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Gdpd5 glycerophosphodiester phosphodiesterase domain containing 5 [ Mus musculus (house mouse) ]

Gene ID: 233552, updated on 12-Nov-2024

Summary

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Official Symbol
Gdpd5provided by MGI
Official Full Name
glycerophosphodiester phosphodiesterase domain containing 5provided by MGI
Primary source
MGI:MGI:2686926
See related
Ensembl:ENSMUSG00000035314 AllianceGenome:MGI:2686926
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Gde2
Summary
Enables glycerophosphocholine phosphodiesterase activity. Involved in negative regulation of Notch signaling pathway; positive regulation of cell cycle; and positive regulation of neuron differentiation. Acts upstream of or within neuron differentiation and regulation of timing of cell differentiation. Located in several cellular components, including axon; neuronal cell body; and perinuclear endoplasmic reticulum. Is expressed in several structures, including nervous system and neural retina. Orthologous to human GDPD5 (glycerophosphodiester phosphodiesterase domain containing 5). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in ovary adult (RPKM 14.1), whole brain E14.5 (RPKM 14.1) and 24 other tissues See more
Orthologs
human all
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Genomic context

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See Gdpd5 in Genome Data Viewer
Location:
7 E1; 7 54.07 cM
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (99027976..99111082)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (99381463..99461875)

Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene microtubule-associated protein 6 Neighboring gene predicted gene, 40449 Neighboring gene STARR-seq mESC enhancer starr_19650 Neighboring gene serine (or cysteine) peptidase inhibitor, clade H, member 1 Neighboring gene STARR-positive B cell enhancer ABC_E4952 Neighboring gene STARR-positive B cell enhancer ABC_E1346 Neighboring gene STARR-seq mESC enhancer starr_19652 Neighboring gene STARR-seq mESC enhancer starr_19653 Neighboring gene STARR-seq mESC enhancer starr_19654 Neighboring gene STARR-seq mESC enhancer starr_19655 Neighboring gene kelch-like 35 Neighboring gene small nucleolar RNA, C/D box 15B 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. High NaCl- and urea-induced posttranslational modifications that increase glycerophosphocholine by inhibiting GDPD5 phosphodiesterase. Topanurak S, et al. Proc Natl Acad Sci U S A, 2013 Apr 30. PMID 23589856, Free PMC Article
  2. GDE2 is essential for neuronal survival in the postnatal mammalian spinal cord. Cave C, et al. Mol Neurodegener, 2017 Jan 19. PMID 28103900, Free PMC Article
  3. GDE2 expression in oligodendroglia regulates the pace of oligodendrocyte maturation. Choi BR, et al. Dev Dyn, 2021 Apr. PMID 33095500, Free PMC Article
  4. Loss of GDE2 leads to complex behavioral changes including memory impairment. Daudelin D, et al. Behav Brain Funct, 2024 Apr 4. PMID 38575965, Free PMC Article
  5. Isolation and characterization of two serpentine membrane proteins containing glycerophosphodiester phosphodiesterase, GDE2 and GDE6. Nogusa Y, et al. Gene, 2004 Aug 4. PMID 15276213

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Loss of GDE2 leads to complex behavioral changes including memory impairment.
    Title: Loss of GDE2 leads to complex behavioral changes including memory impairment.
  2. GDE2 expression in oligodendroglia regulates the pace of oligodendrocyte maturation.
    Title: GDE2 expression in oligodendroglia regulates the pace of oligodendrocyte maturation.
  3. GDE2-Dependent Activation of Canonical Wnt Signaling in Neurons Regulates Oligodendrocyte Maturation.
    Title: GDE2-Dependent Activation of Canonical Wnt Signaling in Neurons Regulates Oligodendrocyte Maturation.
  4. GDE2 is essential for neuronal survival in the postnatal mammalian spinal cord
    Title: GDE2 is essential for neuronal survival in the postnatal mammalian spinal cord.
  5. posttranslational modifications increase glycerophosphocholine by inhibiting GDPD5 phosphodiesterase.
    Title: High NaCl- and urea-induced posttranslational modifications that increase glycerophosphocholine by inhibiting GDPD5 phosphodiesterase.
  6. a key role for Gde2 in controlling cortical neuronal fates by regulating the timing of neurogenesis, and loss of Gde2 uncovers additional mechanisms that trigger remaining neuronal progenitors to differentiate at the end of the neurogenic period.
    Title: Gde2 regulates cortical neuronal identity by controlling the timing of cortical progenitor differentiation.
  7. Data suggest that neuronal GDE2 controls motor neuron subtype diversity through a non-cell-autonomous feedback mechanism that directly regulates progenitor cell differentiation.
    Title: GDE2 regulates subtype-specific motor neuron generation through inhibition of Notch signaling.
  8. Study identified the antioxidant enzyme Prdx1 as an interactor of GDE2 and uncover a developmental role for Prdx1 in regulating neuronal differentiation in the spinal cord.
    Title: The antioxidant enzyme Prdx1 controls neuronal differentiation by thiol-redox-dependent activation of GDE2.
  9. GDPD5 is a glycerophosphocholine phosphodiesterase that osmotically regulates the osmoprotective organic osmolyte glycerophosphocholine.
    Title: GDPD5 is a glycerophosphocholine phosphodiesterase that osmotically regulates the osmoprotective organic osmolyte GPC.
  10. These results demonstrate that GDE2 expression during neuronal differentiation plays an important role for growing neurites.
    Title: Involvement of membrane protein GDE2 in retinoic acid-induced neurite formation in Neuro2A cells.
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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Gene trapped (1) 
  • Targeted (4)  1 citation

