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

CCDC60 Gene

protein-coding   GIFtS: 43
GCID: GC12P119772

Coiled-Coil Domain Containing 60

  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 601 2
Coiled-Coil Domain-Containing Protein 602

External Ids:    HGNC: 286101   Entrez Gene: 1607772   Ensembl: ENSG000001832737   UniProtKB: Q8IWA63   

Export aliases for CCDC60 gene to outside databases

Previous GC identifers: GC12P118238 GC12P116780


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

GeneCards Summary for CCDC60 Gene: 
CCDC60 (coiled-coil domain containing 60) is a protein-coding gene. Diseases associated with CCDC60 include schizophrenia.


(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_000012.11  NT_009775.17  NC_018923.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CCDC60 gene promoter:
         Max1   Tal-1   STAT5A   LCR-F1   Tal-1beta   Evi-1   E47   HOXA5   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC60 promoter sequence
   Search SABiosciences Chromatin IP Primers for CCDC60

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CCDC60


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

Entrez Gene cytogenetic band: 12q24.23   Ensembl cytogenetic band:  12q24.23   HGNC cytogenetic band: 12q24.23

CCDC60 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC60 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P119772:  view genomic region     (about GC identifiers)

Start:
119,772,517 bp from pter      End:
119,978,852 bp from pter
Size:
206,336 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: CCD60_HUMAN, Q8IWA6 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 60  
Size: 550 amino acids; 63091 Da

Explore the universe of human proteins at neXtProt for CCDC60: NX_Q8IWA6

Explore proteomics data for CCDC60 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8IWA6

  • CCDC60 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CCDC60 Protein Expression
    REFSEQ proteins: NP_848594.2  
    ENSEMBL proteins: 
     ENSP00000445505   ENSP00000333374   ENSP00000443403  

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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: Q8IWA6


    (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:
         3 GenomeRNAi human phenotypes for CCDC60:
     Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for CCDC60 
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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 CCDC60

    (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 CCDC60 (CCD60)

    Search CenterWatch for drugs/clinical trials and news about CCDC60 / CCD60

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    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 CCDC60 gene: 
    NM_178499.3  

    Unigene Cluster for CCDC60:

    Coiled-coil domain containing 60
    Hs.98188  [show with all ESTs]
    Unigene Representative Sequence: NM_178499
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000536742 ENST00000327554(uc001txe.3) ENST00000539847 ENST00000546345
    ENST00000535685
    miRNA
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    hsa-miR-1207-3p
    SwitchGear 3'UTR luciferase reporter plasmidCCDC60 3' UTR sequence
    Inhib. RNA
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                         Customized lentivirus expression plasmids for stable overexpression of CCDC60 
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CCDC60

    Additional mRNA sequence: 

    AK310830.1 BC040553.1 

    4 DOTS entries:

    DT.97812399  DT.97803780  DT.75161415  DT.75173171 

    21 AceView cDNA sequences:

    BM705484 AA609446 BM716910 AI420337 BC040553 BM724702 BX098931 BU741364 
    BU685305 AW515677 AW450165 AI810814 BE550336 NM_178499 BM724243 BI603877 
    BU679505 BU738493 AI810534 AW015976 BF847507 

    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

    CCDC60 expression in normal human tissues (normalized intensities)      CCDC60 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GATGCTCTTT
    CCDC60 Expression
    About this image


    CCDC60 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/3 selected tissues (see all 3) fully expand
     
     Epithelium (Respiratory System)    fully expand to see all 2 entries
             bronchial epithelial cells   
     
     Pancreas (Endocrine System)
             Posterior foregut-like cells ( A scalable, suspension protocol for derivation of...
     
