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    CCDC116 coiled-coil domain containing 116 [ Homo sapiens (human) ]

    Gene ID: 164592, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CCDC116provided by HGNC
    Official Full Name
    coiled-coil domain containing 116provided by HGNC
    Primary source
    HGNC:HGNC:26688
    See related
    Ensembl:ENSG00000161180 AllianceGenome:HGNC:26688
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Located in centrosome. Implicated in lung cancer. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 8.7) See more
    Orthologs
    mouse all
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    Genomic context

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    See CCDC116 in Genome Data Viewer
    Location:
    22q11.21
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (21632760..21637329)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (22046244..22050813)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (21987049..21991618)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene RIMS binding protein 3C Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21908512-21908665 Neighboring gene Sharpr-MPRA regulatory region 10827 Neighboring gene ubiquitin conjugating enzyme E2 L3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21914232-21914792 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21920997-21921184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18698 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13509 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21945023-21945836 Neighboring gene VISTA enhancer hs2026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:21977501-21978034 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21979673-21979941 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21982145-21982752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13510 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:21986781-21987280 Neighboring gene YdjC chitooligosaccharide deacetylase homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13512 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr22:22006055-22006725 Neighboring gene stromal cell derived factor 2 like 1 Neighboring gene uncharacterized LOC107985532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:22006726-22007397 Neighboring gene microRNA 301b

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. A cis-eQTL genetic variant of the cancer-testis gene CCDC116 is associated with risk of multiple cancers. Qin N, et al. Hum Genet, 2017 Aug. PMID 28653172
    2. Expression of the coiled coil domain containing protein 116 in the pancreatic islets and endocrine pancreatic tumors. Tsolakis AV, et al. Islets, 2012 Sep-Oct. PMID 23072936, Free PMC Article
    3. Proteomic analysis of mammalian sperm cells identifies new components of the centrosome. Firat-Karalar EN, et al. J Cell Sci, 2014 Oct 1. PMID 25074808, Free PMC Article
    4. Insulin-dependent interactions of proteins with GLUT4 revealed through stable isotope labeling by amino acids in cell culture (SILAC). Foster LJ, et al. J Proteome Res, 2006 Jan. PMID 16396496
    5. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Jostins L, et al. Nature, 2012 Nov 1. PMID 23128233, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Our results suggest that a slight change in CCDC116 expression in normal tissues can confer risk to corresponding cancers.
      Title: A cis-eQTL genetic variant of the cancer-testis gene CCDC116 is associated with risk of multiple cancers.
    2. The CCDC116 protein is expressed in all islet cell types except the glucagon and ghrelin cells.
      Title: Expression of the coiled coil domain containing protein 116 in the pancreatic islets and endocrine pancreatic tumors.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ36046

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 116

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001331066.2 → NP_001317995.1  coiled-coil domain-containing protein 116 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK302030, AP000553
      Consensus CDS
      CCDS87008.1
      UniProtKB/Swiss-Prot
      Q8IYX3
      Related
      ENSP00000476296.1, ENST00000607942.5

    2. NM_152612.3 → NP_689825.2  coiled-coil domain-containing protein 116 isoform 1

      See identical proteins and their annotated locations for NP_689825.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AP000553, BC033499
      Consensus CDS
      CCDS13791.1
      UniProtKB/Swiss-Prot
      B7Z7H5, Q8IYX3, Q8N9Y9
      Related
      ENSP00000292779.3, ENST00000292779.4
      Conserved Domains (1) summary
      pfam15774
      Location:18 → 401
      DUF4702; Domain of unknown function (DUF4702)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      21632760..21637329
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441169.1 → XP_047297125.1  coiled-coil domain-containing protein 116 isoform X2

    2. XM_006724159.3 → XP_006724222.1  coiled-coil domain-containing protein 116 isoform X1

      Conserved Domains (1) summary
      pfam15774
      Location:84 → 467
      DUF4702; Domain of unknown function (DUF4702)

    3. XM_011529985.2 → XP_011528287.1  coiled-coil domain-containing protein 116 isoform X4

      Conserved Domains (1) summary
      pfam15774
      Location:84 → 287
      DUF4702; Domain of unknown function (DUF4702)

    4. XM_011529984.3 → XP_011528286.1  coiled-coil domain-containing protein 116 isoform X3

      Conserved Domains (1) summary
      pfam15774
      Location:1 → 366
      DUF4702; Domain of unknown function (DUF4702)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      22046244..22050813
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325194.1 → XP_054181169.1  coiled-coil domain-containing protein 116 isoform X2

    2. XM_054325193.1 → XP_054181168.1  coiled-coil domain-containing protein 116 isoform X1

    3. XM_054325195.1 → XP_054181170.1  coiled-coil domain-containing protein 116 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IYX3.3 GenPept UniProtKB/Swiss-Prot:Q8IYX3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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