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Aliases for GDE1 Gene

Aliases for GDE1 Gene

  • Glycerophosphodiester Phosphodiesterase 1 2 3 5
  • Membrane Interacting Protein Of RGS16 2 3
  • RGS16-Interacting Membrane Protein 3 4
  • EC 3.1.4.44 4 61
  • MIR16 3 4
  • Membrane-Interacting Protein Of RGS16 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 Metabolism and PI 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 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
GH16F019487 1.2 Ensembl ENCODE 4.6 +33.8 33834 2.2 HDGF PKNOX1 ARNT ZFP64 GATA2 KLF13 ZNF202 NCOA1 REST ZNF518A SYT17 COQ7 KNOP1 CCP110 TMC5 GDE1 ENSG00000260592 GC16P019498
GH16F019554 1.1 ENCODE 5 -33.5 -33481 2.6 HDGF PKNOX1 MLX WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF302 CCP110 ITPRIPL2 ENSG00000263253 ENSG00000263237 ENSG00000260017 TMC5 KNOP1 GDE1 C16orf62 GC16M019687
GH16F019381 0.9 ENCODE 5 +139.5 139527 1.6 HDAC1 KLF17 SIN3A FEZF1 GLIS2 SCRT2 FOS EGR2 CEBPB ZEB2 TMC5 SYT17 GDE1 GC16P019387 GC16P019371
GH16F019515 0.8 ENCODE 4.7 +5.6 5556 3.0 KLF1 KLF17 ZNF384 ZNF121 ZNF316 GATA3 ZNF366 ZNF600 FOS MAFK C16orf62 COQ7 CCP110 KNOP1 GDE1 GC16P019512
GH16F019520 1.4 FANTOM5 ENCODE 0.8 +0.5 504 3.0 HDGF PKNOX1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 CCP110 KNOP1 SYT17 GDE1 GC16P019512
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000504915 645 1801 HDGF PKNOX1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9

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

Selected DME Specific Peptides for GDE1 Gene

Q9NZC3:
  • VCSFLPEVIYKMRQTD
  • HRPWSLSHTGDGKPR
  • KKWSAKGIQVV
  • FSFEPVPS

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:0008889 glycerophosphodiester phosphodiesterase activity IEA,TAS 10760272
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0047395 glycerophosphoinositol glycerophosphodiesterase activity 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

miRNA Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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
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 GDE1 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 2
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for GDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane TAS 10760272
GO:0030659 cytoplasmic vesicle membrane IEA --
GO:0031410 cytoplasmic vesicle IEA --
genes like me logo Genes that share ontologies with GDE1: view

Pathways & Interactions for GDE1 Gene

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

Gene Ontology (GO) - Biological Process for GDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA,TAS 10760272
GO:0046475 glycerophospholipid catabolic process TAS --
genes like me logo Genes that share ontologies with GDE1: view

No data available for SIGNOR curated interactions for GDE1 Gene

Drugs & Compounds for GDE1 Gene

(5) Drugs for GDE1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Choline Approved Nutra 148
Choline alfoscerate Experimental Pharma 0
Ethanolamine Experimental Pharma 0
Magnesium Nutra 0

(4) 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
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:

miRNA Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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 from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for GDE1 Gene



NURSA nuclear receptor signaling pathways regulating expression of GDE1 Gene:

GDE1

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

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
chimpanzee
(Pan troglodytes)
Mammalia GDE1 34 35
  • 99.7 (n)
dog
(Canis familiaris)
Mammalia GDE1 34
  • 91.84 (n)
-- 35
  • 91 (a)
OneToMany
-- 35
  • 80 (a)
OneToMany
cow
(Bos Taurus)
Mammalia GDE1 34 35
  • 89.33 (n)
mouse
(Mus musculus)
Mammalia Gde1 34 16 35
  • 86.4 (n)
rat
(Rattus norvegicus)
Mammalia Gde1 34
  • 86.1 (n)
oppossum
(Monodelphis domestica)
Mammalia GDE1 35
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GDE1 35
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves GDE1 34 35
  • 72.98 (n)
lizard
(Anolis carolinensis)
Reptilia GDE1 35
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gde1 34
  • 65.05 (n)
Str.15048 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.14702 34
zebrafish
(Danio rerio)
Actinopterygii gde1 34 35
  • 61.32 (n)
zgc56068 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001253 34
  • 41.06 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG14883 34 35
  • 39.86 (n)
worm
(Caenorhabditis elegans)
Secernentea T12B3.3 34 35
  • 47.33 (n)
T22G5.1 35
  • 22 (a)
OneToMany
ZC155.4 35
  • 21 (a)
OneToMany
T09B9.3 35
  • 18 (a)
OneToMany
Species where no ortholog for GDE1 was found in the sources mined by GeneCards:
  • 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
rs1053138 -- 19,503,003(-) AAGGA(A/G)CACTa nc-transcript-variant, utr-variant-3-prime
rs10572 -- 19,501,845(+) AGCTA(C/T)GGGGA nc-transcript-variant, utr-variant-3-prime
rs11074400 -- 19,517,881(+) TGAAG(A/T)TTTCT intron-variant
rs111470548 -- 19,507,000(+) TGGGC(A/G)TGGTG intron-variant
rs111659244 -- 19,519,473(+) ATATA(-/TA)CATAC intron-variant

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

Variant ID Type Subtype PubMed ID
esv3407263 CNV insertion 20981092
nsv436835 CNV insertion 17901297
nsv571582 CNV gain 21841781
nsv833163 CNV gain 17160897

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

SNPedia medical, phenotypic, and genealogical associations of SNPs for
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 64
  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 22 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. MIR16, a putative membrane glycerophosphodiester phosphodiesterase, interacts with RGS16. (PMID: 10760272) Zheng B. … Farquhar M.G. (Proc. Natl. Acad. Sci. U.S.A. 2000) 3 4 64
  5. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. (PMID: 10493829) Loftus B.J. … Adams M.D. (Genomics 1999) 3 4 64

Products for GDE1 Gene

Sources for GDE1 Gene

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