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    Pcdh1 protocadherin 1 [ Mus musculus (house mouse) ]

    Gene ID: 75599, updated on 30-Apr-2024

    Summary

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    Official Symbol
    Pcdh1provided by MGI
    Official Full Name
    protocadherin 1provided by MGI
    Primary source
    MGI:MGI:104692
    See related
    Ensembl:ENSMUSG00000051375 AllianceGenome:MGI:104692
    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
    2010005A06Rik
    Summary
    Predicted to be involved in cell adhesion. Predicted to act upstream of or within calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules and homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to be located in cell junction; nucleolus; and nucleoplasm. Predicted to be integral component of plasma membrane. Is expressed in several structures, including central nervous system; genitourinary system; gut; heart; and sensory organ. Orthologous to human PCDH1 (protocadherin 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in lung adult (RPKM 22.2), small intestine adult (RPKM 16.0) and 22 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Pcdh1 in Genome Data Viewer
    Location:
    18 B3; 18 20.08 cM
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (38318967..38345023, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (38185914..38212048, complement)

    Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 30188 Neighboring gene predicted gene, 30142 Neighboring gene predicted gene, 30259 Neighboring gene STARR-seq mESC enhancer starr_44348 Neighboring gene predicted gene, 52328 Neighboring gene RIKEN cDNA 2010320O07 gene Neighboring gene RIKEN cDNA 1700086O06 gene Neighboring gene 60S ribosomal protein L17-like

    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. Mouse protocadherin-1 gene expression is regulated by cigarette smoke exposure in vivo. Koning H, et al. PLoS One, 2014. PMID 24992194, Free PMC Article
    2. Expression of protocadherin-1 (Pcdh1) during mouse development. Redies C, et al. Dev Dyn, 2008 Sep. PMID 18729229
    3. Cloning, expression, and chromosomal localization of a novel cadherin-related protein, protocadherin-3. Sago H, et al. Genomics, 1995 Oct 10. PMID 8575755
    4. delta-Protocadherins: a gene family expressed differentially in the mouse brain. Vanhalst K, et al. Cell Mol Life Sci, 2005 Jun. PMID 15905963, Free PMC Article
    5. An expression profile analysis of ES cell-derived definitive endodermal cells and Pdx1-expressing cells. Ogaki S, et al. BMC Dev Biol, 2011 Mar 1. PMID 21362171, Free PMC Article

    See all (21) 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)
    • Endonuclease-mediated (3) 

    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
    acts_upstream_of_or_within calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within homophilic cell adhesion via plasma membrane adhesion molecules TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell-cell junction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protocadherin-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_001403795.1 → NP_001390724.1  protocadherin-1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC133646

    2. NM_029357.3 → NP_083633.2  protocadherin-1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_083633.2

      Status: VALIDATED

      Source sequence(s)
      AC133646
      Consensus CDS
      CCDS29197.1
      UniProtKB/TrEMBL
      Q8CFX3, Q8QZT6
      Related
      ENSMUSP00000055199.7, ENSMUST00000057185.13
      Conserved Domains (3) summary
      cd11304
      Location:490 → 586
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:793 → 1004
      Protocadherin; Protocadherin
      cl09101
      Location:37 → 116
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    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
      38318967..38345023 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006526320.5 → XP_006526383.1  protocadherin-1 isoform X1

      UniProtKB/TrEMBL
      F7BJK1
      Conserved Domains (3) summary
      cd11304
      Location:512 → 608
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:59 → 138
      Cadherin_2; Cadherin-like
      pfam08374
      Location:815 → 1029
      Protocadherin

    2. XM_006526324.5 → XP_006526387.1  protocadherin-1 isoform X3

      UniProtKB/TrEMBL
      Q8QZT6
      Conserved Domains (3) summary
      cd11304
      Location:512 → 608
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:59 → 138
      Cadherin_2; Cadherin-like
      pfam08374
      Location:815 → 1029
      Protocadherin

    3. XM_006526322.5 → XP_006526385.1  protocadherin-1 isoform X2

      See identical proteins and their annotated locations for XP_006526385.1

      UniProtKB/TrEMBL
      F7BJK1
      Conserved Domains (3) summary
      cd11304
      Location:490 → 586
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:37 → 116
      Cadherin_2; Cadherin-like
      pfam08374
      Location:793 → 1007
      Protocadherin

    4. XM_006526323.5 → XP_006526386.1  protocadherin-1 isoform X2

      See identical proteins and their annotated locations for XP_006526386.1

      UniProtKB/TrEMBL
      F7BJK1
      Related
      ENSMUSP00000125576.2, ENSMUST00000161701.3
      Conserved Domains (3) summary
      cd11304
      Location:490 → 586
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:37 → 116
      Cadherin_2; Cadherin-like
      pfam08374
      Location:793 → 1007
      Protocadherin

    5. XM_017318005.3 → XP_017173494.1  protocadherin-1 isoform X4

      UniProtKB/TrEMBL
      Q8QZT6
      Conserved Domains (3) summary
      cd11304
      Location:512 → 608
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:59 → 138
      Cadherin_2; Cadherin-like
      pfam08374
      Location:815 → 1029
      Protocadherin
    Nucleotide Protein Strain
    Heading Accession and Version

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