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    Gpcpd1 glycerophosphocholine phosphodiesterase 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362219, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Gpcpd1provided by RGD
    Official Full Name
    glycerophosphocholine phosphodiesterase 1provided by RGD
    Primary source
    RGD:735140
    See related
    Ensembl:ENSRNOG00000053201 AllianceGenome:RGD:735140
    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
    Also known as
    Gde5; Prei4; RGD735140
    Summary
    Predicted to enable glycerophosphocholine phosphodiesterase activity. Predicted to be involved in glycerophospholipid catabolic process. Predicted to act upstream of or within skeletal muscle tissue development. Predicted to be located in cytoplasm. Orthologous to human GPCPD1 (glycerophosphocholine phosphodiesterase 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Muscle (RPKM 395.7), Spleen (RPKM 257.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    3q36
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (140240574..140285469, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (119787681..119832550, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (125169131..125213598, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene U2 spliceosomal RNA Neighboring gene prokineticin receptor 2 Neighboring gene uncharacterized LOC120101670 Neighboring gene uncharacterized LOC102552951 Neighboring gene U6 spliceosomal RNA Neighboring gene shieldin complex subunit 1

    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. Blood-brain barrier genomics. Li JY, et al. J Cereb Blood Flow Metab, 2001 Jan. PMID 11149669
    2. A novel glycerophosphodiester phosphodiesterase, GDE5, controls skeletal muscle development via a non-enzymatic mechanism. Okazaki Y, et al. J Biol Chem, 2010 Sep 3. PMID 20576599, Free PMC Article
    3. 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 glycerophosphocholine phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables glycerophosphocholine phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables glycerophosphocholine phosphodiesterase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables starch binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in glycerophospholipid catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in skeletal muscle tissue development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within skeletal muscle tissue development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    glycerophosphocholine phosphodiesterase GPCPD1
    Names
    glycerophosphocholine phosphodiesterase GDE1 homolog
    glycerophosphodiester phosphodiesterase 5
    hypothetical protein LK44
    preimplantation protein 4
    putative glycerophosphocholine phosphodiesterase GPCPD1
    putative glycerophosphodiester phosphodiesterase 5
    NP_942074.1
    XP_038961393.1
    XP_038961394.1
    XP_063140236.1
    XP_063140237.1

    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_198779.2 → NP_942074.1  glycerophosphocholine phosphodiesterase GPCPD1

      See identical proteins and their annotated locations for NP_942074.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/Swiss-Prot
      Q80VJ4
      UniProtKB/TrEMBL
      A0A8I6GDY1, A6HQG6
      Related
      ENSRNOP00000086333.1, ENSRNOT00000109724.1
      Conserved Domains (4) summary
      cd05814
      Location:4 → 125
      CBM20_Prei4; Prei4, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Preimplantation protein 4 (Prei4) is a protein of unknown function that is expressed during mouse preimplantation embryogenesis. In addition to the N-terminal CBM20 domain, Prei4 ...
      cd08607
      Location:319 → 611
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins
      pfam03009
      Location:323 → 611
      GDPD; Glycerophosphoryl diester phosphodiesterase family
      cl21461
      Location:607 → 632
      Globin_like; Globin-like proteins

    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_086021.1 Reference GRCr8

      Range
      140240574..140285469 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063284166.1 → XP_063140236.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X2

      UniProtKB/Swiss-Prot
      Q80VJ4
      UniProtKB/TrEMBL
      A6HQG6

    2. XM_039105465.2 → XP_038961393.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K9B2, A0A8I6GDY1
      Related
      ENSRNOP00000074931.2
      Conserved Domains (2) summary
      cd05814
      Location:4 → 125
      CBM20_Prei4; Prei4, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Preimplantation protein 4 (Prei4) is a protein of unknown function that is expressed during mouse preimplantation embryogenesis. In addition to the N-terminal CBM20 domain, Prei4 ...
      cd08607
      Location:319 → 618
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    3. XM_039105466.2 → XP_038961394.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K9B2, A0A8I6GDY1
      Conserved Domains (2) summary
      cd05814
      Location:4 → 125
      CBM20_Prei4; Prei4, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Preimplantation protein 4 (Prei4) is a protein of unknown function that is expressed during mouse preimplantation embryogenesis. In addition to the N-terminal CBM20 domain, Prei4 ...
      cd08607
      Location:319 → 618
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    4. XM_063284167.1 → XP_063140237.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q80VJ4.1 GenPept UniProtKB/Swiss-Prot:Q80VJ4

    Gene LinkOut

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