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Pcdh1 protocadherin 1 [ Mus musculus (house mouse) ]

Gene ID: 75599, updated on 6-Jun-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
    UniProtKB/TrEMBL
    F7BJK1

  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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