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Aliases for GDPD2 Gene

Aliases for GDPD2 Gene

  • Glycerophosphodiester Phosphodiesterase Domain Containing 2 2 3 5
  • 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
  • Glycerophosphoinositol Inositolphosphodiesterase GDPD2 3
  • 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).

Additional gene information for GDPD2 Gene

No data available for CIViC summary , 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

Enhancers for GDPD2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XH070475 1.2 Ensembl ENCODE 12.5 +56.3 56265 6 ZFP64 INSM2 KLF17 GLIS2 ZNF366 ZSCAN5C SCRT2 FOS EGR2 SP3 DLG3 DLG3-AS1 RNU4-81P GDPD2 ENSG00000230187
GH0XH070398 1.1 FANTOM5 ENCODE 13.2 -24.0 -24035 1 ELF3 SOX13 GATAD2A FOXA2 FOXA3 CEBPG HMG20A RARA ZNF7 NFIL3 GDPD2 ARR3 IGBP1 RNY4P23
GH0XH070433 1.7 FANTOM5 Ensembl ENCODE 0.4 +11.6 11596 2 ATF1 ARID4B SIN3A BRCA1 ZNF2 ETS1 GLIS2 GATA2 ZNF143 KLF7 TAF1 LOC100420758 NONO ENSG00000229601 ARR3 DLG3 KIF4A LOC105373244 GDPD2
GH0XH070422 0.9 Ensembl ENCODE 0.7 +0.4 385 2 SCRT1 CTCF MAZ RFX1 ZSCAN4 ZNF398 RAD21 PRDM2 ZFHX2 GLIS2 ARR3 GDPD2 LOC105373244
GH0XH070421 0.4 ENCODE 0.7 -1.2 -1186 0 NFIC GDPD2 RNY4P23
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around GDPD2 on UCSC Golden Path with GeneCards custom track

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

Genes around GDPD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GDPD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for GDPD2 Gene

  • Glycosylation at isoforms=2, 3442
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for GDPD2 Gene

Domains & Families for GDPD2 Gene

Gene Families for GDPD2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted membrane proteins

Graphical View of Domain Structure for InterPro Entry

Q9HCC8

UniProtKB/Swiss-Prot:

GDPD2_HUMAN :
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
Family:
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
genes like me logo Genes that share domains with GDPD2: view

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 IEA --
GO:0008889 glycerophosphodiester phosphodiesterase activity IEA --
GO:0016787 hydrolase 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
genes like me logo Genes that share phenotypes with GDPD2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for GDPD2

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for GDPD2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GDPD2 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 2

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:0005884 actin filament IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with GDPD2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GDPD2 Gene

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:0006629 lipid metabolic process IEA --
GO:0045669 positive regulation of osteoblast differentiation IEA --
GO:0090527 actin filament reorganization 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

(2) Drugs for GDPD2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glycerol Approved, Investigational Pharma 253
Water Approved Pharma 0

(2) 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
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

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for GDPD2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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



Protein tissue co-expression partners for GDPD2 Gene

NURSA nuclear receptor signaling pathways regulating expression of GDPD2 Gene:

GDPD2

SOURCE GeneReport for Unigene cluster for GDPD2 Gene:

Hs.438712

Evidence on tissue expression from TISSUES for GDPD2 Gene

  • Spleen(4.6)
  • Skin(4.3)
  • Nervous system(4.3)
  • Intestine(4.1)
genes like me logo Genes that share expression patterns with GDPD2: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia GDPD2 33 34
  • 99.66 (n)
dog
(Canis familiaris)
Mammalia GDPD2 33 34
  • 90.23 (n)
cow
(Bos Taurus)
Mammalia GDPD2 33 34
  • 87.26 (n)
mouse
(Mus musculus)
Mammalia Gdpd2 33 16 34
  • 86.18 (n)
rat
(Rattus norvegicus)
Mammalia Gdpd2 33
  • 85.69 (n)
oppossum
(Monodelphis domestica)
Mammalia GDPD2 34
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves GDPD2 33 34
  • 62.29 (n)
lizard
(Anolis carolinensis)
Reptilia GDPD2 34
  • 44 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gdpd2 33
  • 54.74 (n)
zebrafish
(Danio rerio)
Actinopterygii si:dkey-31j3.9 33
  • 51.16 (n)
GDPD2 34
  • 41 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 24 (a)
OneToMany
Species where no ortholog for GDPD2 was found in the sources mined by GeneCards:
  • 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
rs775565226 Benign 70,426,402(+) TGTGG(C/T)GGCTG reference, missense, utr-variant-5-prime
rs1000211326 -- 70,433,874(+) GACTC(C/G)CGGGA downstream-variant-500B, reference, missense
rs1000491069 -- 70,424,254(+) AAAGG(A/G)CAGGA intron-variant
rs1000571794 -- 70,422,269(+) AGAAA(C/T)GACAC upstream-variant-2KB
rs1000689775 -- 70,422,838(+) TATTT(A/C)CAGGG upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
esv1584074 OTHER inversion 17803354
esv33082 CNV loss 17666407
nsv6950 CNV insertion 18451855

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

SNPedia medical, phenotypic, and genealogical associations of SNPs for
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

No disorders were found for GDPD2 Gene.

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 HF … Gray A (Genome research 2003) 2 3 4 60
  2. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  5. Novel membrane protein containing glycerophosphodiester phosphodiesterase motif is transiently expressed during osteoblast differentiation. (PMID: 12933806) Yanaka N … Sakurai N (The Journal of biological chemistry 2003) 3 4 60

Products for GDPD2 Gene

Sources for GDPD2 Gene

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