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    Pcdha1 protocadherin alpha 1 [ Mus musculus (house mouse) ]

    Gene ID: 116731, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Pcdha1provided by MGI
    Official Full Name
    protocadherin alpha 1provided by MGI
    Primary source
    MGI:MGI:2150982
    See related
    Ensembl:ENSMUSG00000103442 AllianceGenome:MGI:2150982
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    CNR
    Summary
    Predicted to be involved in cell adhesion. Located in endoplasmic reticulum and membrane. Is expressed in brain; enteric nervous system; and intestine. Orthologous to human PCDHA1 (protocadherin alpha 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in CNS E18 (RPKM 20.0), cortex adult (RPKM 12.5) and 7 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Pcdha1 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 (37063338..37320710)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (36930285..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 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 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. A variable cytoplasmic domain segment is necessary for γ-protocadherin trafficking and tubulation in the endosome/lysosome pathway. O'Leary R, et al. Mol Biol Cell, 2011 Nov. PMID 21917590, Free PMC Article
    2. Two novel CNRs from the CNR gene cluster have molecular features distinct from those of CNR1 to 8. Takei Y, et al. Genomics, 2001 Mar 15. PMID 11401448
    3. Toward simpler and faster genome-wide mutagenesis in mice. Wu S, et al. Nat Genet, 2007 Jul. PMID 17572674
    4. 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
    5. CNR/Pcdhalpha family in subplate neurons, and developing cortical connectivity. Morishita H, et al. Neuroreport, 2004 Dec 3. PMID 15570159

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC90628

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  

    General protein information

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    Preferred Names
    protocadherin alpha-1
    Names
    protocadherin alpha 2

    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_054072.1 → NP_473413.1  protocadherin alpha-1 precursor

      See identical proteins and their annotated locations for NP_473413.1

      Status: PROVISIONAL

      Source sequence(s)
      AY013756
      Consensus CDS
      CCDS37774.1
      UniProtKB/TrEMBL
      Q641K6, Q91Y21
      Related
      ENSMUSP00000068828.5, ENSMUST00000070797.7
      Conserved Domains (3) summary
      cd11304
      Location:247 → 347
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:31 → 112
      Cadherin_2; Cadherin-like
      pfam15974
      Location:797 → 940
      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
      37063338..37320710
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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