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    Gpcpd1 glycerophosphocholine phosphodiesterase 1 [ Mus musculus (house mouse) ]

    Gene ID: 74182, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Gpcpd1provided by MGI
    Official Full Name
    glycerophosphocholine phosphodiesterase 1provided by MGI
    Primary source
    MGI:MGI:104898
    See related
    Ensembl:ENSMUSG00000027346 AllianceGenome:MGI:104898
    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
    Gde5; Prei4; mKIAA1434; 2310004G06Rik; 2310032D16Rik
    Summary
    Enables glycerophosphocholine phosphodiesterase activity. Acts upstream of or within skeletal muscle tissue development. Located in cytoplasm. Is expressed in early conceptus; primary oocyte; secondary oocyte; and testis. Orthologous to human GPCPD1 (glycerophosphocholine phosphodiesterase 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in cortex adult (RPKM 15.8), frontal lobe adult (RPKM 14.8) and 24 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Gpcpd1 in Genome Data Viewer
    Location:
    2 F2; 2 64.57 cM
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (132371002..132420173, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (132529082..132578248, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_05743 Neighboring gene RIKEN cDNA 1700026D11 gene Neighboring gene predicted gene 14095 Neighboring gene STARR-positive B cell enhancer ABC_E10150 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:132338174-132338621 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:132339740-132339927 Neighboring gene STARR-positive B cell enhancer ABC_E4500 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:132433520-132433703 Neighboring gene expressed sequence AU019990 Neighboring gene STARR-seq mESC enhancer starr_05747 Neighboring gene ribosomal protein L23A, pseudogene 4

    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
    • 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. GDE5 inhibition accumulates intracellular glycerophosphocholine and suppresses adipogenesis at a mitotic clonal expansion stage. Okazaki Y, et al. Am J Physiol Cell Physiol, 2019 Feb 1. PMID 30462540, Free PMC Article
    2. Transient polyadenylation of a maternal mRNA following fertilization of mouse eggs. Temeles GL, et al. J Reprod Fertil, 1997 Mar. PMID 9155731
    3. Gpcpd1-GPC metabolic pathway is dysfunctional in aging and its deficiency severely perturbs glucose metabolism. Cikes D, et al. Nat Aging, 2024 Jan. PMID 38238601
    4. 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
    5. Expression patterns of novel genes during mouse preimplantation embryogenesis. Temeles GL, et al. Mol Reprod Dev, 1994 Feb. PMID 7545925

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Gpcpd1-GPC metabolic pathway is dysfunctional in aging and its deficiency severely perturbs glucose metabolism.
      Title: Gpcpd1-GPC metabolic pathway is dysfunctional in aging and its deficiency severely perturbs glucose metabolism.
    2. Decreased GDE5 expression suppresses adipocyte differentiation by intracellular glycerophosphocholine accumulation.
      Title: GDE5 inhibition accumulates intracellular glycerophosphocholine and suppresses adipogenesis at a mitotic clonal expansion stage.
    3. GDE5 negatively regulates skeletal muscle development.
      Title: A novel glycerophosphodiester phosphodiesterase, GDE5, controls skeletal muscle development via a non-enzymatic mechanism.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (2)  1 citation

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables glycerophosphocholine phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables glycerophosphocholine phosphodiesterase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables glycerophosphocholine phosphodiesterase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables glycerophosphodiester phosphodiesterase activity TAS
    Traceable Author Statement
    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 lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within skeletal muscle tissue development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    glycerophosphocholine phosphodiesterase GPCPD1
    Names
    glycerophosphocholine phosphodiesterase GDE1 homolog
    glycerophosphodiester phosphodiesterase 5
    preimplantation protein 4
    putative glycerophosphocholine phosphodiesterase GPCPD1
    putative glycerophosphodiester phosphodiesterase 5
    NP_001036137.1
    NP_001277979.1
    NP_001277980.1
    NP_001277981.1
    NP_001342577.1
    NP_001342578.1
    NP_001342579.1
    NP_001342580.1
    NP_001342581.1
    NP_081372.1
    NP_083078.3
    XP_006500339.1
    XP_006500340.1
    XP_006500342.1
    XP_006500343.1
    XP_017174782.1
    XP_030107990.1
    XP_030107991.1
    XP_030107992.1

    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_001042672.1 → NP_001036137.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 3' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 8. The resulting isoform (3) has a shorter and distinct C-terminus and lacks an alternate internal segment compared to isoform 4.
      Source sequence(s)
      AK031658, AK141374, AL807386
      Conserved Domains (3) summary
      cd05814
      Location:4 → 127
      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:322 → 613
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins
      pfam03009
      Location:326 → 613
      GDPD; Glycerophosphoryl diester phosphodiesterase family

    2. NM_001291050.1 → NP_001277979.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform 1

      See identical proteins and their annotated locations for NP_001277979.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and lacks an in-frame exon compared to variant 8. The resulting isoform (1) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 4. Variants 1, 5, 6, 7, and 12 all encode the same isoform (1).
      Source sequence(s)
      AK031658, AW125284
      Consensus CDS
      CCDS71151.1
      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 430
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    3. NM_001291051.1 → NP_001277980.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform 1

