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    Ccdc40 coiled-coil domain 40 molecular ruler complex subunit [ Rattus norvegicus (Norway rat) ]

    Gene ID: 287867, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Ccdc40provided by RGD
    Official Full Name
    coiled-coil domain 40 molecular ruler complex subunitprovided by RGD
    Primary source
    RGD:1592118
    See related
    EnsemblRapid:ENSRNOG00000059401 AllianceGenome:RGD:1592118
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to be involved in several processes, including axonemal dynein complex assembly; determination of left/right symmetry; and protein localization to cilium. Predicted to act upstream of or within several processes, including cilium assembly; flagellated sperm motility; and regulation of cilium beat frequency. Predicted to be located in axoneme. Predicted to be active in cytoplasm and motile cilium. 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 Testes (RPKM 21.4), Lung (RPKM 19.5) and 4 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ccdc40 in Genome Data Viewer
    Location:
    10q32.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (104985283..105025813)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (104486748..104527284)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (108055270..108393408)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102551272 Neighboring gene TBC1 domain family, member 16 Neighboring gene alpha glucosidase 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Delineation of CCDC39/CCDC40 mutation spectrum and associated phenotypes in primary ciliary dyskinesia. Blanchon S, et al. J Med Genet, 2012 Jun. PMID 22693285
    2. Mutations in CCDC39 and CCDC40 are the major cause of primary ciliary dyskinesia with axonemal disorganization and absent inner dynein arms. Antony D, et al. Hum Mutat, 2013 Mar. PMID 23255504, Free PMC Article
    3. 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
    4. 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
    5. High prevalence of respiratory ciliary dysfunction in congenital heart disease patients with heterotaxy. Nakhleh N, et al. Circulation, 2012 May 8. PMID 22499950, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in axonemal dynein complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axoneme assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within axoneme assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cilium movement ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 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 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in motile cilium ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 40
    Names
    coiled-coil domain containing 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_001134688.1 → NP_001128160.1  coiled-coil domain-containing protein 40

      See identical proteins and their annotated locations for NP_001128160.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473948
      UniProtKB/TrEMBL
      A0A0G2JUV5, A6HL74
      Related
      ENSRNOP00000095356.1, ENSRNOT00000104773.2
      Conserved Domains (2) summary
      COG1196
      Location:404 → 1249
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam08647
      Location:891 → 989
      BRE1; BRE1 E3 ubiquitin ligase

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      104985283..105025813
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039085685.2 → XP_038941613.1  coiled-coil domain-containing protein 40 isoform X1

      UniProtKB/TrEMBL
      A0A0G2JUV5, A0A0G2JXB9
      Conserved Domains (3) summary
      COG1196
      Location:405 → 1250
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      PRK10811
      Location:71 → 217
      rne; ribonuclease E; Reviewed
      pfam08647
      Location:892 → 990
      BRE1; BRE1 E3 ubiquitin ligase

    2. XM_039085686.2 → XP_038941614.1  coiled-coil domain-containing protein 40 isoform X2

      UniProtKB/TrEMBL
      A0A0G2JUV5, A0A8I6ANF0
      Related
      ENSRNOP00000069245.3, ENSRNOT00000077535.3
      Conserved Domains (3) summary
      COG1196
      Location:404 → 1249
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      PRK10811
      Location:70 → 216
      rne; ribonuclease E; Reviewed
      pfam08647
      Location:891 → 989
      BRE1; BRE1 E3 ubiquitin ligase
    Nucleotide Protein Strain
    Heading Accession and Version

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