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

Gene ID: 74182, updated on 19-Mar-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, Apr 2022]
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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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. 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
  4. Expression patterns of novel genes during mouse preimplantation embryogenesis. Temeles GL, et al. Mol Reprod Dev, 1994 Feb. PMID 7545925
  5. Candidate Agtr2 influenced genes and pathways identified by expression profiling in the developing brain of Agtr2(-/y) mice. Pawlowski TL, et al. Genomics, 2009 Sep. PMID 19501643, Free PMC Article

See all (23) 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)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (1) 

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
  
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 hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphoric diester hydrolase activity IEA
Inferred from Electronic Annotation
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

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