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

CCDC50 Gene

protein-coding   GIFtS: 48
GCID: GC03P191046

coiled-coil domain containing 50

(Previous names: deafness, autosomal dominant 44 )
(Previous symbols: C3orf6, DFNA44)
 Explore 11 diseases affiliated with
CCDC50 via our new
 Human Malady Compendium 
Biological research products
for CCDC50
    

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

Aliases
Coiled-Coil Domain Containing 501 2     Ymer1
C3orf61 2 3 5     Deafness, Autosomal Dominant 441
DFNA441 2 5     YMER2
Protein Ymer2 3     Coiled-Coil Domain-Containing Protein 502

External Ids:    HGNC: 181111   Entrez Gene: 1521372   Ensembl: ENSG000001524927   OMIM: 6110515   UniProtKB: Q8IVM03   

Export aliases for CCDC50 gene to outside databases

Previous GC identifers: GC03P192530 GC03P188446


(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 CCDC50:
This gene encodes a soluble, cytoplasmic, tyrosine-phosphorylated protein with multiple ubiquitin-interacting domains.
Mutations in this gene cause nonsyndromic, postlingual, progressive sensorineural DFNA44 hearing loss. In mouse, the
protein is expressed in the inner ear during development and postnatal maturation and associates with
microtubule-based structures. This protein may also function as a negative regulator of NF-kB signaling and as an
effector of epidermal growth factor (EGF)-mediated cell signaling. Alternative splicing results in multiple transcript
variants encoding distinct isoforms. (provided by RefSeq, Oct 2008)

UniProtKB/Swiss-Prot: CCD50_HUMAN, Q8IVM0
Function: Involved in EGFR signaling

Gene Wiki entry for CCDC50


(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_000003.11  NC_018914.1  NT_005612.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CCDC50 gene promoter:
         c-Fos   LHX3b/Lhx3b   AP-1   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   RORalpha2   Evi-1   LHX3a/Lhx3a   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC50 promoter sequence
   Search SABiosciences Chromatin IP Primers for CCDC50

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CCDC50


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

Entrez Gene cytogenetic band: 3q28   Ensembl cytogenetic band:  3q28   HGNC cytogenetic band: 3q28

CCDC50 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC50 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P191046:  view genomic region     (about GC identifiers)

Start:
191,046,866 bp from pter      End:
191,116,459 bp from pter
Size:
69,594 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: CCD50_HUMAN, Q8IVM0 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 50  
Size: 306 amino acids; 35822 Da
Subcellular location: Cytoplasm. Note=Associated with microtubules of the cytoskeleton and mitotic apparatus (By
similarity)
Miscellaneous: Found in a critical region of hereditary spastic paraplegia (HSP) SPG14 locus. No causative CCDC50
mutations were found in HSP families
Secondary accessions: Q86VH7
Alternative splicing: 2 isoforms:  Q8IVM0-1   Q8IVM0-2   (Major isoform)

Explore the universe of human proteins at neXtProt for CCDC50: NX_Q8IVM0

Post-translational modifications:

  • Phosphorylated on tyrosine residues1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8IVM0

  • CCDC50 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_777568.1  NP_848018.1  

    ENSEMBL proteins: 
     ENSP00000376249   ENSP00000376250  

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    Uscn Proteins for CCDC50

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IDA--


    CCDC50 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

    ProtoNet protein and cluster: Q8IVM0


    (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: CCD50_HUMAN, Q8IVM0
    Function: Involved in EGFR signaling

    miRNA
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    hsa-miR-548j hsa-miR-106a hsa-miR-1245 hsa-miR-605 hsa-miR-519a hsa-miR-502-3p hsa-miR-93 hsa-miR-548a-5p
    SwitchGear 3'UTR luciferase reporter plasmidCCDC50 3' UTR sequence
    Inhib. RNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI18029035


    CCDC50 for ontologies           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 CCDC50

