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Aliases for GDPD2 Gene

Aliases for GDPD2 Gene

  • Glycerophosphodiester Phosphodiesterase Domain Containing 2 2 3
  • Osteoblast Differentiation Promoting Factor 2 3 4
  • Glycerophosphodiester Phosphodiesterase Domain-Containing Protein 2 3 4
  • Glycerophosphodiester Phosphodiesterase 3 3 4
  • OBDPF 3 4
  • GDE3 3 4
  • EC 3.1.4.43 4

External Ids for GDPD2 Gene

Previous GeneCards Identifiers for GDPD2 Gene

  • GC0XP068510
  • GC0XP069426
  • GC0XP069559
  • GC0XP069642
  • GC0XP063464

Summaries for GDPD2 Gene

Entrez Gene Summary for GDPD2 Gene

  • 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]

GeneCards Summary for GDPD2 Gene

GDPD2 (Glycerophosphodiester Phosphodiesterase Domain Containing 2) is a Protein Coding gene. GO annotations related to this gene include phosphoric diester hydrolase activity and glycerophosphoinositol inositolphosphodiesterase activity. An important paralog of this gene is GDPD5.

UniProtKB/Swiss-Prot for GDPD2 Gene

  • Has glycerophosphoinositol inositolphosphodiesterase activity and specifically hydrolyzes glycerophosphoinositol, with no activity for other substrates such as glycerophosphoinositol 4-phosphate, glycerophosphocholine, glycerophosphoethanolamine, and glycerophosphoserine. Accelerates the program of osteoblast differentiation and growth. May play a role in remodeling of the actin cytoskeleton (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GDPD2 Gene

Genomics for GDPD2 Gene

Regulatory Elements for GDPD2 Gene

Genomic Location for GDPD2 Gene

Chromosome:
X
Start:
70,423,031 bp from pter
End:
70,433,391 bp from pter
Size:
10,361 bases
Orientation:
Plus strand

Genomic View for GDPD2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for GDPD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GDPD2 Gene

Proteins for GDPD2 Gene

  • Protein details for GDPD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HCC8-GDPD2_HUMAN
    Recommended name:
    Glycerophosphoinositol inositolphosphodiesterase GDPD2
    Protein Accession:
    Q9HCC8
    Secondary Accessions:
    • B4DRH4
    • B4DVC9
    • Q9NXJ6

    Protein attributes for GDPD2 Gene

    Size:
    539 amino acids
    Molecular mass:
    61729 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA91014.1; Type=Frameshift; Positions=397; Evidence={ECO:0000305};

    Alternative splice isoforms for GDPD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GDPD2 Gene

Proteomics data for GDPD2 Gene at MOPED

Post-translational modifications for GDPD2 Gene

  • Glycosylation at Asn 442
  • Modification sites at PhosphoSitePlus

Other Protein References for GDPD2 Gene

No data available for DME Specific Peptides for GDPD2 Gene

Domains & Families for GDPD2 Gene

Graphical View of Domain Structure for InterPro Entry

Q9HCC8

UniProtKB/Swiss-Prot:

GDPD2_HUMAN :
  • Contains 1 GP-PDE domain.
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
Domain:
  • Contains 1 GP-PDE domain.
Family:
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
genes like me logo Genes that share domains with GDPD2: view

No data available for Gene Families for GDPD2 Gene

Function for GDPD2 Gene

Molecular function for GDPD2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
1-(sn-glycero-3-phospho)-1D-myo-inositol + H(2)O = glycerol + 1D-myo-inositol 1-phosphate
UniProtKB/Swiss-Prot Function:
Has glycerophosphoinositol inositolphosphodiesterase activity and specifically hydrolyzes glycerophosphoinositol, with no activity for other substrates such as glycerophosphoinositol 4-phosphate, glycerophosphocholine, glycerophosphoethanolamine, and glycerophosphoserine. Accelerates the program of osteoblast differentiation and growth. May play a role in remodeling of the actin cytoskeleton (By similarity).

Enzyme Numbers (IUBMB) for GDPD2 Gene

Gene Ontology (GO) - Molecular Function for GDPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008081 phosphoric diester hydrolase activity --
GO:0008889 glycerophosphodiester phosphodiesterase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0047394 glycerophosphoinositol inositolphosphodiesterase activity IEA --
genes like me logo Genes that share ontologies with GDPD2: view

Phenotypes for GDPD2 Gene

genes like me logo Genes that share phenotypes with GDPD2: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for GDPD2

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for GDPD2 Gene

Localization for GDPD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GDPD2 Gene

Cell membrane; Multi-pass membrane protein. Cytoplasm. Cytoplasm, cytoskeleton. Note=Colocalizes with the actin cytoskeleton. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for GDPD2 Gene COMPARTMENTS Subcellular localization image for GDPD2 gene
Compartment Confidence
cytoskeleton 3
plasma membrane 3

Gene Ontology (GO) - Cellular Components for GDPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA --
GO:0005886 plasma membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with GDPD2: view

Pathways & Interactions for GDPD2 Gene

SuperPathways for GDPD2 Gene

No Data Available

Interacting Proteins for GDPD2 Gene

Gene Ontology (GO) - Biological Process for GDPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006071 glycerol metabolic process --
GO:0006629 lipid metabolic process IEA --
genes like me logo Genes that share ontologies with GDPD2: view

