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Aliases for GPCPD1 Gene

Aliases for GPCPD1 Gene

  • Glycerophosphocholine Phosphodiesterase 1 2 3 5
  • Glycerophosphodiester Phosphodiesterase 5 3 4
  • GDE5 3 4
  • Glycerophosphocholine Phosphodiesterase GDE1 Homolog (S. Cerevisiae) 2
  • Putative Glycerophosphocholine Phosphodiesterase GPCPD1 3
  • Glycerophosphocholine Phosphodiesterase GDE1 Homolog 3
  • Putative Glycerophosphodiester Phosphodiesterase 5 3
  • Glycerophosphocholine Phosphodiesterase GPCPD1 3
  • Endometrial Differential 3 3
  • Preimplantation Protein 4 3
  • EC 3.1.4.2 4
  • KIAA1434 4
  • GDPD6 3
  • PREI4 3
  • EDI3 3

External Ids for GPCPD1 Gene

Previous GeneCards Identifiers for GPCPD1 Gene

  • GC20M005525
  • GC20M005481
  • GC20M005582
  • GC20M005800
  • GC20M005860
  • GC20M005923

Summaries for GPCPD1 Gene

GeneCards Summary for GPCPD1 Gene

GPCPD1 (Glycerophosphocholine Phosphodiesterase 1) is a Protein Coding gene. Diseases associated with GPCPD1 include Specific Developmental Disorder. Among its related pathways are Metabolism and Glycerophospholipid biosynthesis. GO annotations related to this gene include carbohydrate binding and starch binding.

UniProtKB/Swiss-Prot for GPCPD1 Gene

  • May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GPCPD1 Gene

Genomics for GPCPD1 Gene

Regulatory Elements for GPCPD1 Gene

Enhancers for GPCPD1 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
GH20F005641 1.8 FANTOM5 Ensembl ENCODE 40 -40.3 -40252 19.0 HDGF PKNOX1 SIN3A YBX1 FEZF1 YY1 ZNF766 ZNF207 FOS KLF13 GPCPD1 TRMT6 C20orf196 PROKR2 LOC105372514
GH20F005607 1.6 FANTOM5 ENCODE 38.1 +0.1 116 6.0 HDGF PKNOX1 ARNT MLX WRNIP1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 GPCPD1 LOC643406 CDS2 LINC00654 TRMT6 C20orf196 EIF4EP1
GH20F005687 1.3 FANTOM5 Ensembl 37.9 -78.1 -78075 2.6 ELF3 ATF1 MLX ARID4B THRB ZNF48 RAD21 DNMT3B RARA SLC30A9 GPCPD1 TRMT6 MCM8 CHGB LOC105372514
GH20F005673 1.6 FANTOM5 Ensembl ENCODE 18.2 -63.8 -63775 3.2 HDGF PKNOX1 ATF1 ARNT CREB3L1 ELK1 GATA2 FOS ZHX2 JUNB GPCPD1 CHGB TRMT6 LOC105372514
GH20F005713 1.6 FANTOM5 Ensembl ENCODE 11.5 -103.9 -103881 1.9 ELF3 PKNOX1 MLX ARID4B SIN3A BMI1 RAD21 DNMT3B THRB YY1 GPCPD1 C20orf196 LOC105372514
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around GPCPD1 on UCSC Golden Path with GeneCards custom track

Promoters for GPCPD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001446841 1326 3801 HDGF ARNT MLX WRNIP1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for GPCPD1 Gene

Chromosome:
20
Start:
5,544,404 bp from pter
End:
5,611,026 bp from pter
Size:
66,623 bases
Orientation:
Minus strand

Genomic View for GPCPD1 Gene

Genes around GPCPD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GPCPD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GPCPD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GPCPD1 Gene

Proteins for GPCPD1 Gene

  • Protein details for GPCPD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NPB8-GPCP1_HUMAN
    Recommended name:
    Glycerophosphocholine phosphodiesterase GPCPD1
    Protein Accession:
    Q9NPB8
    Secondary Accessions:
    • D3DW06
    • Q9BQL8
    • Q9NUX0

    Protein attributes for GPCPD1 Gene

    Size:
    672 amino acids
    Molecular mass:
    76035 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA91994.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA92672.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for GPCPD1 Gene

neXtProt entry for GPCPD1 Gene

Post-translational modifications for GPCPD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for GPCPD1 Gene

