Free for academic non-profit institutions. Other users need a Commercial license

Aliases for GDE1 Gene

Aliases for GDE1 Gene

  • Glycerophosphodiester Phosphodiesterase 1 2 3 5
  • Membrane Interacting Protein Of RGS16 2 3
  • Membrane-Interacting Protein Of RGS16 3 4
  • RGS16-Interacting Membrane Protein 3 4
  • EC 3.1.4.44 4 63
  • MIR16 3 4
  • 363E6.2 3

External Ids for GDE1 Gene

Previous GeneCards Identifiers for GDE1 Gene

  • GC16M019422
  • GC16M018049

Summaries for GDE1 Gene

GeneCards Summary for GDE1 Gene

GDE1 (Glycerophosphodiester Phosphodiesterase 1) is a Protein Coding gene. Among its related pathways are PI Metabolism and Metabolism. GO annotations related to this gene include phosphoric diester hydrolase activity and glycerophosphoinositol glycerophosphodiesterase activity.

UniProtKB/Swiss-Prot for GDE1 Gene

  • Has glycerophosphoinositol phosphodiesterase activity. Has little or no activity towards glycerophosphocholine. GDE1 activity can be modulated by G-protein signaling pathways (By similarity).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GDE1 Gene

Genomics for GDE1 Gene

Regulatory Elements for GDE1 Gene

Enhancers for GDE1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around GDE1 on UCSC Golden Path with GeneCards custom track

Promoters for GDE1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around GDE1 on UCSC Golden Path with GeneCards custom track

Genomic Location for GDE1 Gene

Chromosome:
16
Start:
19,501,689 bp from pter
End:
19,522,145 bp from pter
Size:
20,457 bases
Orientation:
Minus strand

Genomic View for GDE1 Gene

Genes around GDE1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GDE1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GDE1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GDE1 Gene

Proteins for GDE1 Gene

  • Protein details for GDE1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZC3-GDE1_HUMAN
    Recommended name:
    Glycerophosphodiester phosphodiesterase 1
    Protein Accession:
    Q9NZC3
    Secondary Accessions:
    • O43334
    • Q6PKF7
    • Q7KYR4

    Protein attributes for GDE1 Gene

    Size:
    331 amino acids
    Molecular mass:
    37718 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Interacts with RGS16 (By similarity). Interacts with PRAF2.
    SequenceCaution:
    • Sequence=AAC05440.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=AAC05803.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for GDE1 Gene

Proteomics data for GDE1 Gene at MOPED

Selected DME Specific Peptides for GDE1 Gene

Post-translational modifications for GDE1 Gene

Other Protein References for GDE1 Gene

Domains & Families for GDE1 Gene

Suggested Antigen Peptide Sequences for GDE1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NZC3

UniProtKB/Swiss-Prot:

GDE1_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 GDE1: view

No data available for Gene Families for GDE1 Gene

Function for GDE1 Gene

Molecular function for GDE1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
1-(sn-glycero-3-phospho)-1D-myo-inositol + H(2)O = myo-inositol + sn-glycerol 3-phosphate.
UniProtKB/Swiss-Prot Function:
Has glycerophosphoinositol phosphodiesterase activity. Has little or no activity towards glycerophosphocholine. GDE1 activity can be modulated by G-protein signaling pathways (By similarity).

Enzyme Numbers (IUBMB) for GDE1 Gene

Gene Ontology (GO) - Molecular Function for GDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008081 phosphoric diester hydrolase activity IEA --
GO:0047395 glycerophosphoinositol glycerophosphodiesterase activity IEA,TAS --
genes like me logo Genes that share ontologies with GDE1: view

Phenotypes for GDE1 Gene

genes like me logo Genes that share phenotypes with GDE1: view

Animal Models for GDE1 Gene

MGI Knock Outs for GDE1:

Animal Model Products

  • Taconic Biosciences Mouse Models for GDE1

miRNA for GDE1 Gene

miRTarBase miRNAs that target GDE1

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for GDE1 Gene

Localization for GDE1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GDE1 Gene

Cell membrane; Multi-pass membrane protein. Cytoplasmic vesicle membrane; Multi-pass membrane protein. Note=Perinuclear vesicles and cell membrane. {ECO:0000250 UniProtKB:Q9JL55}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for GDE1 Gene COMPARTMENTS Subcellular localization image for GDE1 gene
Compartment Confidence
plasma membrane 4
endoplasmic reticulum 2
extracellular 1
peroxisome 1

No data available for Gene Ontology (GO) - Cellular Components for GDE1 Gene

Pathways & Interactions for GDE1 Gene

genes like me logo Genes that share pathways with GDE1: view

Gene Ontology (GO) - Biological Process for GDE1 Gene

None

No data available for SIGNOR curated interactions for GDE1 Gene

Drugs & Compounds for GDE1 Gene

(3) Drugs for GDE1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Choline Approved Nutra 139
Ethanolamine Experimental Pharma 0
Magnesium Nutra 0

(6) Additional Compounds for GDE1 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
glycerol 3-phosphate
  • 1-(Dihydrogen phosphate) Glycerol
  • 1-Glycerophosphate
  • 1-Glycerophosphorate
  • 1-Glycerophosphoric acid
  • 3-Glycerophosphate
57-03-4
glycerophosphocholine
  • 2-[[(2,3-Dihydroxypropoxy)hydroxyphosphinyl]oxy]-N,N,N-trimethyl-Ethanaminium inner salt
  • a-Glycerophosphorylcholine
  • a-Glycerylphosphorylcholine
  • alpha-Glycerophosphorylcholine
  • alpha-Glycerylphosphorylcholine
28319-77-9
Glycerylphosphorylethanolamine
  • 2-Aminoethyl ester 1-Glycerophosphoric acid
  • a-Glycerophosphorylethanolamine
  • alpha-Glycerophosphorylethanolamine
  • Glycerol 3-phosphoethanolamine
  • Glycerol 3-phosphorylethanolamine
1190-00-7
Myoinositol
  • cis-1,2,3,5-trans-4,6-Cyclohexanehexol
  • i-Inositol
  • Iso-Inositol
  • Meat sugar
  • Meso-Inositol
87-89-8
genes like me logo Genes that share compounds with GDE1: view