General gene information

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Markers

Homology

Clone Names

  • MGC31332, MGC37148

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables glycerophosphocholine phosphodiesterase activity EXP
Inferred from Experiment
more info
 PubMed 
enables glycerophosphocholine phosphodiesterase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables glycerophosphodiester phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycerophosphodiester phosphodiesterase activity ISO
Inferred from Sequence Orthology
more info
  
enables phosphatidylinositol phospholipase C activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of Notch signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within cerebral cortex neuron differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lipid metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of Notch signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within negative regulation of Notch signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of Notch signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within negative regulation of Notch signaling pathway ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of neuron differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within neuron projection development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of neuron differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of timing of cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within spinal cord motor neuron differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in axon IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in growth cone IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in neuronal cell body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
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
Names
glycerophosphocholine phosphodiesterase GDPD5
glycerophosphodiester phosphodiesterase 2
phosphoinositide phospholipase C GDPD5
NP_001349095.1
NP_001349096.1
NP_001349097.1
NP_958740.2
XP_006507696.1
XP_006507697.1
XP_006507698.1
XP_006507700.1
XP_006507702.1
XP_011240040.1
XP_030098348.1
XP_030098349.1
XP_036008885.1
XP_036008886.1
XP_036008887.1

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_001362166.1 → NP_001349095.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC115858, AC158748
    Consensus CDS
    CCDS21481.1
    UniProtKB/Swiss-Prot
    Q640M6, Q8R0T5, Q8R3N5
    Conserved Domains (1) summary
    cl14615
    Location:227 → 576
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  2. NM_001362167.1 → NP_001349096.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC115858, AC158748
    Consensus CDS
    CCDS90276.1
    UniProtKB/TrEMBL
    A0A1L1STK0
    Related
    ENSMUSP00000150361.2, ENSMUST00000213887.2
    Conserved Domains (1) summary
    cl14615
    Location:227 → 581
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  3. NM_001362168.1 → NP_001349097.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC115858, AC158748
    Conserved Domains (1) summary
    cl14615
    Location:170 → 524
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  4. NM_201352.3 → NP_958740.2  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 1

    See identical proteins and their annotated locations for NP_958740.2

    Status: VALIDATED

    Source sequence(s)
    AC115858, AK141189, BC082585, CO039911
    Consensus CDS
    CCDS21481.1
    UniProtKB/Swiss-Prot
    Q640M6, Q8R0T5, Q8R3N5
    Related
    ENSMUSP00000036175.9, ENSMUST00000037528.10
    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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000073.7 Reference GRCm39 C57BL/6J

    Range
    99027976..99111082
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011241738.3 → XP_011240040.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    See identical proteins and their annotated locations for XP_011240040.1

    UniProtKB/TrEMBL
    A0A1L1STK0
    Conserved Domains (1) summary
    cl14615
    Location:227 → 581
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  2. XM_036152992.1 → XP_036008885.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

    UniProtKB/Swiss-Prot
    Q640M6, Q8R0T5, Q8R3N5
    Conserved Domains (1) summary
    cl14615
    Location:227 → 576
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  3. XM_006507634.3 → XP_006507697.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    See identical proteins and their annotated locations for XP_006507697.1

    UniProtKB/TrEMBL
    A0A1L1STK0
    Conserved Domains (1) summary
    cl14615
    Location:227 → 581
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  4. XM_006507633.3 → XP_006507696.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    See identical proteins and their annotated locations for XP_006507696.1

    UniProtKB/TrEMBL
    A0A1L1STK0
    Conserved Domains (1) summary
    cl14615
    Location:227 → 581
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  5. XM_006507635.3 → XP_006507698.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X3

    Conserved Domains (1) summary
    cl14615
    Location:207 → 561
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  6. XM_036152993.1 → XP_036008886.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X4

    Conserved Domains (1) summary
    cl14615
    Location:170 → 519
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  7. XM_030242488.2 → XP_030098348.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X5

    Conserved Domains (1) summary
    cl14615
    Location:150 → 504
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  8. XM_006507637.3 → XP_006507700.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X6

    Conserved Domains (1) summary
    cl14615
    Location:148 → 502
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  9. XM_036152994.1 → XP_036008887.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X7

    Conserved Domains (1) summary
    cl14615
    Location:148 → 497
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  10. XM_030242489.2 → XP_030098349.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X8

    Conserved Domains (1) summary
    cl14615
    Location:128 → 482
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  11. XM_006507639.3 → XP_006507702.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X9

    Conserved Domains (1) summary
    cl14615
    Location:227 → 316
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q640M6.1 GenPept UniProtKB/Swiss-Prot:Q640M6

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