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

Gene ID: 116731, updated on 11-Apr-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, Apr 2022]
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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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. 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 (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

Gene LinkOut

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