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

CCDC9 Gene

protein-coding   GIFtS: 44
GCID: GC19P047759

Coiled-Coil Domain Containing 9

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Coiled-Coil Domain Containing 91 2
Coiled-Coil Domain-Containing Protein 92

External Ids:    HGNC: 245601   Entrez Gene: 260932   Ensembl: ENSG000001053217   UniProtKB: Q9Y3X03   

Export aliases for CCDC9 gene to outside databases

Previous GC identifers: GC00U914334 GC19P052452 GC19P052453 GC19P044183


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

GeneCards Summary for CCDC9 Gene: 
CCDC9 (coiled-coil domain containing 9) is a protein-coding gene. Diseases associated with CCDC9 include gastric cancer. An important paralog of this gene is C15orf52.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NT_011109.16  NC_018930.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CCDC9 gene promoter:
         PPAR-gamma1   Sp1   STAT5A   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC9 promoter sequence
   Search SABiosciences Chromatin IP Primers for CCDC9

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CCDC9


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

Entrez Gene cytogenetic band: 19q13.32   Ensembl cytogenetic band:  19q13.32   HGNC cytogenetic band: 19q13.33

CCDC9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC9 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P047759:  view genomic region     (about GC identifiers)

Start:
47,759,237 bp from pter      End:
47,775,210 bp from pter
Size:
15,974 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CCDC9_HUMAN, Q9Y3X0 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 9  
Size: 531 amino acids; 59703 Da

Explore the universe of human proteins at neXtProt for CCDC9: NX_Q9Y3X0

Explore proteomics data for CCDC9 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y3X0

  • CCDC9 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CCDC9 Protein Expression
    REFSEQ proteins: NP_056418.1  
    ENSEMBL proteins: 
     ENSP00000221922   ENSP00000469717   ENSP00000470706   ENSP00000472843  

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

    ProtoNet protein and cluster: Q9Y3X0


    (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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Phenotypes:
         1 GenomeRNAi human phenotype for CCDC9:
     Decreased Hepatitis C virus re 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for CCDC9 
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section




    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CCDC9

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for CCDC9 (ENSP000002219224) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    POT1ENSP000003502494STRING: ENSP00000350249
    TERF1ENSP000002766034STRING: ENSP00000276603
    TINF2ENSP000002674154STRING: ENSP00000267415
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 CCDC9

    Search CenterWatch for drugs/clinical trials and news about CCDC9

    (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,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CCDC9 gene: 
    NM_015603.2  

    Unigene Cluster for CCDC9:

    Coiled-coil domain containing 9
    Hs.227782  [show with all ESTs]
    Unigene Representative Sequence: NM_015603
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000601154 ENST00000221922(uc010xym.2) ENST00000599398 ENST00000595659
    ENST00000596938 ENST00000600117
    miRNA
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    hsa-miR-3151 hsa-miR-3150a-3p
    SwitchGear 3'UTR luciferase reporter plasmidCCDC9 3' UTR sequence
    Inhib. RNA
    Products:
         
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    OriGene RNAi products in human, mouse, rat for CCDC9
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CCDC9
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCDC9
    Sirion Biotech Customized lentivirus for stable overexpression of CCDC9 
                         Customized lentivirus expression plasmids for stable overexpression of CCDC9 
    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CCDC9

    Additional mRNA sequence: 

    AK302153.1 AL050284.1 BC002787.2 BC009743.2 

    7 DOTS entries:

    DT.422753  DT.100748439  DT.100008073  DT.91669788  DT.92003159  DT.97813310  DT.107365 

    24/40 AceView cDNA sequences (see all 40):

    BX282055 BM737911 BE159048 NM_015603 BX432961 BI754362 BU855140 BG680123 
    BC002787 BQ434271 BF341006 BM737780 BX432962 BC009743 AA584799 BG110455 
    AL050284 AA306074 BM476311 BX406409 BQ777926 CF139548 BE159113 AW468183 

    GeneLoc Exon Structure


    (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

    CCDC9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCCGTCTCTG
    CCDC9 Expression
    About this image


    See CCDC9 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CCDC9

    SOURCE GeneReport for Unigene cluster: Hs.227782
        SABiosciences Custom PCR Arrays for CCDC9
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC9

    (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 chordates.

