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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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