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    Pcdhga1 protocadherin gamma subfamily A, 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 553129, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Pcdhga1provided by RGD
    Official Full Name
    protocadherin gamma subfamily A, 1provided by RGD
    Primary source
    RGD:1590761
    See related
    AllianceGenome:RGD:1590761
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable calcium ion binding activity. Predicted to be involved in homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to be located in membrane. Orthologous to human PCDHGA1 (protocadherin gamma subfamily A, 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 156.2), Lung (RPKM 92.7) and 9 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Pcdhga1 in Genome Data Viewer
    Location:
    18p11
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (29738639..29919095)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (29487404..29667865)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (30808404..30971113)

    Chromosome 18 - NC_086036.1Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 2 Neighboring gene TATA-box binding protein associated factor 7 Neighboring gene zinc finger protein 605 like 1 Neighboring gene protocadherin gamma subfamily A, 2 Neighboring gene protocadherin gamma subfamily A, 3 Neighboring gene protocadherin gamma subfamily B, 1 Neighboring gene uncharacterized LOC103694196 Neighboring gene protocadherin gamma subfamily A, 4 Neighboring gene small nucleolar RNA SNORA40 Neighboring gene protocadherin gamma subfamily A, 5 Neighboring gene protocadherin gamma subfamily A, 7 Neighboring gene protocadherin gamma subfamily A, 8 Neighboring gene protocadherin gamma subfamily A, 9 Neighboring gene protocadherin gamma subfamily A, 10 Neighboring gene protocadherin gamma subfamily B, 7 Neighboring gene protocadherin gamma subfamily A, 11 Neighboring gene protocadherin gamma subfamily B, 8 Neighboring gene protocadherin gamma subfamily A, 12 Neighboring gene protocadherin gamma subfamily C, 3 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene diaphanous-related formin 1 Neighboring gene uncharacterized LOC120098325 Neighboring gene histone deacetylase 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Sequence analysis and expression mapping of the rat clustered protocadherin gene repertoires. Zou C, et al. Neuroscience, 2007 Jan 19. PMID 17110050
    2. Interaction with protocadherin-gamma regulates the cell surface expression of protocadherin-alpha. Murata Y, et al. J Biol Chem, 2004 Nov 19. PMID 15347688
    3. Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. Zhang T, et al. Genome Res, 2004 Jan. PMID 14672974, Free PMC Article
    4. Comparative genomics and diversifying selection of the clustered vertebrate protocadherin genes. Wu Q. Genetics, 2005 Apr. PMID 15744052, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin gamma-A1
    Names
    protocadherin gamma a1

    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_001037140.1 → NP_001032217.1  protocadherin gamma-A1 precursor

      See identical proteins and their annotated locations for NP_001032217.1

      Status: PROVISIONAL

      Source sequence(s)
      AY574008
      UniProtKB/TrEMBL
      A6J383, I6LBW6
      Conserved Domains (4) summary
      cd11304
      Location:246 → 343
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:31 → 112
      Cadherin_2; Cadherin-like
      pfam15974
      Location:808 → 904
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
      pfam16492
      Location:688 → 772
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086036.1 Reference GRCr8

      Range
      29738639..29919095
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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