    Orthologs for CCDC9 gene from 4/8 species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc91 , 5 coiled-coil domain containing 91, 5 81.76(n)1
    83.43(a)1
      7 (8.78 cM)5
    2438461  NM_172297.11  NP_758501.21 
     162740425 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC96
    Uncharacterized protein
    48(a)
    1 ↔ 1
    LGf(1695052-1707583)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.188082 Transcribed sequence with weak similarity to protein more 77.98(n)    AL846991.2 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1527851 zgc:152785 60.97(n)
    67.97(a)
      550140  NM_001075106.1  NP_001068574.1 


    ENSEMBL Gene Tree for CCDC9 (if available)
    TreeFam Gene Tree for CCDC9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CCDC9 gene
    C15orf522  

    CCDC9 for paralogs           About GeneDecksing



    (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) 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

    10/500 SNPs in CCDC9 are shown (see all 500)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1491669031,2
    --47758115(+) GGCACG/TATCTT 1 -- us2k10--------
    rs72543711,2
    C--47758145(+) ctcccA/Gggttc 1 -- us2k10--------
    rs1899803381,2
    --47758166(+) CTATCC/TCAGCC 1 -- us2k10--------
    rs1392909661,2
    --47758220(+) TAAATG/TTTGTA 1 -- us2k10--------
    rs1823446531,2
    --47758320(+) CTGGGA/GTTACA 1 -- us2k10--------
    rs735705391,2
    C--47758375(+) GTAGTG/CTTGCT 1 -- us2k11Minor allele frequency- C:0.50WA 2
    rs1475451271,2
    --47758409(+) TGGCAC/TGATCT 1 -- us2k10--------
    rs1866779721,2
    --47758654(+) GCCTAC/TTTTAT 1 -- us2k10--------
    rs104231011,2
    C,F,H--47758928(+) ttctcC/Ttggct 1 -- us2k15Minor allele frequency- T:0.33NS NA WA 128
    rs1419886431,2
    C--47758974(+) CACCAC/GGCCGG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CCDC9 (47759237 - 47775210 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for CCDC9:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv912196CNV Loss21882294
    nsv833852CNV Loss17160897
    nsv912199CNV Loss21882294
    dgv3963n71CNV Loss21882294

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    2 diseases for CCDC9:    About MalaCards
    gastric cancer    


    CCDC9 for disorders           About GeneDecksing


    Export disorders for CCDC9 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 CCDC9 gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with CCDC9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2, 3 Wiemann S.... Poustka A. (2001)
    2. 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)
    3. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. (PubMed id 23084401)1 Singh G....Moore M.J. (2012)
    4. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
    5. Genome-wide YFP fluorescence complementation screen id entifies new regulators for telomere signaling in human cells. (PubMed id 21044950)1 Lee O.H....Songyang Z. (2011)
    6. Systematic analysis of human protein complexes identi fies chromosome segregation proteins. (PubMed id 20360068)1 Hutchins J.R....Peters J.M. (2010)
    7. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    8. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. (PubMed id 19413330)2 Gauci S....Mohammed S. (2009)
    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. Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. (PubMed id 18220336)2 Cantin G.T....Yates J.R. III (2008)

    (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)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 26093 HGNC: 24560 AceView: CCDC9 Ensembl:ENSG00000105321 euGenes: HUgn26093
    ECgene: CCDC9 H-InvDB: CCDC9

    (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 CCDC9 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 CCDC9 gene:
    Search GeneIP for patents involving CCDC9

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
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