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GDPD5 glycerophosphodiester phosphodiesterase domain containing 5 [ Homo sapiens (human) ]

Gene ID: 81544, updated on 21-Oct-2018

Summary

Official Symbol
GDPD5provided by HGNC
Official Full Name
glycerophosphodiester phosphodiesterase domain containing 5provided by HGNC
Primary source
HGNC:HGNC:28804
See related
Ensembl:ENSG00000158555 MIM:609632; Vega:OTTHUMG00000165484
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
GDE2; PP1665
Summary
Glycerophosphodiester phosphodiesterases (GDPDs; EC 3.1.4.46), such as GDPD5, are involved in glycerol metabolism (Lang et al., 2008 [PubMed 17578682]).[supplied by OMIM, Jan 2010]
Expression
Broad expression in spleen (RPKM 16.9), fat (RPKM 8.6) and 14 other tissues See more
Orthologs

Genomic context

See GDPD5 in Genome Data Viewer
Location:
11q13.4-q13.5
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (75434640..75525916, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (75145683..75236991, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA, C/D box 15B Neighboring gene ribosomal protein S3 Neighboring gene Sharpr-MPRA regulatory regions 6111 and 12908 Neighboring gene kelch like family member 35 Neighboring gene uncharacterized LOC105369389 Neighboring gene VISTA enhancer hs1748 Neighboring gene serpin family H member 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Glycerophospholipid catabolism, organism-specific biosystem (from REACTOME)
    Glycerophospholipid catabolism, organism-specific biosystemReactions grouped in this pathway because of their shared chemistry - the hydrolysis of various phosphatidyl inositols and related phospholipids. They differ, however, in the tissues in which they oc...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • PI Metabolism, organism-specific biosystem (from REACTOME)
    PI Metabolism, organism-specific biosystemPhosphatidylinositol (PI), a membrane phospholipid, can be reversibly phosphorylated at the 3, 4, and 5 positions of the inositol ring to generate seven phosphoinositides: phosphatidylinositol 3-phos...
  • Phospholipid metabolism, organism-specific biosystem (from REACTOME)
    Phospholipid metabolism, organism-specific biosystemPhospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
glycerophosphocholine phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
 
glycerophosphodiester phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cerebral cortex neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
lipid metabolic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
neuron projection development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell cycle IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of timing of cell differentiation IEA
Inferred from Electronic Annotation
more info
 
spinal cord motor neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
growth cone IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
perinuclear endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
glycerophosphodiester phosphodiesterase domain-containing protein 5
Names
glycerophosphodiester phosphodiesterase 2

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_001351167.1NP_001338096.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' structure, resulting in a novel 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AF318351, AP002815, BC033391
    Consensus CDS
    CCDS86230.1
    Related
    ENSP00000434050.1, ENST00000526177.5
    Conserved Domains (1) summary
    cd08608
    Location:89438
    GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
  2. NM_001351168.1NP_001338097.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate exon, resulting in a novel 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AF318351, AP002815
    Consensus CDS
    CCDS86229.1
    Related
    ENSP00000435196.1, ENST00000533805.5
    Conserved Domains (1) summary
    cl14615
    Location:1331
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
  3. NM_030792.7NP_110419.5  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 1

    See identical proteins and their annotated locations for NP_110419.5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF318351, AF318377, AK074848, AP002815
    Consensus CDS
    CCDS8238.1
    UniProtKB/Swiss-Prot
    Q8WTR4
    Related
    ENSP00000337972.3, OTTHUMP00000229940, ENST00000336898.7
    Conserved Domains (2) summary
    cd08608
    Location:227576
    GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
    COG0584
    Location:227468
    UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    75434640..75525916 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545276.2XP_011543578.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    See identical proteins and their annotated locations for XP_011543578.1

    Conserved Domains (2) summary
    cd08608
    Location:227577
    GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
    COG0584
    Location:227468
    UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
  2. XM_011545279.2XP_011543581.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    See identical proteins and their annotated locations for XP_011543581.1

    Conserved Domains (2) summary
    cd08608
    Location:227577
    GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
    COG0584
    Location:227468
    UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
  3. XM_011545278.2XP_011543580.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    See identical proteins and their annotated locations for XP_011543580.1

    Conserved Domains (2) summary
    cd08608
    Location:227577
    GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
    COG0584
    Location:227468
    UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
  4. XM_011545277.2XP_011543579.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    See identical proteins and their annotated locations for XP_011543579.1

    Conserved Domains (2) summary
    cd08608
    Location:227577
    GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
    COG0584
    Location:227468
    UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
  5. XM_006718697.3XP_006718760.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

    See identical proteins and their annotated locations for XP_006718760.1

    UniProtKB/Swiss-Prot
    Q8WTR4
    Related
    ENSP00000433214.1, OTTHUMP00000229939, ENST00000529721.5, OTTHUMT00000384408
    Conserved Domains (2) summary
    cd08608
    Location:227576
    GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
    COG0584
    Location:227468
    UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
  6. XM_011545280.1XP_011543582.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X3

    Conserved Domains (2) summary
    cd08608
    Location:170520
    GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
    COG0584
    Location:170411
    UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
  7. XM_011545281.2XP_011543583.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X4

    See identical proteins and their annotated locations for XP_011543583.1

    Related
    ENSP00000437049.1, OTTHUMP00000229938, ENST00000533784.5, OTTHUMT00000384407
    Conserved Domains (2) summary
    cd08608
    Location:89439
    GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
    COG0584
    Location:89330
    UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
  8. XM_011545286.1XP_011543588.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X5

    Conserved Domains (1) summary
    cl14615
    Location:1332
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
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