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

Gene ID: 499211, updated on 13-Apr-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
Ensembl: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. Predicted to be involved in positive regulation of cell cycle. Predicted to act upstream of or within several processes, including 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. Orthologous to human GDPD5 (glycerophosphodiester phosphodiesterase domain containing 5). [provided by Alliance of Genome Resources, Apr 2022]
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, ENSRNOT00000055321.5
    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
    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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