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CCDC116 Gene

protein-coding   GIFtS: 42
GCID: GC22P021987

Coiled-Coil Domain Containing 116

  Search for CCDC116
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Coiled-Coil Domain Containing 1161 2
Coiled-Coil Domain-Containing Protein 1162

External Ids:    HGNC: 266881   Entrez Gene: 1645922   Ensembl: ENSG000001611807   UniProtKB: Q8IYX33   

Export aliases for CCDC116 gene to outside databases

Previous GC identifers: GC22P020317 GC22P004944


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for CCDC116 Gene:
CCDC116 (coiled-coil domain containing 116) is a protein-coding gene.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000022.10  NT_011520.13  NC_018933.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CCDC116 gene promoter:
         AML1a   Pax-5   Brachyury   E47   YY1   GATA-1   CREB   MEF-2A   deltaCREB   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC116 promoter sequence
   Search Chromatin IP Primers for CCDC116

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC116


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

Entrez Gene cytogenetic band: 22q11.21   Ensembl cytogenetic band:  22q11.21   HGNC cytogenetic band: 22q11.21

CCDC116 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC116 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P021987:  view genomic region     (about GC identifiers)

Start:
21,987,005 bp from pter      End:
21,991,616 bp from pter
Size:
4,612 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CC116_HUMAN, Q8IYX3 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 116  
Size: 515 amino acids; 56940 Da
Secondary accessions: Q8N9Y9
Alternative splicing: 2 isoforms:  Q8IYX3-1   Q8IYX3-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CCDC116: NX_Q8IYX3

Explore proteomics data for CCDC116 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See CCDC116 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689825.2  
    ENSEMBL proteins: 
     ENSP00000476296   ENSP00000401637   ENSP00000292779  

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    Search eBioscience for ELISAs for CCDC116 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    ProtoNet protein and cluster: Q8IYX3


    (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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CCDC116
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol1

    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CCDC116
    Interactions:

        Search GeneGlobe Interaction Network for CCDC116

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

    Selected Interacting proteins for CCDC116 (Q8IYX33 ENSP000002927794) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCDC85BQ158343, ENSP000003116954I2D: score=3 STRING: ENSP00000311695
    KRTAP4-12Q9BQ663, ENSP000003775824I2D: score=3 STRING: ENSP00000377582
    MDFIQ997503, ENSP000002303214I2D: score=3 STRING: ENSP00000230321
    SLC2A4P146723I2D: score=3 
    CEP44Q9C0F13I2D: score=1 
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CCDC116 (CC116)



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CCDC116 gene: 
    NM_152612.2  

    Unigene Cluster for CCDC116:

    Coiled-coil domain containing 116
    Hs.131615  [show with all ESTs]
    Unigene Representative Sequence: NM_152612
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000607942 ENST00000425975 ENST00000292779(uc011aih.1 uc002zve.3)

    miRNA
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    1 qRT-PCR Assays for microRNA that regulate CCDC116:
    hsa-miR-922
    SwitchGear 3'UTR luciferase reporter plasmidCCDC116 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat CCDC116
      QuantiFast Probe-based Assays in human, mouse, rat CCDC116

    Additional mRNA sequence: 

    AK302030.1 BC033499.1 

    3 DOTS entries:

    DT.100019822  DT.40296004  DT.100742855 

    15 AceView cDNA sequences:

    AI216430 CD557807 BI831230 NM_152612 BC033499 AI025315 BM553010 BM560353 
    BU585082 AI285916 AA745185 BI831251 BI831297 AX748079 AK093365 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for CCDC116    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5
    SP1:              -     -                                 
    SP2:              -                                       
    SP3:                                                      


    ECgene alternative splicing isoforms for CCDC116

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CCDC116 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GACAATGAGG
    CCDC116 Expression
    About this image

    CCDC116 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CCDC116 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.131615
        Custom PCR Arrays for CCDC116
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC116

    (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)
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    This gene was present in the common ancestor of human and mouse.

    Orthologs for CCDC116 gene from Selected species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc1161 , 5 coiled-coil domain containing 1161, 5 74.9(n)1
    69.77(a)1
      16 (10.62 cM)5
    768721  NM_001164606.11  NP_001158078.11 
     171390645 


    ENSEMBL Gene Tree for CCDC116 (if available)
    TreeFam Gene Tree for CCDC116 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CCDC116 gene
    1 SIMAP similar gene for CCDC116 using alignment to 2 protein entries:     CC116_HUMAN (see all proteins):
    FLJ36046

    Find genes that share paralogs with CCDC116           About GenesLikeMe



    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CCDC116 (see all 210)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1465078101,2
    Cuntested121990989(+) GTCCTC/TGGAGA 2 S L mis10--------
    rs57544791,2
    C--21986346(+) cactgC/Aactcc 1 -- us2k11Minor allele frequency- A:0.00EA 180
    rs1113866711,2
    C,F--21986361(+) TGGGCG/AACTGA 1 -- us2k11Minor allele frequency- A:0.50WA 2
    rs1427802011,2
    --21986436(+) TACTGA/GGTGTG 1 -- us2k10--------
    rs1474106461,2
    --21986589(+) AGAGCC/TGGCAC 1 -- us2k10--------
    rs1397297961,2
    --21986703(+) GGCTGC/TGCAGC 1 -- us2k10--------
    rs793196661,2
    F--21986711(+) AGCAAC/GCAAGG 1 -- us2k11Minor allele frequency- G:0.03WA 118
    rs1452871291,2
    --21986784(+) TCGGGA/GCAGGA 1 -- us2k10--------
    rs2010687111,2
    --21986823(+) GTGGT-/GGGGTG 1 -- us2k10--------
    rs8618551,2
    C,F,H--21986827(-) CCCCCA/CCCCAC 1 -- us2k111Minor allele frequency- C:0.17NS EA CSA 1633

    HapMap Linkage Disequilibrium report for CCDC116 (21987005 - 21991616 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for CCDC116:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv4882n71CNV Loss21882294
    nsv516806CNV Loss19592680
    nsv914458CNV Loss21882294
    nsv914469CNV Loss21882294
    dgv4881n71CNV Loss21882294
    nsv7350OTHER Inversion18451855

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for CCDC116

    (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.)
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      --

    (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)
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    PubMed articles for CCDC116 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with CCDC116)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    4. Expression of the coiled coil domain containing protein 116 in the pancreatic islets and endocrine pancreatic tumors. (PubMed id 23072936)1 Tsolakis A.V....Islam M.S. (Islets 2012)
    5. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. (PubMed id 23128233)1 Jostins L....Cho J.H. (Nature 2012)
    6. Insulin-dependent interactions of proteins with GLUT4 revealed through stable isotope labeling by amino acids in cell culture (SILAC). (PubMed id 16396496)1 Foster L.J....Klip A. (J. Proteome Res. 2006)
    7. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 164592 HGNC: 26688 AceView: FLJ36046 Ensembl:ENSG00000161180 euGenes: HUgn164592
    ECgene: CCDC116 H-InvDB: CCDC116

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for CCDC116 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CCDC116 gene:
    Search GeneIP for patents involving CCDC116

    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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