. Orthologous to human PCDHA5 (protocadherin alpha 5). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in CNS E18 (RPKM 21.9), cortex adult (RPKM 13.0) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    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 (37093329..37320716)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (36960276..37187663)

    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 protocadherin alpha 4 Neighboring gene predicted gene, 38667 Neighboring gene predicted gene, 36858 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. Diversity revealed by a novel family of cadherins expressed in neurons at a synaptic complex. Kohmura N, et al. Neuron, 1998 Jun. PMID 9655502
    2. Proteins of the CNR family are multiple receptors for Reelin. Senzaki K, et al. Cell, 1999 Dec 10. PMID 10612399
    3. Monoallelic yet combinatorial expression of variable exons of the protocadherin-alpha gene cluster in single neurons. Esumi S, et al. Nat Genet, 2005 Feb. PMID 15640798
    4. Molecular mechanisms governing Pcdh-gamma gene expression: evidence for a multiple promoter and cis-alternative splicing model. Wang X, et al. Genes Dev, 2002 Aug 1. PMID 12154121, Free PMC Article
    5. Alpha protocadherins and Pyk2 kinase regulate cortical neuron migration and cytoskeletal dynamics via Rac1 GTPase and WAVE complex in mice. Fan L, et al. Elife, 2018 Jun 18. PMID 29911975, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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
    		  

    General protein information

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    Preferred Names
    protocadherin alpha-5
    Names
    cadherin-related neuronal receptor 6

    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_009959.2 → NP_034089.1  protocadherin alpha-5 precursor

      See identical proteins and their annotated locations for NP_034089.1

      Status: VALIDATED

      Source sequence(s)
      AC020968, AC020972, AC020973
      Consensus CDS
      CCDS79617.1
      UniProtKB/TrEMBL
      O88193, Q91Y15
      Related
      ENSMUSP00000142293.2, ENSMUST00000192168.2
      Conserved Domains (3) summary
      cd11304
      Location:246 → 346
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30 → 111
      Cadherin_2; Cadherin-like
      pfam15974
      Location:783 → 926
      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
      37093329..37320716
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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