No data available for DME Specific Peptides for GPCPD1 Gene

Domains & Families for GPCPD1 Gene

Suggested Antigen Peptide Sequences for GPCPD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NPB8

UniProtKB/Swiss-Prot:

GPCP1_HUMAN :
  • Contains 1 CBM20 (carbohydrate binding type-20) domain.
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
Domain:
  • Contains 1 CBM20 (carbohydrate binding type-20) domain.
  • Contains 1 GP-PDE domain.
Family:
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
genes like me logo Genes that share domains with GPCPD1: view

No data available for Gene Families for GPCPD1 Gene

Function for GPCPD1 Gene

Molecular function for GPCPD1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
sn-glycero-3-phosphocholine + H(2)O = choline + sn-glycerol 3-phosphate.
UniProtKB/Swiss-Prot Function:
May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity.

Enzyme Numbers (IUBMB) for GPCPD1 Gene

Gene Ontology (GO) - Molecular Function for GPCPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008081 phosphoric diester hydrolase activity IEA --
GO:0008889 glycerophosphodiester phosphodiesterase activity IBA --
GO:0016787 hydrolase activity IEA --
GO:0030246 carbohydrate binding IEA --
GO:0047389 glycerophosphocholine phosphodiesterase activity IEA,IBA --
genes like me logo Genes that share ontologies with GPCPD1: view
genes like me logo Genes that share phenotypes with GPCPD1: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GPCPD1 Gene

Localization for GPCPD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GPCPD1 Gene

Cytoplasm, cytosol.

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 GPCPD1 gene
Compartment Confidence
cytosol 4
nucleus 3
plasma membrane 2
extracellular 1

Gene Ontology (GO) - Cellular Components for GPCPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with GPCPD1: view

Pathways & Interactions for GPCPD1 Gene

genes like me logo Genes that share pathways with GPCPD1: view

Interacting Proteins for GPCPD1 Gene

Gene Ontology (GO) - Biological Process for GPCPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0007519 skeletal muscle tissue development IEA --
GO:0030643 cellular phosphate ion homeostasis IBA --
GO:0046475 glycerophospholipid catabolic process IEA,IBA --
genes like me logo Genes that share ontologies with GPCPD1: view

No data available for SIGNOR curated interactions for GPCPD1 Gene

Drugs & Compounds for GPCPD1 Gene

(3) Drugs for GPCPD1 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

(1) Additional Compounds for GPCPD1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
glycerol 3-phosphate
  • 1-(Dihydrogen phosphate) Glycerol
  • 1-Glycerophosphate
  • 1-Glycerophosphorate
  • 1-Glycerophosphoric acid
  • 3-Glycerophosphate
57-03-4
genes like me logo Genes that share compounds with GPCPD1: view

Transcripts for GPCPD1 Gene

Unigene Clusters for GPCPD1 Gene

Glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae):
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for GPCPD1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^
SP1: - - - - -
SP2: - -
SP3: - -
SP4: - - -
SP5: - - - -
SP6: - - - -
SP7:
SP8:
SP9:
SP10:
SP11:

ExUns: 18 ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23a · 23b · 23c
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7: - - -
SP8:
SP9:
SP10:
SP11:

Relevant External Links for GPCPD1 Gene

GeneLoc Exon Structure for
GPCPD1
ECgene alternative splicing isoforms for
GPCPD1

Expression for GPCPD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GPCPD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GPCPD1 Gene

This gene is overexpressed in Whole Blood (x5.2).

Protein differential expression in normal tissues from HIPED for GPCPD1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.6), Monocytes (7.7), Fetal heart (7.3), Frontal cortex (6.8), and Testis (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for GPCPD1 Gene



Protein tissue co-expression partners for GPCPD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GPCPD1 Gene:

GPCPD1

SOURCE GeneReport for Unigene cluster for GPCPD1 Gene:

Hs.636359

mRNA Expression by UniProt/SwissProt for GPCPD1 Gene:

Q9NPB8-GPCP1_HUMAN
Tissue specificity: Widely expressed, with highest expression in spinal chord.
genes like me logo Genes that share expression patterns with GPCPD1: view

