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

Gene ID: 164592, updated on 10-Dec-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, Dec 2024]
Expression
Restricted expression toward testis (RPKM 8.7) See more
Orthologs
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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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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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