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

DDX50 Gene

protein-coding   GIFtS: 52
GCID: GC10P070661

DEAD (Asp-Glu-Ala-Asp) box polypeptide 50

 Explore 1 disease affiliated with
DDX50 via our new
 Human Malady Compendium 
Biological research products
for DDX50
    

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

Aliases
DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 501 2     Gu-Beta1
GU21 2     Malignant Cell Derived RNA Helicase2
GUB1 2     Mcdrh1
RH-II/GuB1 2     RNA Helicase II/Gu Beta2
Nucleolar Protein Gu22 3     EC 3.6.4.133
DEAD Box Protein 502 3     Gu-Beta1
MGC31991     EC 3.6.18
ATP-Dependent RNA Helicase DDX502     

External Ids:    HGNC: 179061   Entrez Gene: 790092   Ensembl: ENSG000001076257   OMIM: 6103735   UniProtKB: Q9BQ393   

Export aliases for DDX50 gene to outside databases

Previous GC identifers: GC10P070553 GC10P070005 GC10P070331 GC10P064662


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

Entrez Gene summary for DDX50:
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are
implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation
initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution
patterns, some members of this DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis,
and cellular growth and division. This gene encodes a DEAD box enzyme that may be involved in ribosomal RNA synthesis
or processing. This gene and DDX21, also called RH-II/GuA, have similar genomic structures and are in tandem
orientation on chromosome 10, suggesting that the two genes arose by gene duplication in evolution. This gene has
pseudogenes on chromosomes 2, 3 and 4. Alternative splicing of this gene generates multiple transcript variants, but
the full length nature of all the other variants but one has not been defined. (provided by RefSeq, Jul 2008)

Gene Wiki entry for DDX50


(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_000010.10  NC_018921.1  NT_030059.13  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the DDX50 gene promoter:
         HOXA9   HOXA9B   MAZR   p53   POU3F2   MEF-2A   N-Myc   aMEF-2   Meis-1a   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDDX50 promoter sequence
   Search SABiosciences Chromatin IP Primers for DDX50

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat DDX50


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

Entrez Gene cytogenetic band: 10q22.1   Ensembl cytogenetic band:  10q22.1   HGNC cytogenetic band: 10q22.2

DDX50 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DDX50 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P070661:  view genomic region     (about GC identifiers)

Start:
70,661,034 bp from pter      End:
70,706,603 bp from pter
Size:
45,570 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: DDX50_HUMAN, Q9BQ39 (See protein sequence)
Recommended Name: ATP-dependent RNA helicase DDX50  
Size: 737 amino acids; 82565 Da
Subunit: Interacts with C1QBP
Subcellular location: Nucleus, nucleolus
1 PDB 3D structure from and Proteopedia for DDX50:
2E29 (3D)    
Secondary accessions: Q5VX37 Q8WV76 Q9BWI8

Explore the universe of human proteins at neXtProt for DDX50: NX_Q9BQ39

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9BQ39

  • 4/14 DME Specific Peptides for DDX50 (Q9BQ39) (see all 14)
     GRTGRAG  LAPTREL  VGTPGRI  APTRELA 

    DDX50 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_076950.1  
    ENSEMBL proteins: 
     ENSP00000362687  

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    Uscn Proteins for DDX50

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005730nucleolus IDA--
    GO:0005886plasma membrane IDA--


    DDX50 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

    DDX50 for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR011545 DNA/RNA_helicase_DEAD/DEAH_N
     IPR014014 RNA_helicase_DEAD_Q_motif
     IPR012562 GUCT
     IPR014001 Helicase_ATP-bd
     IPR001650 Helicase_C

    Graphical View of Domain Structure for InterPro Entry Q9BQ39

    ProtoNet protein and cluster: Q9BQ39

    1 Blocks protein family: IPB012562 GUCT

    UniProtKB/Swiss-Prot: DDX50_HUMAN, Q9BQ39
    Similarity: Belongs to the DEAD box helicase family. DDX21/DDX50 subfamily
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal 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: DDX50_HUMAN, Q9BQ39
    Catalytic activity: ATP + H(2)O = ADP + phosphate

    Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.131

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    hsa-miR-4311 hsa-miR-578 hsa-miR-342-3p hsa-miR-548m hsa-miR-493* hsa-miR-518a-5p hsa-miR-1243 hsa-miR-3165
    SwitchGear 3'UTR luciferase reporter plasmidDDX50 3' UTR sequence
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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:0003723RNA binding IEA--
    GO:0005524ATP binding IEA--
    GO:0008026ATP-dependent helicase activity IEA--


    DDX50 for ontologies           About GeneDecksing


    Animal Models:
         1 MGI phenotypic allele for Ddx50 (no phenotypes)

    DDX50 for phenotypes           About GeneDecksing


    (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 DDX50

    STRING Interaction Network Preview (showing 5 interactants - click image to see 13)

    5/126 Interacting proteins for DDX50 (Q9BQ392, 3 ENSP000003626874) via UniProtKB, MINT, STRING, and/or I2D (see all 126)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ESR2Q927313, ENSP000003439254I2D: score=1 STRING: ENSP00000343925
    MED19A0JLT23, ENSP000003373404STRING: ENSP00000337340 I2D: score=1 
    SRRM2Q9UQ353, ENSP000003017404I2D: score=1 STRING: ENSP00000301740
    STAU1O957933, ENSP000003609224I2D: score=1 STRING: ENSP00000360922
    UBCP0CG482, ENSP000003448184MINT-6488791 STRING: ENSP00000344818
    About this table

    (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 DDX50
    Search CenterWatch for drugs/clinical trials and news about DDX50 

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    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 DDX50 gene: 
    NM_024045.1  

    Unigene Cluster for DDX50:

    DEAD (Asp-Glu-Ala-Asp) box polypeptide 50
    Hs.522984  [show with all ESTs]
    Unigene Representative Sequence: BC000272
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000373585(uc001jot.3 uc001jou.3) ENST00000483593 ENST00000471475
    ENST00000494889 ENST00000475535 ENST00000460470 ENST00000466265

    miRNA
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    hsa-miR-4311 hsa-miR-578 hsa-miR-342-3p hsa-miR-548m hsa-miR-493* hsa-miR-518a-5p hsa-miR-1243 hsa-miR-3165
    SwitchGear 3'UTR luciferase reporter plasmidDDX50 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AB051075.1 AF334103.1 AK223297.1 AK293577.1 AK301431.1 AL137423.1 BC000210.1 BC000272.1 
    BC014263.2 BC018637.2 

    12 DOTS entries:

    DT.100792166  DT.212281  DT.100769536  DT.99972890  DT.101966618  DT.92437423  DT.100792163  DT.92437425 
    DT.95359183  DT.121226078  DT.91649131  DT.95117151 

    24/199 AceView cDNA sequences (see all 199):

    BQ069789 BP345450 BM786121 CA436265 BI769874 BI222798 NM_024045 CK903662 
    BC000210 CF994796 AF334103 BF513490 AI567697 BG055710 CR618753 BX333581 
    BM786089 CR620490 BQ935244 BM786122 CB989252 AW328636 AI688898 BQ948049 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for DDX50    About this scheme

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


    ECgene alternative splicing isoforms for DDX50

    (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

    DDX50 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TACATTATCC

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

    About this image
    See DDX50 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for DDX50

    SOURCE GeneReport for Unigene cluster: Hs.522984
        SABiosciences Custom PCR Arrays for DDX50
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    In Situ
    Assay Products:
     

     
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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 last universal common ancestor (LUCA).

    Orthologs for DDX50 gene from 6/25 species (see all 25)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves DDX506
    Uncharacterized protein
    61(a)
    1 ↔ 1
    6(11877942-11891369)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.60152 Transcribed sequence with weak similarity to protein more 73.44(n)    142005932 
    zebrafish
    (Danio rerio)
    Actinopterygii ddx216
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 21
    48(a)
    1 → many
    13(174494-184799)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons emb11381 DEAD-box ATP-dependent RNA helicase 3 48.78(n)
    40.68(a)
      832713  NM_001036866.3  NP_001031943.1 
    rice
    (Oryza sativa)
    Liliopsida Os03g08277001 hypothetical protein 47.27(n)
    39.75(a)
      4334649  NM_001058308.1  NP_001051773.1 
    E. coli
    (Escherichia coli)
    Gamma proteobacteria dbpA6
    srmB6
    ATP-dependent RNA helicase
    28(a)
    27(a)
    possible ortholog
    possible ortholog
    Chromosome(1407535-1408908)
    Chromosome(2710918-2712252)