No data available for Pathways by source and SIGNOR curated interactions for GDPD2 Gene

Drugs & Compounds for GDPD2 Gene

(1) Drugs for GDPD2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glycerol Experimental Pharma 176

(3) Additional Compounds for GDPD2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
1-(sn-Glycero-3-phospho)-1D-myo-inositol
  • 1-(Sn-glycero-3-Phospho)-1D-myo-inositol
  • 3-Phosphoglyceroinositol
  • Glyerophosphoinositol
  • GroPIns
  • Sn-glycero-3-Phospho-1-inositol
Inositol phosphate
  • 1D-Myo-Inositol 1-monophosphate
  • 1D-Myo-Inositol 1-phosphate
  • D-Myo-Inositol-1-Phosphate
  • Inositol 1-monophosphate
15421-51-9
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
genes like me logo Genes that share compounds with GDPD2: view

Transcripts for GDPD2 Gene

Unigene Clusters for GDPD2 Gene

Glycerophosphodiester phosphodiesterase domain containing 2:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for GDPD2

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for GDPD2 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - -
SP2: - -
SP3: - -
SP4: - - - -
SP5: - - - - -
SP6:

Relevant External Links for GDPD2 Gene

GeneLoc Exon Structure for
GDPD2
ECgene alternative splicing isoforms for
GDPD2

Expression for GDPD2 Gene

mRNA expression in normal human tissues for GDPD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GDPD2 Gene

This gene is overexpressed in Spleen (x22.2) and Skin - Not Sun Exposed (Suprapubic) (x4.9).

Protein differential expression in normal tissues from HIPED for GDPD2 Gene

This gene is overexpressed in Spleen (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for GDPD2 Gene



SOURCE GeneReport for Unigene cluster for GDPD2 Gene Hs.438712

genes like me logo Genes that share expression patterns with GDPD2: view

Protein tissue co-expression partners for GDPD2 Gene

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for GDPD2 Gene

Orthologs for GDPD2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for GDPD2 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia GDPD2 35
  • 87.26 (n)
  • 82.37 (a)
GDPD2 36
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia GDPD2 35
  • 90.23 (n)
  • 88.68 (a)
GDPD2 36
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gdpd2 35
  • 86.18 (n)
  • 85.13 (a)
Gdpd2 16
Gdpd2 36
  • 85 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia GDPD2 35
  • 99.66 (n)
  • 100 (a)
GDPD2 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Gdpd2 35
  • 85.69 (n)
  • 84.57 (a)
oppossum
(Monodelphis domestica)
Mammalia GDPD2 36
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves GDPD2 35
  • 62.29 (n)
  • 55.24 (a)
GDPD2 36
  • 55 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GDPD2 36
  • 44 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gdpd2 35
  • 54.74 (n)
  • 47.5 (a)
zebrafish
(Danio rerio)
Actinopterygii si:dkey-31j3.9 35
  • 51.16 (n)
  • 42.35 (a)
GDPD2 36
  • 41 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 24 (a)
OneToMany
Species with no ortholog for GDPD2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for GDPD2 Gene

ENSEMBL:
Gene Tree for GDPD2 (if available)
TreeFam:
Gene Tree for GDPD2 (if available)

Paralogs for GDPD2 Gene

Paralogs for GDPD2 Gene

(2) SIMAP similar genes for GDPD2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with GDPD2: view

Variants for GDPD2 Gene

Sequence variations from dbSNP and Humsavar for GDPD2 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs781687274 -- 70,423,217(+) CTGCA(C/G)GCCTT utr-variant-5-prime
rs781376413 -- 70,423,906(+) ACACA(G/T)GCTCA intron-variant
rs781349552 -- 70,425,889(+) CCACC(C/T)CAGCC intron-variant
rs781088307 -- 70,425,031(+) CCTCC(A/G)CTGCC intron-variant, reference, missense
rs781034905 -- 70,425,356(+) CAGTG(C/T)GACTG intron-variant, reference, synonymous-codon, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for GDPD2 Gene

Variant ID Type Subtype PubMed ID
esv1584074 OTHER Inversion 17803354
nsv6950 CNV Insertion 18451855
esv33082 CNV Loss 17666407

Variation tolerance for GDPD2 Gene

Residual Variation Intolerance Score: 67.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.03; 21.09% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GDPD2 Gene

HapMap Linkage Disequilibrium report
GDPD2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GDPD2 Gene

Disorders for GDPD2 Gene

Relevant External Links for GDPD2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GDPD2
genes like me logo Genes that share disorders with GDPD2: view

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for GDPD2 Gene

Publications for GDPD2 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 2003) 2 67
  2. The developmentally regulated osteoblast phosphodiesterase GDE3 is glycerophosphoinositol-specific and modulates cell growth. (PMID: 19596859) Corda D. … MariggiA^ S. (J. Biol. Chem. 2009) 67
  3. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L. … Andersson-Svahn H. (Mol. Cell Proteomics 2008) 67
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PMID: 16344560) Kimura K. … Sugano S. (Genome Res. 2006) 67
  5. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross M.T. … Bentley D.R. (Nature 2005) 67

Products for GDPD2 Gene

Sources for GDPD2 Gene

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