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    Gdpd5 glycerophosphodiester phosphodiesterase domain containing 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 499211, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Gdpd5provided by RGD
    Official Full Name
    glycerophosphodiester phosphodiesterase domain containing 5provided by RGD
    Primary source
    RGD:1559673
    See related
    EnsemblRapid:ENSRNOG00000036859 AllianceGenome:RGD:1559673
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1559673
    Summary
    Predicted to enable glycerophosphocholine phosphodiesterase activity and glycerophosphodiester phosphodiesterase activity. Predicted to be involved in positive regulation of cell cycle and positive regulation of neuron differentiation. Predicted to act upstream of or within negative regulation of Notch signaling pathway; neuron differentiation; and regulation of timing of cell differentiation. Predicted to be located in several cellular components, including axon; neuronal cell body; and perinuclear endoplasmic reticulum. Predicted to be active in plasma membrane. Orthologous to human GDPD5 (glycerophosphodiester phosphodiesterase domain containing 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 78.9), Lung (RPKM 37.3) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Gdpd5 in Genome Data Viewer
    Location:
    1q32
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (163091844..163173559)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (153679718..153761452)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (164337176..164418056)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene serpin family H member 1 Neighboring gene uncharacterized LOC134483761 Neighboring gene uncharacterized LOC134483762 Neighboring gene kelch-like family member 35 Neighboring gene small nucleolar RNA, C/D box 15B Neighboring gene small nucleolar RNA, C/D box 15A Neighboring gene ribosomal protein S3

    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. GDPD5 is a glycerophosphocholine phosphodiesterase that osmotically regulates the osmoprotective organic osmolyte GPC. Gallazzini M, et al. Proc Natl Acad Sci U S A, 2008 Aug 5. PMID 18667693, Free PMC Article
    2. Involvement of membrane protein GDE2 in retinoic acid-induced neurite formation in Neuro2A cells. Yanaka N, et al. FEBS Lett, 2007 Feb 20. PMID 17275818
    3. GDE2 promotes neurogenesis by glycosylphosphatidylinositol-anchor cleavage of RECK. Park S, et al. Science, 2013 Jan 18. PMID 23329048, Free PMC Article
    4. Gde2 regulates cortical neuronal identity by controlling the timing of cortical progenitor differentiation. Rodriguez M, et al. Development, 2012 Oct. PMID 22951639
    5. GDE2 regulates subtype-specific motor neuron generation through inhibition of Notch signaling. Sabharwal P, et al. Neuron, 2011 Sep 22. PMID 21943603, Free PMC Article

    See all (7) citations in PubMed

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables glycerophosphodiester phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of Notch signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cerebral cortex neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of Notch signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of Notch signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuron projection development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cell cycle ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of timing of cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within spinal cord motor neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in neuronal cell body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    glycerophosphodiester phosphodiesterase domain-containing protein 5
    NP_001102622.2
    XP_006229876.1
    XP_006229879.1
    XP_017445679.1
    XP_017445680.1
    XP_063127325.1

    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_001109152.2 → NP_001102622.2  glycerophosphodiester phosphodiesterase domain-containing protein 5

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A6I6H1, G3V9L7
      Related
      ENSRNOP00000052189.4, ENSRNOT00000055321.6
      Conserved Domains (1) summary
      cl14615
      Location:227 → 576
      PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

    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_086019.1 Reference GRCr8

      Range
      163091844..163173559
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006229814.5 → XP_006229876.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_006229876.1

      UniProtKB/TrEMBL
      A0A8I6GK08
      Conserved Domains (1) summary
      cl14615
      Location:227 → 581
      PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

    2. XM_006229817.5 → XP_006229879.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      See identical proteins and their annotated locations for XP_006229879.1

      UniProtKB/TrEMBL
      A6I6H1, G3V9L7
      Conserved Domains (1) summary
      cl14615
      Location:227 → 576
      PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

    3. XM_017590190.3 → XP_017445679.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

      UniProtKB/TrEMBL
      A0A8I6GK08
      Related
      ENSRNOP00000092047.1, ENSRNOT00000111969.2
      Conserved Domains (1) summary
      cl14615
      Location:227 → 581
      PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

    4. XM_017590191.3 → XP_017445680.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

      UniProtKB/TrEMBL
      A0A8I6GK08
      Conserved Domains (1) summary
      cl14615
      Location:227 → 581
      PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

    5. XM_063271255.1 → XP_063127325.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/TrEMBL
      A6I6H1, G3V9L7
    Nucleotide Protein Strain
    Heading Accession and Version

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