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CCDC13 coiled-coil domain containing 13 [ Homo sapiens (human) ]

Gene ID: 152206, updated on 27-Nov-2024

Summary

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Official Symbol
CCDC13provided by HGNC
Official Full Name
coiled-coil domain containing 13provided by HGNC
Primary source
HGNC:HGNC:26358
See related
Ensembl:ENSG00000244607 AllianceGenome:HGNC:26358
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
Acts upstream of or within DNA damage response; cytoplasmic microtubule organization; and non-motile cilium assembly. Located in centriolar satellite; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in testis (RPKM 1.5), brain (RPKM 0.5) and 10 other tissues See more
Orthologs
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Genomic context

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See CCDC13 in Genome Data Viewer
Location:
3p22.1
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (42704118..42773253, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (42722128..42791300, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (42747248..42814745, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr3:42729552-42729776 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42737916-42738518 Neighboring gene kelch like family member 40 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14249 Neighboring gene hedgehog acyltransferase like Neighboring gene HHATL antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42771937-42772436 Neighboring gene Sharpr-MPRA regulatory region 2509 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42774613-42775298 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42775299-42775982 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:42777355-42778040 Neighboring gene CCDC13 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42788170-42788670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42788671-42789171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19750 Neighboring gene CCDC13 antisense RNA 2 Neighboring gene HIG1 hypoxia inducible domain family member 1A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14251 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:42847019-42847816 Neighboring gene MIX23 pseudogene 4 Neighboring gene Sharpr-MPRA regulatory region 10622 Neighboring gene atypical chemokine receptor 2 Neighboring gene uncharacterized LOC124909373 Neighboring gene Sharpr-MPRA regulatory region 4247

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
  • 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. Ccdc13 is a novel human centriolar satellite protein required for ciliogenesis and genome stability. Staples CJ, et al. J Cell Sci, 2014 Jul 1. PMID 24816561
  2. Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles. Goldstein JI, et al. Nat Commun, 2014 Sep 4. PMID 25187353, Free PMC Article
  3. Genome-wide association study of chronic periodontitis in a general German population. Teumer A, et al. J Clin Periodontol, 2013 Nov. PMID 24024966
  4. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article
  5. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
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
Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
EBI GWAS Catalog
Genome-wide association study of chronic periodontitis in a general German population.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
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

  • FLJ25467

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cytoplasmic microtubule organization IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within cytoplasmic microtubule organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in non-motile cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within non-motile cilium assembly IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
is_active_in centriolar satellite IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in centriolar satellite IDA
Inferred from Direct Assay
more info
 PubMed 
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
coiled-coil domain-containing protein 13

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_144719.4 → NP_653320.3  coiled-coil domain-containing protein 13

    See identical proteins and their annotated locations for NP_653320.3

    Status: VALIDATED

    Source sequence(s)
    AC006059, AK058196, BC036050, BM664398
    Consensus CDS
    CCDS2705.1
    UniProtKB/Swiss-Prot
    Q8IYE1
    UniProtKB/TrEMBL
    A0A3B3IRZ5
    Related
    ENSP00000309836.6, ENST00000310232.11
    Conserved Domains (2) summary
    COG1196
    Location:76 → 444
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    TIGR02168
    Location:316 → 612
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    42704118..42773253 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533418.3 → XP_011531720.1  coiled-coil domain-containing protein 13 isoform X2

    UniProtKB/TrEMBL
    A0A3B3IRZ5
    Conserved Domains (1) summary
    COG1196
    Location:76 → 444
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

  2. XM_005264898.4 → XP_005264955.1  coiled-coil domain-containing protein 13 isoform X1

    UniProtKB/TrEMBL
    A0A3B3IRZ5
    Conserved Domains (1) summary
    COG1196
    Location:76 → 444
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

  3. XM_017005781.2 → XP_016861270.1  coiled-coil domain-containing protein 13 isoform X3

    Conserved Domains (1) summary
    TIGR02168
    Location:4 → 234
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  4. XM_011533419.3 → XP_011531721.1  coiled-coil domain-containing protein 13 isoform X3

    Conserved Domains (1) summary
    TIGR02168
    Location:4 → 234
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  5. XM_005264899.5 → XP_005264956.1  coiled-coil domain-containing protein 13 isoform X6

    Conserved Domains (1) summary
    COG1196
    Location:76 → 444
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

  6. XM_011533420.2 → XP_011531722.1  coiled-coil domain-containing protein 13 isoform X4

    Conserved Domains (1) summary
    COG1196
    Location:76 → 444
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

  7. XM_011533421.3 → XP_011531723.1  coiled-coil domain-containing protein 13 isoform X5

    Conserved Domains (1) summary
    COG1196
    Location:76 → 444
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

RNA

  1. XR_940385.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    42722128..42791300 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345389.1 → XP_054201364.1  coiled-coil domain-containing protein 13 isoform X2

  2. XM_054345388.1 → XP_054201363.1  coiled-coil domain-containing protein 13 isoform X1

  3. XM_054345391.1 → XP_054201366.1  coiled-coil domain-containing protein 13 isoform X3

  4. XM_054345390.1 → XP_054201365.1  coiled-coil domain-containing protein 13 isoform X3

  5. XM_054345394.1 → XP_054201369.1  coiled-coil domain-containing protein 13 isoform X6

  6. XM_054345392.1 → XP_054201367.1  coiled-coil domain-containing protein 13 isoform X4

  7. XM_054345393.1 → XP_054201368.1  coiled-coil domain-containing protein 13 isoform X5

RNA

  1. XR_008486665.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IYE1.2 GenPept UniProtKB/Swiss-Prot:Q8IYE1

Gene LinkOut

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