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GPCPD1 glycerophosphocholine phosphodiesterase 1 [ Homo sapiens (human) ]

Gene ID: 56261, updated on 13-Mar-2020

Summary

Official Symbol
GPCPD1provided by HGNC
Official Full Name
glycerophosphocholine phosphodiesterase 1provided by HGNC
Primary source
HGNC:HGNC:26957
See related
Ensembl:ENSG00000125772 MIM:614124
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EDI3; GDE5; GDPD6; PREI4
Expression
Ubiquitous expression in bone marrow (RPKM 31.5), spleen (RPKM 13.3) and 24 other tissues See more
Orthologs

Genomic context

See GPCPD1 in Genome Data Viewer
Location:
20p12.3
Exon count:
24
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (5544439..5611046, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (5525080..5591672, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1729 Neighboring gene ribosomal protein S18 pseudogene 1 Neighboring gene eukaryotic translation initiation factor 4E pseudogene 1 Neighboring gene uncharacterized LOC105372514 Neighboring gene shieldin complex subunit 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Phenotypes

NHGRI GWAS Catalog

Description
Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ11085, KIAA1434, MGC26147

Gene Ontology Provided by GOA

Function Evidence Code Pubs
glycerophosphocholine phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
starch binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
glycerophospholipid catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
skeletal muscle tissue development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
glycerophosphocholine phosphodiesterase GPCPD1
Names
endometrial differential 3
glycerophosphocholine phosphodiesterase GDE1 homolog
glycerophosphodiester phosphodiesterase 5
preimplantation protein 4
putative glycerophosphocholine phosphodiesterase GPCPD1
putative glycerophosphodiester phosphodiesterase 5
NP_062539.1
XP_005260815.1
XP_005260818.1
XP_006723659.1
XP_024307716.1
XP_024307717.1

NCBI Reference Sequences (RefSeq)

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_019593.5NP_062539.1  glycerophosphocholine phosphodiesterase GPCPD1

    See identical proteins and their annotated locations for NP_062539.1

    Status: VALIDATED

    Source sequence(s)
    AB037855, AL049446, BC027588, BG674365, BI561344, BP421674, T79323
    Consensus CDS
    CCDS13090.1
    UniProtKB/Swiss-Prot
    Q9NPB8
    Related
    ENSP00000368305.4, ENST00000379019.7
    Conserved Domains (2) summary
    cd05814
    Location:4127
    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:319611
    GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    5544439..5611046 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024451949.1XP_024307717.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X2

    Conserved Domains (2) summary
    cd08607
    Location:270562
    GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins
    cl15347
    Location:178
    CBM20; The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is ...
  2. XM_024451948.1XP_024307716.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X2

    Conserved Domains (2) summary
    cd08607
    Location:270562
    GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins
    cl15347
    Location:178
    CBM20; The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is ...
  3. XM_005260761.2XP_005260818.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X3

    Conserved Domains (3) summary
    cd08607
    Location:138430
    GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins
    pfam03009
    Location:142430
    GDPD; Glycerophosphoryl diester phosphodiesterase family
    cl21461
    Location:426451
    Globin_like; Globin-like proteins
  4. XM_005260758.5XP_005260815.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

    See identical proteins and their annotated locations for XP_005260815.1

    UniProtKB/Swiss-Prot
    Q9NPB8
    Conserved Domains (2) summary
    cd05814
    Location:4127
    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:319611
    GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins
  5. XM_006723596.4XP_006723659.1  glycerophosphocholine phosphodiesterase GPCPD1 isoform X1

    See identical proteins and their annotated locations for XP_006723659.1

    UniProtKB/Swiss-Prot
    Q9NPB8
    Conserved Domains (2) summary
    cd05814
    Location:4127
    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:319611
    GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

RNA

  1. XR_001754345.2 RNA Sequence

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