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    5/58 Interacting proteins for CCDC50 (Q8IVM01, 2, 3 ENSP000003762504) via UniProtKB, MINT, STRING, and/or I2D (see all 58)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    OTUD7BQ6GQQ91, 3, ENSP000003581314EBI-723996,EBI-527784 I2D: score=1 STRING: ENSP00000358131
    UBBP0CG471, 3, ENSP000003046974EBI-723996,EBI-413034 I2D: score=1 STRING: ENSP00000304697
    RIPK1Q135461, 3, ENSP000002598084EBI-723996,EBI-358507 I2D: score=3 STRING: ENSP00000259808
    RPS3AP612472, 3, ENSP000003460504MINT-64849 I2D: score=3 STRING: ENSP00000346050
    UBCP0CG483, ENSP000003448184I2D: score=2 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 CCDC50
    Search CenterWatch for drugs/clinical trials and news about CCDC50 / CCD50 

    (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 CCDC50 gene (2 alternative transcripts): 
    NM_174908.3  NM_178335.2  

    Unigene Cluster for CCDC50:

    Coiled-coil domain containing 50
    Hs.478682  [show with all ESTs]
    Unigene Representative Sequence: NM_178335
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000392455(uc003fsv.3 uc003fsw.3) ENST00000392456 ENST00000460064


    miRNA
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    8/80 QIAGEN miScript miRNA Assays for microRNAs that regulate CCDC50 (see all 80):
    hsa-miR-548j hsa-miR-106a hsa-miR-1245 hsa-miR-605 hsa-miR-519a hsa-miR-502-3p hsa-miR-93 hsa-miR-548a-5p
    SwitchGear 3'UTR luciferase reporter plasmidCCDC50 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AJ416916.2 AJ557013.1 AK055652.1 AK092045.1 AK093660.1 AL512753.1 BC065004.1 

    10 DOTS entries:

    DT.445499  DT.95080968  DT.216377  DT.100774449  DT.120881814  DT.92017035  DT.92025937  DT.100798370 
    DT.100798380  DT.91741772 

    24/330 AceView cDNA sequences (see all 330):

    AA278800 AA665991 CR618316 AA513091 AA376060 BM760943 AW150632 AW296132 
    BQ776280 BM848116 AW148472 AL512753 CA419775 CR614299 AW074000 CA390285 
    AI803500 AJ416916 AI857877 AI608839 AA771842 AW518889 BE550167 CR618301 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for CCDC50    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
    SP1:                                                                        
    SP2:                                -                                       


    ECgene alternative splicing isoforms for CCDC50

    (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

    CCDC50 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
    See CCDC50 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CCDC50

    SOURCE GeneReport for Unigene cluster: Hs.478682

    UniProtKB/Swiss-Prot: CCD50_HUMAN, Q8IVM0
    Tissue specificity: Isoform 1 and isoform 2 are coexpressed in placenta, liver, lung, kidney and pancreas. Only isoform
    1 is detected in skeletal muscle, brain and heart

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC50

    (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 CCDC50 gene from 6/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc505 coiled-coil domain containing 50   --   16 (18.98 cM) 27388869 
    chicken
    (Gallus gallus)
    Aves CCDC506
    Uncharacterized protein
    58(a)
    1 ↔ 1
    9(14748009-14783046)
    lizard
    (Anolis carolinensis)
    Reptilia CCDC506
    --
    63(a)
    1 ↔ 1
    GL343386.1(938784-963884)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.148962 Xenopus laevis transcribed sequence with weak similarity more 77.21(n)    BM004828.1 
    zebrafish
    (Danio rerio)
    Actinopterygii si:ch73-6k16.16
    CT009593.26
    --
    22(a)
    17(a)
    many → 1
    many → 1
    22(23453199-23490125)
    22(23654750-23671694)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG102836
    --
    12(a)
    1 ↔ 1
    2L(18472964-18484513)


    ENSEMBL Gene Tree for CCDC50 (if available)
    TreeFam Gene Tree for CCDC50 (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

