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    Pcdh1 protocadherin 1 [ Mus musculus (house mouse) ]

    Gene ID: 75599, updated on 3-Dec-2024

    Summary

    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 active in 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, Nov 2024]
    Expression
    Broad expression in lung adult (RPKM 22.2), small intestine adult (RPKM 16.0) and 22 other tissues See more
    Orthologs
    NEW
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    Genomic context

    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

    Expression

    • 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

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    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 

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001403795.1NP_001390724.1  protocadherin-1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC133646
      UniProtKB/TrEMBL
      F7BJK1
    2. NM_029357.3NP_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:490586
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:7931004
      Protocadherin; Protocadherin
      cl09101
      Location:37116
      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_006526320.5XP_006526383.1  protocadherin-1 isoform X1

      UniProtKB/TrEMBL
      F7BJK1
      Conserved Domains (3) summary
      cd11304
      Location:512608
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:59138
      Cadherin_2; Cadherin-like
      pfam08374
      Location:8151029
      Protocadherin
    2. XM_006526324.5XP_006526387.1  protocadherin-1 isoform X3

      UniProtKB/TrEMBL
      Q8QZT6
      Conserved Domains (3) summary
      cd11304
      Location:512608
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:59138
      Cadherin_2; Cadherin-like
      pfam08374
      Location:8151029
      Protocadherin
    3. XM_006526322.5XP_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:490586
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:37116
      Cadherin_2; Cadherin-like
      pfam08374
      Location:7931007
      Protocadherin
    4. XM_006526323.5XP_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:490586
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:37116
      Cadherin_2; Cadherin-like
      pfam08374
      Location:7931007
      Protocadherin
    5. XM_017318005.3XP_017173494.1  protocadherin-1 isoform X4

      UniProtKB/TrEMBL
      Q8QZT6
      Conserved Domains (3) summary
      cd11304
      Location:512608
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:59138
      Cadherin_2; Cadherin-like
      pfam08374
      Location:8151029
      Protocadherin