Primer Products

Orthologs for GPCPD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GPCPD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GPCPD1 34 35
  • 99.45 (n)
cow
(Bos Taurus)
Mammalia GPCPD1 34 35
  • 94.35 (n)
dog
(Canis familiaris)
Mammalia GPCPD1 34 35
  • 93.9 (n)
mouse
(Mus musculus)
Mammalia Gpcpd1 34 16 35
  • 89.24 (n)
rat
(Rattus norvegicus)
Mammalia Gpcpd1 34
  • 88.71 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 88 (a)
OneToMany
-- 35
  • 86 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia GPCPD1 35
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves -- 35
  • 77 (a)
OneToMany
GPCPD1 34
  • 75.85 (n)
-- 35
  • 60 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia GPCPD1 35
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gpcpd1 34
  • 72.73 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.15092 34
zebrafish
(Danio rerio)
Actinopterygii gpcpd1 34 35
  • 64.57 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG2818 34 35
  • 48.54 (n)
CG18135 35
  • 24 (a)
OneToMany
CG3942 35
  • 24 (a)
OneToMany
CG11619 35
  • 23 (a)
OneToMany
CG9394 35
  • 23 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009843 34
worm
(Caenorhabditis elegans)
Secernentea K10B3.6 35
  • 28 (a)
OneToMany
T05H10.7 35
  • 27 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GDE1 35 37
  • 14 (a)
OneToOne
rice
(Oryza sativa)
Liliopsida Os08g0535700 34
  • 44.78 (n)
Species where no ortholog for GPCPD1 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)
  • 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 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 GPCPD1 Gene

ENSEMBL:
Gene Tree for GPCPD1 (if available)
TreeFam:
Gene Tree for GPCPD1 (if available)

Paralogs for GPCPD1 Gene

(1) SIMAP similar genes for GPCPD1 Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for GPCPD1 Gene

genes like me logo Genes that share paralogs with GPCPD1: view

No data available for Paralogs for GPCPD1 Gene

Variants for GPCPD1 Gene

Sequence variations from dbSNP and Humsavar for GPCPD1 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs1033660 -- 5,592,714(+) CTTTA(C/G)AATAA intron-variant
rs10470056 -- 5,554,232(+) gctca(C/T)ctcgg intron-variant
rs10470067 -- 5,552,686(+) GAAGA(C/G)CGCTA intron-variant
rs1053399 -- 5,545,340(-) GCTGC(A/G)GGCTC nc-transcript-variant, utr-variant-3-prime
rs1056244 -- 5,570,388(-) GAAAA(C/G)CCATT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for GPCPD1 Gene

Variant ID Type Subtype PubMed ID
nsv585330 CNV gain 21841781
nsv585329 CNV loss 21841781
nsv585328 CNV loss 21841781
nsv1138915 CNV deletion 24896259
nsv1071345 CNV deletion 25765185
nsv1066860 CNV gain 25217958
esv5676 CNV loss 19470904
esv3556775 CNV deletion 23714750
esv3077124 CNV deletion 24192839
esv2762059 CNV gain 21179565
esv2722141 CNV deletion 23290073
esv2678474 CNV deletion 23128226
dgv4242n100 CNV gain 25217958
dgv4241n100 CNV gain 25217958

Variation tolerance for GPCPD1 Gene

Residual Variation Intolerance Score: 35.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.55; 77.86% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GPCPD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GPCPD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GPCPD1 Gene

Disorders for GPCPD1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for GPCPD1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
specific developmental disorder
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for GPCPD1

Genetic Association Database (GAD)
GPCPD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GPCPD1
genes like me logo Genes that share disorders with GPCPD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GPCPD1 Gene

Publications for GPCPD1 Gene

  1. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T. … Ohara O. (DNA Res. 2000) 2 3 4 64
  2. Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans. (PMID: 22343285) Bakken T.E. … Carlson H. (Proc. Natl. Acad. Sci. U.S.A. 2012) 3 46 64
  3. A novel glycerophosphodiester phosphodiesterase, GDE5, controls skeletal muscle development via a non-enzymatic mechanism. (PMID: 20576599) Okazaki Y. … Yanaka N. (J. Biol. Chem. 2010) 2 3 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. 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

Products for GPCPD1 Gene

Sources for GPCPD1 Gene

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