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GDPD1 glycerophosphodiester phosphodiesterase domain containing 1 [ Homo sapiens (human) ]

Gene ID: 284161, updated on 1-Jun-2020

Summary

Official Symbol
GDPD1provided by HGNC
Official Full Name
glycerophosphodiester phosphodiesterase domain containing 1provided by HGNC
Primary source
HGNC:HGNC:20883
See related
Ensembl:ENSG00000153982 MIM:616317
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GDE4
Summary
This gene encodes a member of the glycerophosphodiester phosphodiesterase family of enzymes that catalyze the hydrolysis of deacylated glycerophospholipids to glycerol phosphate and alcohol. The encoded protein is localized to the cytoplasm and concentrates near the perinuclear region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
Expression
Broad expression in brain (RPKM 4.9), testis (RPKM 3.0) and 22 other tissues See more
Orthologs

Genomic context

See GDPD1 in Genome Data Viewer
Location:
17q22
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (59220470..59275970)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (57297828..57353331)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene proline rich 11 Neighboring gene speedy/RINGO cell cycle regulator family member E22, pseudogene Neighboring gene SMG8 nonsense mediated mRNA decay factor Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 17 Neighboring gene yippee like 2 Neighboring gene microRNA 4729

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ27503, FLJ37451, MGC35046

Gene Ontology Provided by GOA

Function Evidence Code Pubs
alkylglycerophosphoethanolamine phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
 
lysophospholipase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lysophospholipase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
phosphoric diester hydrolase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
N-acylethanolamine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
N-acylethanolamine metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
glycerophospholipid catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phospholipid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
lysophospholipase D GDPD1
Names
glycerophosphodiester phosphodiesterase 4
glycerophosphodiester phosphodiesterase domain-containing protein 1
NP_001159465.1
NP_001159466.1
NP_872375.2
XP_016880010.1

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_001165993.2NP_001159465.1  lysophospholipase D GDPD1 isoform 3

    See identical proteins and their annotated locations for NP_001159465.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR and 3' coding region, compared to variant 1. The resulting isoform (3) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC099850, AI478202, AY271346
    Consensus CDS
    CCDS58583.1
    UniProtKB/Swiss-Prot
    Q8N9F7
    Related
    ENSP00000463273.1, ENST00000581140.5
    Conserved Domains (1) summary
    cd08612
    Location:14269
    GDPD_GDE4; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins
  2. NM_001165994.2NP_001159466.1  lysophospholipase D GDPD1 isoform 2

    See identical proteins and their annotated locations for NP_001159466.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and 3' coding region, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC099850, BC034432
    Consensus CDS
    CCDS58584.1
    UniProtKB/Swiss-Prot
    Q8N9F7
    Related
    ENSP00000464690.1, ENST00000581276.5
    Conserved Domains (1) summary
    cd08612
    Location:14279
    GDPD_GDE4; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins
  3. NM_182569.4NP_872375.2  lysophospholipase D GDPD1 isoform 1

    See identical proteins and their annotated locations for NP_872375.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC091059, AC099850, AI478202, AK094770
    Consensus CDS
    CCDS11616.1
    UniProtKB/Swiss-Prot
    Q8N9F7
    Related
    ENSP00000284116.4, ENST00000284116.9
    Conserved Domains (1) summary
    cd08612
    Location:14311
    GDPD_GDE4; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 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_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    59220470..59275970
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017024521.1XP_016880010.1  lysophospholipase D GDPD1 isoform X1

RNA

  1. XR_001752500.2 RNA Sequence

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