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    Ccdc40 coiled-coil domain containing 40 [ Mus musculus (house mouse) ]

    Gene ID: 207607, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Ccdc40provided by MGI
    Official Full Name
    coiled-coil domain containing 40provided by MGI
    Primary source
    MGI:MGI:2443893
    See related
    Ensembl:ENSMUSG00000039963 AllianceGenome:MGI:2443893
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    B930008I02Rik
    Summary
    Involved in epithelial cilium movement involved in determination of left/right asymmetry; lung development; and protein localization to cilium. Acts upstream of or within axoneme assembly and determination of left/right symmetry. Located in cilium and cytoplasm. Is active in motile cilium. Is expressed in several structures, including central nervous system; node; olfactory epithelium; and respiratory system. Human ortholog(s) of this gene implicated in primary ciliary dyskinesia 15. Orthologous to human CCDC40 (coiled-coil domain 40 molecular ruler complex subunit). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in testis adult (RPKM 14.7), CNS E11.5 (RPKM 3.1) and 5 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ccdc40 in Genome Data Viewer
    Location:
    11 E2; 11 83.35 cM
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (119119328..119156074)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (119228490..119265248)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene TBC1 domain family, member 16 Neighboring gene STARR-seq mESC enhancer starr_31313 Neighboring gene predicted gene 11753 Neighboring gene predicted gene, 36111 Neighboring gene STARR-seq mESC enhancer starr_31314 Neighboring gene predicted gene, 35932 Neighboring gene predicted gene, 46303 Neighboring gene STARR-positive B cell enhancer mm9_chr11:119129170-119129471 Neighboring gene glucosidase, alpha, acid Neighboring gene predicted gene, 39483 Neighboring gene STARR-positive B cell enhancer ABC_E7111 Neighboring gene eukaryotic translation initiation factor 4A3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. The coiled-coil domain containing protein CCDC40 is essential for motile cilia function and left-right axis formation. Becker-Heck A, et al. Nat Genet, 2011 Jan. PMID 21131974, Free PMC Article
    2. Loss-of-Function GAS8 Mutations Cause Primary Ciliary Dyskinesia and Disrupt the Nexin-Dynein Regulatory Complex. Olbrich H, et al. Am J Hum Genet, 2015 Oct 1. PMID 26387594, Free PMC Article
    3. Mechanism for generation of left isomerism in Ccdc40 mutant embryos. Sugrue KF, et al. PLoS One, 2017. PMID 28182636, Free PMC Article
    4. Repurposing of the multiciliation gene regulatory network in fate specification of Cajal-Retzius neurons. Moreau MX, et al. Dev Cell, 2023 Aug 7. PMID 37321213
    5. Choroid plexuses carry nodal-like cilia that undergo axoneme regression from early adult stage. Ho KH, et al. Dev Cell, 2023 Dec 4. PMID 37890489

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A model to explain how left isomerism arises in a proportion of Ccdc40lnks mutants is proposed.
      Title: Mechanism for generation of left isomerism in Ccdc40 mutant embryos.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Chemically induced (ENU) (1)  1 citation
    • Endonuclease-mediated (3) 

    General gene information

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    Homology

    Clone Names

    • MGC109697

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in axonemal dynein complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axonemal dynein complex assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in axoneme assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within axoneme assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cilium movement IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cilium movement ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in determination of digestive tract left/right asymmetry ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within determination of left/right symmetry IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in determination of liver left/right asymmetry ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in determination of pancreatic left/right asymmetry ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in epithelial cilium movement involved in determination of left/right asymmetry IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in epithelial cilium movement involved in determination of left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in epithelial cilium movement involved in determination of left/right asymmetry ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in epithelial cilium movement involved in extracellular fluid movement ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within flagellated sperm motility ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in heart looping IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in heart looping ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within inner dynein arm assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lung development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lung development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within motile cilium assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to cilium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of cilium beat frequency ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cilium beat frequency ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in axoneme ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cilium ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in motile cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 40

    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_001364767.2 → NP_001351696.1  coiled-coil domain-containing protein 40 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL672140
      Consensus CDS
      CCDS88294.1
      UniProtKB/TrEMBL
      A0A494BAF9
      Related
      ENSMUSP00000158069.2, ENSMUST00000236813.2
      Conserved Domains (3) summary
      PHA03169
      Location:2 → 146
      PHA03169; hypothetical protein; Provisional
      pfam08647
      Location:900 → 998
      BRE1; BRE1 E3 ubiquitin ligase
      cl25732
      Location:418 → 1257
      SMC_N; RecF/RecN/SMC N terminal domain

    2. NM_001408391.1 → NP_001395320.1  coiled-coil domain-containing protein 40 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL672140

    3. NM_001408393.1 → NP_001395322.1  coiled-coil domain-containing protein 40 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL672140
      UniProtKB/Swiss-Prot
      A2AFL0, Q5U4C0, Q8BI59, Q8BI79

    4. NM_001408394.1 → NP_001395323.1  coiled-coil domain-containing protein 40 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL672140
      UniProtKB/TrEMBL
      Q8BI54
      Related
      ENSMUST00000126652.2

    5. NM_001408395.1 → NP_001395324.1  coiled-coil domain-containing protein 40 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL672140

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      119119328..119156074
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006532698.4 → XP_006532761.1  coiled-coil domain-containing protein 40 isoform X1

      Conserved Domains (3) summary
      PHA03169
      Location:5 → 147
      PHA03169; hypothetical protein; Provisional
      COG1196
      Location:419 → 1258
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam08647
      Location:901 → 999
      BRE1; BRE1 E3 ubiquitin ligase

    2. XM_030245744.1 → XP_030101604.1  coiled-coil domain-containing protein 40 isoform X2

      Conserved Domains (3) summary
      COG1196
      Location:44 → 395
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02169
      Location:294 → 575
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
      pfam08647
      Location:275 → 373
      BRE1; BRE1 E3 ubiquitin ligase

    RNA

    1. XR_388387.4 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_175430.4: Suppressed sequence

      Description
      NM_175430.4: This RefSeq was removed because currently there is insufficient support for the transcript and protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BI79.1 GenPept UniProtKB/Swiss-Prot:Q8BI79

    Gene LinkOut

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

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