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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
    mouse all
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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

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

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