Transcripts for GDE1 Gene

Unigene Clusters for GDE1 Gene

Glycerophosphodiester phosphodiesterase 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for GDE1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b
SP1: - -
SP2: - -
SP3: - - -
SP4:
SP5:

Relevant External Links for GDE1 Gene

GeneLoc Exon Structure for
GDE1
ECgene alternative splicing isoforms for
GDE1

Expression for GDE1 Gene

mRNA expression in normal human tissues for GDE1 Gene

Protein differential expression in normal tissues from HIPED for GDE1 Gene

This gene is overexpressed in Nasal epithelium (55.1) and Pancreas (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for GDE1 Gene



SOURCE GeneReport for Unigene cluster for GDE1 Gene Hs.512607

mRNA Expression by UniProt/SwissProt for GDE1 Gene

Q9NZC3-GDE1_HUMAN
Tissue specificity: Widely expressed.
genes like me logo Genes that share expression patterns with GDE1: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for GDE1 Gene

Orthologs for GDE1 Gene

This gene was present in the common ancestor of animals.

Orthologs for GDE1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia GDE1 35
  • 89.33 (n)
  • 87.31 (a)
GDE1 36
  • 87 (a)
OneToOne
dog
(Canis familiaris)
Mammalia GDE1 35
  • 91.84 (n)
  • 91.54 (a)
-- 36
  • 80 (a)
OneToMany
-- 36
  • 91 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Gde1 35
  • 86.4 (n)
  • 87.31 (a)
Gde1 16
Gde1 36
  • 87 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia GDE1 35
  • 99.7 (n)
  • 99.7 (a)
GDE1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Gde1 35
  • 86.1 (n)
  • 87.92 (a)
oppossum
(Monodelphis domestica)
Mammalia GDE1 36
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GDE1 36
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves GDE1 35
  • 72.98 (n)
  • 69.55 (a)
GDE1 36
  • 64 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GDE1 36
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gde1 35
  • 65.05 (n)
  • 67.64 (a)
Str.15048 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.14702 35
zebrafish
(Danio rerio)
Actinopterygii gde1 35
  • 61.32 (n)
  • 59.12 (a)
zgc56068 35
gde1 36
  • 56 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001253 35
  • 41.06 (n)
  • 26.83 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG14883 35
  • 39.86 (n)
  • 26.67 (a)
CG14883 36
  • 21 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea T12B3.3 35
  • 47.33 (n)
  • 32 (a)
T09B9.3 36
  • 18 (a)
OneToMany
T12B3.3 36
  • 26 (a)
OneToMany
T22G5.1 36
  • 22 (a)
OneToMany
ZC155.4 36
  • 21 (a)
OneToMany
Species with no ortholog for GDE1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for GDE1 Gene

ENSEMBL:
Gene Tree for GDE1 (if available)
TreeFam:
Gene Tree for GDE1 (if available)

Paralogs for GDE1 Gene

No data available for Paralogs for GDE1 Gene

Variants for GDE1 Gene

Sequence variations from dbSNP and Humsavar for GDE1 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs2072086 - 19,505,076(+) CATCC(C/T)GATCT reference, missense
rs34137361 - 19,503,484(+) AGGTT(C/T)GCAGT reference, missense
rs7135 -- 19,503,161(-) GTACA(A/G)TTTGC utr-variant-3-prime
rs10572 -- 19,501,845(+) AGCTA(C/T)GGGGA utr-variant-3-prime
rs226886 -- 19,518,029(+) ACTAC(C/T)GGCAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for GDE1 Gene

Variant ID Type Subtype PubMed ID
nsv436835 CNV Insertion 17901297
nsv833163 CNV Gain 17160897
esv272811 CNV Insertion 20981092

Variation tolerance for GDE1 Gene

Residual Variation Intolerance Score: 53.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.38; 27.17% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GDE1 Gene

HapMap Linkage Disequilibrium report
GDE1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GDE1 Gene

Disorders for GDE1 Gene

Relevant External Links for GDE1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GDE1

No disorders were found for GDE1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for GDE1 Gene

Publications for GDE1 Gene

  1. Genomic organization, characterization, and molecular 3D model of GDE1, a novel mammalian glycerophosphoinositol phosphodiesterase. (PMID: 16472945) Bachmann A.S. … Mocz G. (Gene 2006) 2 3 4 67
  2. GDE1/MIR16 is a glycerophosphoinositol phosphodiesterase regulated by stimulation of G protein-coupled receptors. (PMID: 12576545) Zheng B. … Farquhar M.G. (Proc. Natl. Acad. Sci. U.S.A. 2003) 2 3 23
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  4. Aberrant plasma levels of circulating miR-16, miR-107, miR-130a and miR-146a are associated with lymph node metastasis and receptor status of breast cancer patients. (PMID: 26033453) StA1ckrath I. … Schwarzenbach H. (Oncotarget 2015) 3
  5. Targeting of YAP1 by microRNA-15a and microRNA-16-1 exerts tumor suppressor function in gastric adenocarcinoma. (PMID: 25743273) Kang W. … To K.F. (Mol. Cancer 2015) 3

Products for GDE1 Gene

Sources for GDE1 Gene

Content