    ENSEMBL Gene Tree for DDX50 (if available)
    TreeFam Gene Tree for DDX50 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for DDX50 gene
    DDX212  
    6 SIMAP similar genes for DDX50 using alignment to 1 protein entry:     DDX50_HUMAN:
    DKFZp761E0323    mcdrh    DDX21    DDX54    EIF4A2    DDX47

    DDX50 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for DDX50
    PGOHUM00000240615 PGOHUM00000237825


    (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

    10/917 NCBI SNPs in DDX50 are shown (see all 917    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1825155441,2
    --70659075(+) AAAATC/GATATC 1 -- us2k10--------
    rs1407775351,2
    --70659173(+) CCCTTC/TCCATC 1 -- us2k10--------
    rs1169481571,2
    C,F,--70659242(+) TCTGTA/GGNNNN 1 -- us2k11Minor allele frequency- G:0.02NA 120
    rs1872247831,2
    C,--70659336(+) TTTTTC/TTCAGG 1 -- us2k10--------
    rs1497044201,2
    --70659342(+) TCAGGC/TCCGCT 1 -- us2k10--------
    rs1455074411,2
    --70659388(+) GTGCTC/TAGGAG 1 -- us2k10--------
    rs1402527111,2
    --70659398(+) GCTCAA/GCTTTT 1 -- us2k10--------
    rs1452161151,2
    --70659473(+) CGTGCA/GGCATT 1 -- us2k10--------
    rs780374911,2
    C,--70659659(+) TCTCCG/ATCATC 1 -- us2k11Minor allele frequency- A:0.01EA 120
    rs782757521,2
    F,--70659689(+) TGTTTC/GTAAGT 1 -- us2k11Minor allele frequency- G:0.02WA 118

    HapMap Linkage Disequilibrium report for DDX50 (70661034 - 70706603 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for DDX50
         1 CNV: 48614
         1 Indel: 100974

    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for DDX50

    (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

    DDX50 for disorders           About GeneDecksing

    OMIM gene information: 610373    OMIM disorders: --

    1 disease for DDX50:    About MalaCards
    malaria


    Export disorders for DDX50 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 DDX50 gene, integrated from 9 sources (see all 25):
    (articles sorted by number of sources associating them with DDX50)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genomic structure of newly identified paralogue of RNA helicase II/Gu: detection of pseudogenes and multiple alternatively spliced mRNAs. (PubMed id 11891046)1, 2, 3, 9 Valdez B.C.... Sequitin A.M. (2002)
    2. Solution structure of the GUCT domain from human RNA helicase II/Gu beta reveals the RRM fold, but implausible RNA interactions. (PubMed id 18615715)1, 2, 9 Ohnishi S....Yokoyama S. (2009)
    3. 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)
    4. Functional proteomic analysis of human nucleolus. (PubMed id 12429849)1, 2 Scherl A.... Diaz J.-J. (2002)
    5. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (2012)
    6. Interactome study suggests multiple cellular functions of hepatoma-derived growth factor (HDGF). (PubMed id 21907836)1 Zhao J....Yang P. (2011)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    8. Splicing factor 2-associated protein p32 participates in ribosome biogenesis by regulating the binding of Nop52 and fibrillarin to pre ribosome particles. (PubMed id 21536856)2 Yoshikawa H....Takahashi N. (2011)
    9. Integrative analysis of the ubiquitin proteome isolat ed using Tandem Ubiquitin Binding Entities (TUBEs). (PubMed id 22178446)1 Lopitz-Otsoa F....Rodriguez M.S. (2011)
    10. Proliferating cell nuclear antigen (PCNA)-associated KIAA0101/PAF15 protein is a cell cycle-regulated anaphase-promoting complex/cyc losome substrate. (PubMed id 21628590)1 Emanuele M.J....Elledge S.J. (2011)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 79009 HGNC: 17906 AceView: DDX50 Ensembl:ENSG00000107625 euGenes: HUgn79009
    ECgene: DDX50 H-InvDB: DDX50

    (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 DDX50 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 DDX50 gene:
    Search GeneIP for patents involving DDX50

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



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