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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

GDPD3 Gene

protein-coding   GIFtS: 40
GCID: GC16M030116

glycerophosphodiester phosphodiesterase domain containing...
  Search for GDPD3
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Biological research products
for GDPD3    

Aliases
for GDPD3 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Glycerophosphodiester Phosphodiesterase Domain Containing 31 2
MGC41711
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


Summaries
for GDPD3 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
  --

Genomic Views
for GDPD3 gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NC_018927.1  NT_010393.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the GDPD3 gene promoter:
         CREB   ATF-2   deltaCREB   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: GDPD3 promoter sequence
   Search SABiosciences Chromatin IP Primers for GDPD3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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

Proteins
for GDPD3 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: GDPD3_HUMAN, Q7L5L3 (See protein sequence)
Recommended Name: Glycerophosphodiester phosphodiesterase domain-containing protein 3  
Size: 318 amino acids; 36596 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q7L5L3

    • GDPD3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

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

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    Uscn Proteins for GDPD3

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--


    GDPD3 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for GDPD3 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    GDPD3 for domains           About GeneDecksing

    2 InterPro domains/families:
     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 family: IPB004129 Glycerophosphoryl diester phosphodiesterase

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


    Function
    for GDPD3 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Enzyme Number (IUBMB): EC 3.1.-.-1

    miRNA
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008889glycerophosphodiester phosphodiesterase activity IEA--
    GO:0046872metal ion binding IEA--


    GDPD3 for ontologies           About GeneDecksing



    Pathways & Interactions
    for GDPD3 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for GDPD3

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

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


    GDPD3 for ontologies           About GeneDecksing



    Drugs & Compounds
    for GDPD3 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for GDPD3
    Search CenterWatch for drugs/clinical trials and news about GDPD3 

    Transcripts
    for GDPD3 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
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    About This Section
    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

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    Additional cDNA 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 

    24/477 AceView cDNA sequences (see all 477):

    H80909 BQ068059 CR596064 BI769652 CR607536 CR621688 T16143 CR621455 
    BM672391 AA359549 AY033608 AW138059 BG386083 BE700056 AI628474 BQ446853 
    NM_024307 BM707953 BM721417 BM468615 BM041252 BF115305 BI767377 BU838396 

    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

    Expression
    for GDPD3 gene

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    GDPD3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    GDPD3 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    PureStem™ mesenchymal progenitor 7PEND24 (Embryonic Progenitor Cell)Cartilage, Neural Crest
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See GDPD3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for GDPD3

    SOURCE GeneReport for Unigene cluster: Hs.289015
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    In Situ
    Assay Products:     
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    Orthologs
    for GDPD3 gene

    (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)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for GDPD3 gene from 3/15 species (see all 15)    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 81.26(n)1
    79.08(a)1    		   7 (69.25 cM)5
    686161  NM_024228.21  NP_077190.21 
     1267664145 
    zebrafish
    (Danio rerio)    		 Actinopterygii LOC5672861 glycerophosphodiester phosphodiesterase domain-containing more 55.18(n)
    49.83(a)    		   567286  XM_690578.3  XP_695670.3 
    honey bee
    (Apis mellifera)    		 Insecta --
    		 --
    		 37(a)
    		 1 → many
    		 Group3.20(59185-60750)


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

    Paralogs
    for GDPD3 gene

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

    GDPD3 for paralogs           About GeneDecksing



    Genomic Variants
    for GDPD3 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/174 NCBI SNPs in GDPD3 are shown (see all 174)     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 -- int10--------
    rs1919096431,2
    		--30115654(+) GTGAAA/TATGGC 1 -- int10--------
    rs1458313291,2
    		--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 (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for GDPD3
         3 CNVs: 4940 35383 4001

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    Disorders / Diseases
    for GDPD3 gene

    (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.)
    About This Section
    		   --

    Publications
    for GDPD3 gene

    (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)
    About This Section

    PubMed articles for GDPD3 gene integrated from 9 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. (2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Dynamics of cullin-RING ubiquitin ligase network revea led by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (2010)
    4. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)2 Martin J.... Pennacchio L.A. (2004)
    5. 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. (2002)

    External Searches for GDPD3 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing GDPD3 gene

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

    Other Databases showing GDPD3 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing GDPD3 gene

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

    Intellectual Property
    for GDPD3 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		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



    Products
    for GDPD3 gene

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    About This Section

     
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    von Willebrand factor
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