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GDPD3 Gene

protein-coding   GIFtS: 42
GCID: GC16M030116

Glycerophosphodiester Phosphodiesterase Domain Containing...

  Search for GDPD3
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Glycerophosphodiester Phosphodiesterase Domain Containing 31 2
Glycerophosphodiester Phosphodiesterase Domain-Containing Protein 32
EC 3.1.-.-3

External Ids:    HGNC: 286381   Entrez Gene: 791532   Ensembl: ENSG000001028867   UniProtKB: Q7L5L33   

Export aliases for GDPD3 gene to outside databases

Previous GC identifers: GC16M030024 GC16M027777


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for GDPD3 Gene:
GDPD3 (glycerophosphodiester phosphodiesterase domain containing 3) is a protein-coding gene. GO annotations related to this gene include glycerophosphodiester phosphodiesterase activity. An important paralog of this gene is GDPD1.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000016.10  NT_187260.1  NC_018927.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the GDPD3 gene promoter:
         CREB   ATF-2   deltaCREB   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidGDPD3 promoter sequence
   Search Chromatin IP Primers for GDPD3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat GDPD3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p11.2   Ensembl cytogenetic band:  16p11.2   HGNC cytogenetic band: 16p11.2

GDPD3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
GDPD3 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M030116:  view genomic region     (about GC identifiers)

Start:
30,116,131 bp from pter      End:
30,125,177 bp from pter
Size:
9,047 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: GDPD3_HUMAN, Q7L5L3 (See protein sequence)
Recommended Name: Glycerophosphodiester phosphodiesterase domain-containing protein 3  
Size: 318 amino acids; 36596 Da
Sequence caution: Sequence=AAH02714.2; Type=Erroneous initiation;
Secondary accessions: Q9H652
Alternative splicing: 2 isoforms:  Q7L5L3-2   Q7L5L3-1   

Explore the universe of human proteins at neXtProt for GDPD3: NX_Q7L5L3

Explore proteomics data for GDPD3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See GDPD3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_077283.2  
    ENSEMBL proteins: 
     ENSP00000384363   ENSP00000455508   ENSP00000454472  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR004129 GlyceroP-diester-Pdiesterase
     IPR017946 PLC-like_Pdiesterase_TIM-brl

    Graphical View of Domain Structure for InterPro Entry Q7L5L3

    ProtoNet protein and cluster: Q7L5L3

    1 Blocks protein domain: IPB004129 Glycerophosphoryl diester phosphodiesterase

    UniProtKB/Swiss-Prot: GDPD3_HUMAN, Q7L5L3
    Similarity: Belongs to the glycerophosphoryl diester phosphodiesterase family
    Similarity: Contains 1 GP-PDE domain


    Find genes that share domains with GDPD3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Enzyme Number (IUBMB): EC 3.1.-.-1

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008081phosphoric diester hydrolase activity ----
    GO:0008889glycerophosphodiester phosphodiesterase activity IEA--
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with GDPD3           About GenesLikeMe


    Animal Models:
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    GDPD3_HUMAN, Q7L5L3: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular2
    mitochondrion2
    cytosol1
    golgi apparatus1
    lysosome1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--
    GO:0070062extracellular vesicular exosome IDA19056867

    Find genes that share ontologies with GDPD3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for GDPD3
    Interactions:

        Search GeneGlobe Interaction Network for GDPD3

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006071glycerol metabolic process IEA--
    GO:0006629lipid metabolic process IEA--

    Find genes that share ontologies with GDPD3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for GDPD3



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for GDPD3 gene: 
    NM_024307.2  

    Unigene Cluster for GDPD3:

    Glycerophosphodiester phosphodiesterase domain containing 3
    Hs.289015  [show with all ESTs]
    Unigene Representative Sequence: AK026256
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000565704 ENST00000360688(uc002dwq.3) ENST00000406256(uc002dwp.3)
    ENST00000566434 ENST00000566613
    miRNA
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    Additional mRNA sequence: 

    AK026256.1 AK225450.1 BC002714.2 Z36775.1 

    9 DOTS entries:

    DT.212967  DT.100815233  DT.91932345  DT.95365223  DT.100775463  DT.91667947  DT.120696421  DT.120697739 
    DT.421428 

    Selected AceView cDNA sequences (see all 477):