     Blood (Hematopoietic System)
             Hematopoietic Stem Cells Hematopoietic Bone Marrow

    See CCDC60 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CCDC60

    SOURCE GeneReport for Unigene cluster: Hs.98188
        SABiosciences Custom PCR Arrays for CCDC60
    Primer
    Products:
    OriGene qSTAR qPCR primer pairs in human, mouse for CCDC60
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC60

    (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 CCDC60 gene from 3/8 species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc601 , 5 coiled-coil domain containing 601, 5 77.84(n)1
    78.28(a)1
      5 (56.12 cM)5
    2696931  NM_177759.31  NP_808427.11 
     1161246415 
    chicken
    (Gallus gallus)
    Aves CCDC606
    Uncharacterized protein
    31(a)
    1 ↔ 1
    15(9672623-9717861)
    lizard
    (Anolis carolinensis)
    Reptilia CCDC606
    Uncharacterized protein
    36(a)
    1 ↔ 1
    GL343338.1(488655-497152)


    ENSEMBL Gene Tree for CCDC60 (if available)
    TreeFam Gene Tree for CCDC60 (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, 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

    10/3987 SNPs in CCDC60 are shown (see all 3987)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs681047611,2
    C--116789642(+) CAAAC-/TA    
       
    /TATA
    TATAT
    1 -- int11NA 2
    rs601001651,2
    C--116823250(+) AAAAA-/A/A   
       AAAAA
    GAAAA
    1 -- int11NA 2
    rs1915940291,2
    --119770603(+) GAAGCC/TGGAGA 1 -- us2k10--------
    rs1143744691,2
    F--119770652(+) TTTAGG/ACAATG 1 -- us2k11Minor allele frequency- A:0.01WA 118
    rs1837355071,2
    --119770678(+) CTTTCA/GGGCAC 1 -- us2k10--------
    rs1116525961,2
    F--119770708(+) GCTAGG/ATATTT 1 -- us2k12Minor allele frequency- A:0.04CSA WA 120
    rs1167312221,2
    F--119770742(+) GCAGTA/GGATGC 1 -- us2k11Minor allele frequency- G:0.01WA 118
    rs1490813461,2
    --119770958(+) CGGGAA/GGCGGA 1 -- us2k10--------
    rs1431463751,2
    --119770961(+) GAGGCA/GGAGGT 1 -- us2k10--------
    rs110647501,2
    C,F,A--119770977(+) TGAGCT/CGAGAT 1 -- us2k13Minor allele frequency- C:0.33NA 6

    HapMap Linkage Disequilibrium report for CCDC60 (119772517 - 119978852 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for CCDC60:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2127888CNV Deletion18987734
    esv3817CNV Deletion18987735
    esv2674874CNV Deletion23128226
    esv2746459CNV Deletion23290073
    dgv318e199CNV Deletion23128226
    nsv899552CNV Loss21882294
    nsv832529CNV Loss17160897
    esv7481CNV Loss19470904
    nsv832528CNV Gain17160897
    nsv899553CNV Gain21882294

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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 CCDC60:    About MalaCards
    schizophrenia    


    CCDC60 for disorders           About GeneDecksing

    Genetic Association Database (GAD): CCDC60
    Human Genome Epidemiology (HuGE) Navigator: CCDC60 (1 document)

    Export disorders for CCDC60 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 CCDC60 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with CCDC60)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A genome-wide association study in 574 schizophrenia trios using DNA pooling. (PubMed id 18332876)1, 4 Kirov G....O'Donovan M.C. (2008)
    2. Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study. (PubMed id 17903295)1, 4 Lunetta K.L....Murabito J.M. (2007)
    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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    5. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    6. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. (PubMed id 17463248)4 Scott L.J....Boehnke M. (2007)
    7. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    8. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (2006)
    9. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)

    (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: 160777 HGNC: 28610 AceView: MGC39827 Ensembl:ENSG00000183273 euGenes: HUgn160777
    ECgene: CCDC60 H-InvDB: CCDC60

    (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 CCDC60 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 CCDC60 gene:
    Search GeneIP for patents involving CCDC60

    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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