      See identical proteins and their annotated locations for NP_001277980.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and lacks an in-frame exon compared to variant 8. The resulting isoform (1) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 4. Variants 1, 5, 6, 7, and 12 all encode the same isoform (1).
      Source sequence(s)
      AK031658, AK163419, AW125284
      Consensus CDS
      CCDS71151.1
      UniProtKB/TrEMBL
      B0R058
      Related
      ENSMUSP00000105763.2, ENSMUST00000110136.8
      Conserved Domains (1) summary
      cd08607
      Location:138 → 430
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    4. NM_001291052.1 → NP_001277981.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform 1

      See identical proteins and their annotated locations for NP_001277981.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and coding sequence and lacks an in-frame exon compared to variant 8. The resulting isoform (1) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 4. Variants 1, 5, 6, 7, and 12 all encode the same isoform (1).
      Source sequence(s)
      AK031658, AL807386, AW125284
      Consensus CDS
      CCDS71151.1
      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 430
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    5. NM_001355648.1 → NP_001342577.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (12) differs in the 5' UTR and coding sequence and lacks an in-frame exon compared to variant 8. The resulting isoform (1) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 4. Variants 1, 5, 6, 7, and 12 all encode the same isoform (1).
      Source sequence(s)
      AL807386
      Consensus CDS
      CCDS71151.1
      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 430
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    6. NM_001355649.1 → NP_001342578.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) represents the longest transcript and encodes the longest isoform (4). Variants 8 and 9 both encode isoform 4.
      Source sequence(s)
      AL807386
      Conserved Domains (2) summary
      cd05814
      Location:4 → 127
      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:322 → 621
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    7. NM_001355650.1 → NP_001342579.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) differs in the 5' UTR compared to variant 8. Variants 8 and 9 both encode the same isoform (4).
      Source sequence(s)
      AL807386
      Conserved Domains (2) summary
      cd05814
      Location:4 → 127
      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:322 → 621
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    8. NM_001355651.1 → NP_001342580.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10) lacks an alternate in-frame exon compared to variant 8. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 4. Variants 2 and 10 both encode the same isoform (2).
      Source sequence(s)
      AL807386
      Consensus CDS
      CCDS38246.1
      UniProtKB/Swiss-Prot
      A2AMD5, Q3TLV6, Q80TD5, Q8BKJ7, Q8BKW7, Q8C0L9, Q8CFW2, Q9D759
      Related
      ENSMUSP00000105769.2, ENSMUST00000110142.8
      Conserved Domains (2) summary
      cd05814
      Location:4 → 127
      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:322 → 614
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    9. NM_001355652.1 → NP_001342581.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (11) differs in the 5' UTR and coding sequence compared to variant 8. The resulting isoform (5) is shorter at the N-terminus compared to isoform 4.
      Source sequence(s)
      AL807386
      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 437
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    10. NM_027096.2 → NP_081372.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform 1

      See identical proteins and their annotated locations for NP_081372.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence and lacks an in-frame exon compared to variant 8. The resulting isoform (1) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 4. Variants 1, 5, 6, 7, and 12 all encode the same isoform (1).
      Source sequence(s)
      AK031658, AK050318, AW125284, BC033408
      Consensus CDS
      CCDS71151.1
      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 430
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    11. NM_028802.3 → NP_083078.3  glycerophosphocholine phosphodiesterase GPCPD1 isoform 2

      See identical proteins and their annotated locations for NP_083078.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 8. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 4. Variants 2 and 10 both encode the same isoform (2).
      Source sequence(s)
      AK030645, AK031658, AK050318, AW125284
      Consensus CDS
      CCDS38246.1
      UniProtKB/Swiss-Prot
      A2AMD5, Q3TLV6, Q80TD5, Q8BKJ7, Q8BKW7, Q8C0L9, Q8CFW2, Q9D759
      Related
      ENSMUSP00000062221.6, ENSMUST00000060955.12
      Conserved Domains (2) summary
      cd05814
      Location:4 → 127
      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:322 → 614
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    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_000068.8 Reference GRCm39 C57BL/6J

      Range
      132371002..132420173 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006500276.5 → XP_006500339.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

      See identical proteins and their annotated locations for XP_006500339.1

      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 437
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    2. XM_030252132.1 → XP_030107992.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X2

      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 430
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    3. XM_030252130.1 → XP_030107990.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 437
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    4. XM_006500280.4 → XP_006500343.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

      See identical proteins and their annotated locations for XP_006500343.1

      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 437
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    5. XM_006500279.4 → XP_006500342.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

      See identical proteins and their annotated locations for XP_006500342.1

      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 437
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    6. XM_030252131.2 → XP_030107991.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 437
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    7. XM_006500277.5 → XP_006500340.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

      See identical proteins and their annotated locations for XP_006500340.1

      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 437
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    8. XM_017319293.3 → XP_017174782.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

      UniProtKB/TrEMBL
      B0R058
      Conserved Domains (1) summary
      cd08607
      Location:138 → 437
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    RNA

    1. XR_003953728.2 RNA Sequence

    2. XR_003953727.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001042671.1: Suppressed sequence

      Description
      NM_001042671.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8C0L9.1 GenPept UniProtKB/Swiss-Prot:Q8C0L9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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