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    CCDC42 coiled-coil domain containing 42 [ Homo sapiens (human) ]

    Gene ID: 146849, updated on 11-Apr-2024

    Summary

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    Official Symbol
    CCDC42provided by HGNC
    Official Full Name
    coiled-coil domain containing 42provided by HGNC
    Primary source
    HGNC:HGNC:26528
    See related
    Ensembl:ENSG00000161973 AllianceGenome:HGNC:26528
    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
    Also known as
    CCDC42A
    Summary
    Predicted to be involved in spermatid development. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Restricted expression toward testis (RPKM 43.4) See more
    Orthologs
    mouse all
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    Genomic context

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    See CCDC42 in Genome Data Viewer
    Location:
    17p13.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (8729935..8744836, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (8636013..8650898, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (8633253..8648154, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene myosin heavy chain 10 Neighboring gene ribosomal protein S26 pseudogene 53 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11699 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:8532416-8533194 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:8533195-8533972 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:8533973-8534750 Neighboring gene Sharpr-MPRA regulatory region 9864 Neighboring gene uncharacterized LOC105371525 Neighboring gene VISTA enhancer hs2548 Neighboring gene Sharpr-MPRA regulatory region 493 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:8599868-8600378 Neighboring gene uncharacterized LOC105371526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:8642150-8642650 Neighboring gene uncharacterized LOC105371529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11701 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8186 Neighboring gene uncharacterized LOC105371530 Neighboring gene uncharacterized LOC124903918 Neighboring gene speedy/RINGO cell cycle regulator family member E4

    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. Human ORFeome version 1.1: a platform for reverse proteomics. Rual JF, et al. Genome Res, 2004 Oct. PMID 15489335, Free PMC Article
    2. Transcriptional repressor ZBTB1 promotes chromatin remodeling and translesion DNA synthesis. Kim H, et al. Mol Cell, 2014 Apr 10. PMID 24657165, Free PMC Article
    3. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Yachie N, et al. Mol Syst Biol, 2016 Apr 22. PMID 27107012, Free PMC Article
    4. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Fragoza R, et al. Nat Commun, 2019 Sep 12. PMID 31515488, Free PMC Article
    5. Towards a proteome-scale map of the human protein-protein interaction network. Rual JF, et al. Nature, 2005 Oct 20. PMID 16189514

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ32734

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in acrosome assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in centrosome cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cilium assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatid development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermatid development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in centrosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in manchette ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in sperm connecting piece ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in sperm principal piece ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 42
    Names
    coiled-coil domain-containing protein 42A

    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_001158261.2 → NP_001151733.1  coiled-coil domain-containing protein 42 isoform 2

      See identical proteins and their annotated locations for NP_001151733.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the coding region compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
      Source sequence(s)
      AI204372, AK057296, BC029224
      Consensus CDS
      CCDS54088.1
      UniProtKB/Swiss-Prot
      Q96M95
      Related
      ENSP00000444359.2, ENST00000539522.2
      Conserved Domains (1) summary
      pfam13863
      Location:44 → 162
      DUF4200; Domain of unknown function (DUF4200)

    2. NM_144681.3 → NP_653282.2  coiled-coil domain-containing protein 42 isoform 1

      See identical proteins and their annotated locations for NP_653282.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK057296, CV030241
      Consensus CDS
      CCDS11145.1
      UniProtKB/Swiss-Prot
      Q8N6Q0, Q96M95
      Related
      ENSP00000293845.3, ENST00000293845.8
      Conserved Domains (1) summary
      pfam13863
      Location:44 → 162
      DUF4200; Domain of unknown function (DUF4200)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      8729935..8744836 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      8636013..8650898 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96M95.2 GenPept UniProtKB/Swiss-Prot:Q96M95

    Gene LinkOut

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

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