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GDPD2 glycerophosphodiester phosphodiesterase domain containing 2 [ Homo sapiens (human) ]

Gene ID: 54857, updated on 26-Nov-2021

Summary

Official Symbol
GDPD2provided by HGNC
Official Full Name
glycerophosphodiester phosphodiesterase domain containing 2provided by HGNC
Primary source
HGNC:HGNC:25974
See related
Ensembl:ENSG00000130055 MIM:300940
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
GDE3; OBDPF
Summary
This gene encodes a member of the glycerophosphodiester phosphodiesterase enzyme family. The encoded protein hydrolyzes glycerophosphoinositol to produce inositol 1-phosphate and glycerol. This protein may have a role in osteoblast differentiation and growth. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2010]
Expression
Biased expression in spleen (RPKM 25.5), skin (RPKM 21.4) and 4 other tissues See more
Orthologs
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Genomic context

See GDPD2 in Genome Data Viewer
Location:
Xq13.1
Exon count:
17
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (70423031..70433391)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (69643164..69653231)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene kinesin family member 4A Neighboring gene TRAPPC2L pseudogene 1 Neighboring gene RNY4 pseudogene 23 Neighboring gene uncharacterized LOC105373244 Neighboring gene RNA, U4 small nuclear 81, pseudogene Neighboring gene DLG3 antisense RNA 1 Neighboring gene discs large MAGUK scaffold protein 3

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20207

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables glycerophosphodiester phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables glycerophosphoinositol inositolphosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in actin filament reorganization IEA
Inferred from Electronic Annotation
more info
 
involved_in lipid metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of osteoblast differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in actin filament IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
located_in lamellipodium IEA
Inferred from Electronic Annotation
more info
 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
glycerophosphoinositol inositolphosphodiesterase GDPD2
Names
glycerophosphodiester phosphodiesterase 3
glycerophosphodiester phosphodiesterase domain-containing protein 2
osteoblast differentiation promoting factor
NP_001164662.1
NP_001164663.1
NP_001164664.1
NP_060181.2
XP_011529279.1
XP_016885103.1

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.

Genomic

  1. NG_016413.1 RefSeqGene

    Range
    5001..15361
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001171191.2NP_001164662.1  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform 3

    See identical proteins and their annotated locations for NP_001164662.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG. Variants 3 and 4 encode the same isoform (3), which is shorter than isoform 1.
    Source sequence(s)
    AI277430, AK299255
    Consensus CDS
    CCDS55438.1
    UniProtKB/Swiss-Prot
    Q9HCC8
    Related
    ENSP00000444601.1, ENST00000538649.5
    Conserved Domains (1) summary
    cd08609
    Location:123433
    GDPD_GDE3; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE3 and similar proteins
  2. NM_001171192.2NP_001164663.1  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform 1

    See identical proteins and their annotated locations for NP_001164663.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AI277430, AK301025, AL139398
    Consensus CDS
    CCDS55437.1
    UniProtKB/Swiss-Prot
    Q9HCC8
    Related
    ENSP00000414019.2, ENST00000453994.6
    Conserved Domains (1) summary
    cl14615
    Location:202563
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
  3. NM_001171193.2NP_001164664.1  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform 3

    See identical proteins and their annotated locations for NP_001164664.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG. Variants 3 and 4 encode the same isoform (3), which is shorter than isoform 1.
    Source sequence(s)
    AI277430, AK316035, AL139398
    Consensus CDS
    CCDS55438.1
    UniProtKB/Swiss-Prot
    Q9HCC8
    Related
    ENSP00000445982.1, ENST00000536730.5
    Conserved Domains (1) summary
    cd08609
    Location:123433
    GDPD_GDE3; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE3 and similar proteins
  4. NM_017711.4NP_060181.2  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform 2

    See identical proteins and their annotated locations for NP_060181.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, which results in a frameshift, compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
    Source sequence(s)
    AB048363, AL139398
    Consensus CDS
    CCDS14402.1
    UniProtKB/Swiss-Prot
    Q9HCC8
    Related
    ENSP00000363503.3, ENST00000374382.4
    Conserved Domains (1) summary
    cd08609
    Location:202512
    GDPD_GDE3; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE3 and similar proteins

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    70423031..70433391
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029614.1XP_016885103.1  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform X2

  2. XM_011530977.1XP_011529279.1  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform X1

    Conserved Domains (2) summary
    cd08609
    Location:75385
    GDPD_GDE3; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE3 and similar proteins
    pfam03009
    Location:102344
    GDPD; Glycerophosphoryl diester phosphodiesterase family
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