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

TDRD3 Gene

protein-coding   GIFtS: 49
GCID: GC13P060970

tudor domain containing 3

 Explore 2 diseases affiliated with
TDRD3 via our new
 Human Malady Compendium 
Biological research products
for TDRD3
    

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

Aliases
Tudor Domain Containing 31 2
FLJ210071
Tudor Domain-Containing Protein 32

External Ids:    HGNC: 206121   Entrez Gene: 815502   Ensembl: ENSG000000835447   OMIM: 6143925   UniProtKB: Q9H7E23   

Export aliases for TDRD3 gene to outside databases

Previous GC identifers: GC13P054966 GC13P059907 GC13P058768 GC13P058769 GC13P059868 GC13P041662


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

UniProtKB/Swiss-Prot: TDRD3_HUMAN, Q9H7E2
Function: Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus,
acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with
transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In
cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of
translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins

Gene Wiki entry for TDRD3


(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_000013.10  NC_018924.1  NT_024524.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TDRD3 gene promoter:
         TBP   Sox5   AP-4   NF-kappaB   Evi-1   MEF-2A   SRY   HFH-1   aMEF-2   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTDRD3 promoter sequence
   Search SABiosciences Chromatin IP Primers for TDRD3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TDRD3


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

Entrez Gene cytogenetic band: 13q21.2   Ensembl cytogenetic band:  13q21.2   HGNC cytogenetic band: 13q14.3

TDRD3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TDRD3 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P060970:  view genomic region     (about GC identifiers)

Start:
60,970,591 bp from pter      End:
61,148,013 bp from pter
Size:
177,423 bases      Orientation:
plus strand

(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: TDRD3_HUMAN, Q9H7E2 (See protein sequence)
Recommended Name: Tudor domain-containing protein 3  
Size: 651 amino acids; 73185 Da
Subunit: Component of mRNA stress granules. Interacts with FMR1, FXR1, FXR2, EWSR1, FUS, SERBP1, EEF1A1 and DDX3X or
DDX3Y, and with the small nuclear ribonucleoprotein-associated proteins SNRPB and SNRPN. Interacts with
'Lys-48'-linked tetra-ubiquitin, but not with monoubiquitin or 'Lys-63'-linked ubiquitin chains
Subcellular location: Cytoplasm. Nucleus. Note=Predominantly cytoplasmic. Associated with actively translating
polyribosomes and with mRNA stress granules
5 PDB 3D structures from and Proteopedia for TDRD3:
1WJI (3D)        2LTO (3D)        3PMT (3D)        3PNW (3D)        3S6W (3D)    
Secondary accessions: B2MWP9 Q53XA6 Q6P992
Alternative splicing: 3 isoforms:  Q9H7E2-1   Q9H7E2-2   Q9H7E2-3   

Explore the universe of human proteins at neXtProt for TDRD3: NX_Q9H7E2

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H7E2

  • TDRD3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001139542.1  NP_001139543.1  NP_110421.1  

    ENSEMBL proteins: 
     ENSP00000432703   ENSP00000367113   ENSP00000367126   ENSP00000367114   ENSP00000440190  
     ENSP00000196169  

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    Uscn Proteins for TDRD3

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005737cytoplasm IEA--


    TDRD3 for ontologies           About GeneDecksing



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

    TDRD3 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR000449 UBA/transl_elong_EF1B_N
     IPR015940 UBA/transl_elong_EF1B_N_euk
     IPR002999 Tudor
     IPR009060 UBA-like

    Graphical View of Domain Structure for InterPro Entry Q9H7E2

    ProtoNet protein and cluster: Q9H7E2

    1 Blocks protein family: IPB008191 Maternal tudor protein

    UniProtKB/Swiss-Prot: TDRD3_HUMAN, Q9H7E2
    Domain: The Tudor domain specifically recognizes and binds asymmetric dimethylation of histone H3 'Arg-17' (H3R17me2a)
    and histones H4 'Arg-3', 2 tags for epigenetic transcriptional activation
    Similarity: Contains 1 Tudor domain
    Similarity: Contains 1 UBA domain


    (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

    Function Summary:

