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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
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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

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