    10/1353 NCBI SNPs in CCDC50 are shown (see all 1353    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1127633161,2
    --188445212(+) GCCTAG/ATGATT 2 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs561341511,2
    C,F,--188445391(+) TACCAC/TTTCCT 2 -- us2k15Minor allele frequency- T:0.23NA CSA WA 244
    rs1137149991,2
    C,--188445399(+) CCTTCT/GTATTC 2 -- us2k12Minor allele frequency- G:0.03NA 122
    rs98790121,2
    C,F,--188445653(+) TGCTAG/ACCTAA 2 -- us2k11Minor allele frequency- A:0.16WA 118
    rs1166103311,2
    C,F,--188446333(+) ATTCAT/CGCGAT 2 -- us2k11Minor allele frequency- C:0.02NA 120
    rs1127246491,2
    --188446442(+) GTATTT/CGGGGT 2 -- us2k13Minor allele frequency- C:0.03CSA WA 121
    rs46872101,2
    C,F,A,H,--188446482(+) ATTCCG/AGGTGC 2 -- us2k117Minor allele frequency- A:0.09EA NS NA 1972
    rs1150649061,2
    C,F,--188446589(+) CGGGAA/GAGACT 2 -- ut511Minor allele frequency- G:0.02WA 118
    rs794887111,2
    F,--188446642(+) GGATAC/GAAGGC 2 -- ut511Minor allele frequency- G:0.09WA 118
    rs561412141,2
    --188446954(+) GGCCGC/TGGCGG 2 -- ut510--------

    HapMap Linkage Disequilibrium report for CCDC50 (191046866 - 191116459 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 37 variations for CCDC50
         15/34 CNVs (see all 34): 10029 59119 23177 10031 1659 9464 51052 51058 51053 91781 3469 63689 91779 91780 51051
         3 Indels: 51055 33747 51050
    Human Gene Mutation Database (HGMD): CCDC50

    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

    CCDC50 for disorders           About GeneDecksing

    OMIM gene information: 611051   
    OMIM disorders: 607453  
    UniProtKB/Swiss-Prot: CCD50_HUMAN, Q8IVM0
  • Defects in CCDC50 are the cause of deafness autosomal dominant type 44 (DFNA44) [MIM:607453]. A form of
  • non-syndromic hearing loss. It is initially moderate and affects mainly low to mid frequencies. Later, it progresses
    to involve all the frequencies and leads to a profound hearing loss by the 6th decade. The onset of the hearing loss
    occurs in the first decade of life

    11 diseases for CCDC50:    About MalaCards
    deafness, autosomal dominant 44    hearing loss    spastic paraplegia    hereditary spastic paraplegia
    paraplegia    mantle cell lymphoma    optic atrophy    spasticity
    chronic lymphocytic leukemia    lymphocytic leukemia    leukemia

    Human Genome Epidemiology (HuGE) Navigator: CCDC50 (1 document)

    Export disorders for CCDC50 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 CCDC50 gene, integrated from 9 sources (see all 28):
    (articles sorted by number of sources associating them with CCDC50)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A mutation in CCDC50, a gene encoding an effector of epidermal growth factor-mediated cell signaling, causes progressive hearing loss. (PubMed id 17503326)1, 2, 3 Modamio-Hoeybjoer S.... Moreno-Pelayo M.A. (2007)
    2. Identification and characterization of C3orf6, a new conserved human gene mapping to chromosome 3q28. (PubMed id 14527723)1, 2, 9 Vazza G.... Mostacciuolo M.L. (2003)
    3. Suppression of the ligand-mediated down-regulation of epidermal growth factor receptor by Ymer, a novel tyrosine-phosphorylated and ubiquitinated protein. (PubMed id 16803894)1, 3 Tashiro K....Taniguchi H. (2006)
    4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    5. 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)
    6. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. (PubMed id 15314609)1, 2 Blagoev B.... Mann M. (2004)
    7. Proteome-wide identification of ubiquitylation sites b y conjugation of engineered lysine-less ubiquitin. (PubMed id 22053931)1 Oshikawa K....Nakayama K.I. (2012)
    8. Ymer acts as a multifunctional regulator in nuclear fa ctor-kB and Fas signaling pathways. (PubMed id 22331027)1 Tsukiyama T....Hatakeyama S. (2012)
    9. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    10. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (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: 152137 HGNC: 18111 AceView: C3orf6 Ensembl:ENSG00000152492 euGenes: HUgn152137
    ECgene: CCDC50 H-InvDB: CCDC50

    (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 CCDC50 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 CCDC50 gene:
    Search GeneIP for patents involving CCDC50

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



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