         UniProtKB/Swiss-Prot: TDRD3_HUMAN, Q9H7E2
    Function: Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus,
    acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with
    transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In
    cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of
    translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins

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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003682chromatin binding IDA--
    GO:0003713transcription coactivator activity IDA--
    GO:0035064methylated histone residue binding IDA--


    TDRD3 for ontologies           About GeneDecksing


    2 GenomeRNAi human phenotypes for TDRD3:
     Decreased number of cells in m  Increased cell death in HCC-19 


    (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 TDRD3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 11)

    5/11 Interacting proteins for TDRD3 (Q9H7E23 ENSP000001961694) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST3H3Q166953, ENSP000003556574I2D: score=1 STRING: ENSP00000355657
    FMR1ENSP000003595064STRING: ENSP00000359506
    FUSENSP000002541084STRING: ENSP00000254108
    FXR1ENSP000003501704STRING: ENSP00000350170
    FXR2ENSP000002501134STRING: ENSP00000250113
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016568chromatin modification IEA--


    TDRD3 for ontologies           About GeneDecksing



    (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
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TDRD3
    Search CenterWatch for drugs/clinical trials and news about TDRD3 

    (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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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for TDRD3 gene (3 alternative transcripts): 
    NM_001146070.1  NM_001146071.1  NM_030794.2  

    Unigene Cluster for TDRD3:

    Tudor domain containing 3
    Hs.525061  [show with all ESTs]
    Unigene Representative Sequence: NM_001146071
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000484389 ENST00000377881 ENST00000377894 ENST00000377882 ENST00000463109
    ENST00000471710 ENST00000535286(uc010aeg.3 uc001vib.4) ENST00000196169(uc010aef.2 uc001vhz.4 uc001via.3)


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    Additional cDNA sequence: 

    AK023578.1 AK024660.1 BC020604.1 BC030514.1 BC060876.1 BX537910.1 EU643838.1 

    14 DOTS entries:

    DT.100736815  DT.120775377  DT.116068  DT.97843170  DT.92453974  DT.97843173  DT.100783955  DT.100026255 
    DT.100783957  DT.95262705  DT.95166958  DT.95219820  DT.120775370  DT.92453975 

    24/250 AceView cDNA sequences (see all 250):

    BG211535 AI373857 AA635921 AK024660 AI086727 AI342429 CB149421 NM_030794 
    BC020604 BP370193 BM700162 AA417561 AA805345 BM699010 AI394194 BC030514 
    BU737450 BM669837 AI037896 AA136563 AA953993 AA668599 BU727273 BQ439903 

    GeneLoc Exon Structure

    5/8 Alternative Splicing Database (ASD) splice patterns (SP) for TDRD3 (see all 8)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18
    SP1:        -     -                             -                                                           -     -     -               
    SP2:                                            -                                                           -     -     -               
    SP3:                                            -                                                           -     -     -               
    SP4:                                                                                                                                    
    SP5:                                                                                                                                    


    ECgene alternative splicing isoforms for TDRD3

    (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

    TDRD3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGAGGAAGAA

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

    About this image
    See TDRD3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TDRD3

    SOURCE GeneReport for Unigene cluster: Hs.525061

    UniProtKB/Swiss-Prot: TDRD3_HUMAN, Q9H7E2
    Tissue specificity: Detected in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas

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    In Situ
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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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for TDRD3 gene from 9/22 species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tdrd31 , 5 tudor domain containing 31, 5 85.6(n)1
    85.06(a)1
      14 (44.17 cM)5
    2192491  NM_172605.31  NP_766193.31 
     874166395 
    chicken
    (Gallus gallus)
    Aves TDRD31 tudor domain containing 3 77(n)
    76.59(a)
      418823  NM_001030822.1  NP_001025993.1 
    lizard
    (Anolis carolinensis)
    Reptilia TDRD36
    --
    74(a)
    1 ↔ 1
    3(75747851-75809219)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.80872 Xenopus laevis transcribed sequence with weak similarity more 80.23(n)    BJ057467.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.168282 Danio rerio cDNA clone IMAGE5604109, partial cds 74.07(n)    BC055609.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG134721 CG13472 46.43(n)
    38.68(a)
      39612  NM_140467.2  NP_648724.1 
    worm
    (Caenorhabditis elegans)
    Secernentea Y50D4C.31 Protein Y50D4C.3 43.08(n)
    30.82(a)
      178599  NM_070957.2  NP_503358.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G199506
    uncharacterized protein
    21(a)
    1 ↔ 1
    5(6740777-6743773)
    rice
    (Oryza sativa)
    Liliopsida --
    expressed protein
    20(a)
    1 ↔ 1
    1(4058510-4062190)