    BM784739 CR621688 BF685468 BU740487 BI829198 CA397310 AL516647 AY033608 
    CR600245 AI968273 AL515713 BI769652 CA405450 BQ890149 BQ030332 AA357613 
    BQ446853 BQ639471 BQ066864 BF115305 BQ653432 BQ935076 BU608224 CD672252 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for GDPD3    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b · 10c
    SP1:                    -                                                               
    SP2:                                                                                    
    SP3:                                                                                    
    SP4:                                                              -                     


    ECgene alternative splicing isoforms for GDPD3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    GDPD3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    GDPD3 Expression
    About this image


    GDPD3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Epiblast (Early Embryonic Tissues)    fully expand to see all 2 entries
             Epiblast Stem Cell line 5
     
     Blood (Hematopoietic System)
             Granulocytes Peripheral Blood
     
     Epidermis (Integumentary System)
     
     Esophagus (Gastrointestinal Tract)
    GDPD3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    GDPD3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.289015
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for GDPD3 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Gdpd31 , 5 glycerophosphodiester phosphodiesterase domain containing more1, 5 81.49(n)1
    78.93(a)1
      7 (69.25 cM)5
    686161  NM_024228.21  NP_077190.21 
     1267664145 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1001251071 uncharacterized LOC100125107 56.32(n)
    50.33(a)
      100125107  NM_001103015.1  NP_001096485.1 
    zebrafish
    (Danio rerio)
    Actinopterygii gdpd3b1 glycerophosphodiester phosphodiesterase domain containing more 55.18(n)
    49.83(a)
      567286  XM_690578.4  XP_695670.3 


    ENSEMBL Gene Tree for GDPD3 (if available)
    TreeFam Gene Tree for GDPD3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for GDPD3 gene
    GDPD12  
    1 SIMAP similar gene for GDPD3 using alignment to 3 protein entries:     GDPD3_HUMAN (see all proteins):
    GDPD1

    Find genes that share paralogs with GDPD3           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for GDPD3 (see all 256)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs803133291,2
    C--30115644(+) GTTCC-/ATCTTCAG 1 -- cds10--------
    rs1919096431,2
    --30115654(+) GTGAAA/TATGGC 1 -- int10--------
    rs1458313291,2
    C--30115734(+) AATGGC/TGGGGG 1 -- int10--------
    rs617578611,2
    C,F--30115795(-) TTCTCG/AGGCTG 1 -- int12Minor allele frequency- A:0.02NS 94
    rs1876095201,2
    --30115820(+) CAAGAC/TATGGA 1 -- int10--------
    rs617578601,2
    C,F--30115982(-) CCTGCC/TACACC 1 -- int13Minor allele frequency- T:0.03NS NA 214
    rs1998166231,2
    --30116256(+) TAATCC/TGTTAT 2 T syn10--------
    rs1426905571,2
    C,F--30116257(+) AATCCG/ATTATG 2 /T /M mis11Minor allele frequency- A:0.00NA 4550
    rs1464365291,2
    C,F--30116302(+) AATCCG/AACTCT 2 /S /L mis11Minor allele frequency- A:0.00NA 4490
    rs1489749841,2
    C--30116306(+) CGACTC/TTTCAT 2 K E mis11Minor allele frequency- T:0.00NA 4478

    HapMap Linkage Disequilibrium report for GDPD3 (30116131 - 30125177 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for GDPD3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv833187CNV Loss17160897
    dgv2668n71CNV Loss21882294
    nsv905720CNV Loss21882294
    dgv846e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for GDPD3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with GDPD3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)
    4. Large-scale proteomics and phosphoproteomics of urinary exosomes. (PubMed id 19056867)1 Gonzales P.A....Knepper M.A. (J. Am. Soc. Nephrol. 2009)
    5. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)2 Martin J.... Pennacchio L.A. (Nature 2004)
    6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    7. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. (PubMed id 8125298)1 Maruyama K. and Sugano S. (Gene 1994)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 79153 HGNC: 28638 AceView: MAPK3andMGC4171 Ensembl:ENSG00000102886 euGenes: HUgn79153
    ECgene: GDPD3 H-InvDB: GDPD3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for GDPD3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for GDPD3 gene:
    Search GeneIP for patents involving GDPD3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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