    ENSEMBL Gene Tree for TDRD3 (if available)
    TreeFam Gene Tree for TDRD3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    10/2584 NCBI SNPs in TDRD3 are shown (see all 2584    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1409883261,2
    C,Fother61102603(+) TCCTCG/AAAATG 6 /Q /R mis12Minor allele frequency- A:0.00NA EU 5791
    rs80022391,2
    C,F,A,--60968740(+) gaggcG/Cgaggt 2 -- us2k14Minor allele frequency- C:0.50NA CSA 8
    rs1503922571,2
    --60968884(+) ATGTGC/TCTGCG 2 -- us2k10--------
    rs1382210171,2
    --60968903(+) TTTAAC/TTTGCT 2 -- us2k10--------
    rs1491553941,2
    --60969019(+) TTGTAG/TGATAT 2 -- us2k10--------
    rs95281281,2
    C,F,A,H,--60969094(+) CAACCT/CAGACA 2 -- us2k126Minor allele frequency- C:0.40NS EA NA CSA WA 2764
    rs732080481,2
    C,F,--60969158(+) GCTTGG/CTTAAA 2 -- us2k11Minor allele frequency- C:0.12NA 120
    rs113673061,2
    C--60969295(+) AGTGA-/TTTTTT 2 -- us2k1 trp30--------
    rs1999244221,2
    C--60969354(+) GGCTTG/TAAACT 2 -- us2k10--------
    rs1909577291,2
    --60969486(+) CATTTG/TTTCTA 3 -- us2k10--------

    HapMap Linkage Disequilibrium report for TDRD3 (60970591 - 61148013 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for TDRD3
         1 CNV: 71726

    SABiosciences Cancer Mutation 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.)
    About This Section

    TDRD3 for disorders           About GeneDecksing

    OMIM gene information: 614392    OMIM disorders: --

    2 diseases for TDRD3:    About MalaCards
    sertoli cell-only syndrome    fragile x syndrome

    1 disease from the University of Copenhagen DISEASES database for TDRD3:
    Sertoli cell-only syndrome

    Export disorders for TDRD3 gene to outside databases

    (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 TDRD3 gene, integrated from 9 sources (see all 21):
    (articles sorted by number of sources associating them with TDRD3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. TDRD3 is an effector molecule for arginine-methylated histone marks. (PubMed id 21172665)1, 2 Yang Y.... Bedford M.T. (2010)
    2. Tdrd3 is a novel stress granule-associated protein interacting with the Fragile-X syndrome protein FMRP. (PubMed id 18664458)1, 2 Linder B.... Fischer U. (2008)
    3. TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules. (PubMed id 18632687)1, 2 Goulet I.... Cote J. (2008)
    4. 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)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. Crystal structure of TDRD3 and methyl-arginine binding characterization of TDRD3, SMN and SPF30. (PubMed id 22363433)1 Liu K....Min J. (2012)
    7. Genetic variants associated with breast size also infl uence breast cancer risk. (PubMed id 22747683)1 Eriksson N....Tung J.Y. (2012)
    8. Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. (PubMed id 22267201)1 Stolk L....Lunetta K.L. (2012)
    9. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (2009)
    10. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 81550 HGNC: 20612 AceView: TDRD3 Ensembl:ENSG00000083544 euGenes: HUgn81550
    ECgene: TDRD3 H-InvDB: TDRD3

    (According to HUGE)
    About This Section
      --

    (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 TDRD3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for TDRD3 gene:
    Search GeneIP for patents involving TDRD3

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



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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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