U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 207607, updated on 21-Apr-2024

Summary

Go to the top of the page Help
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 containing 40). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis adult (RPKM 14.7), CNS E11.5 (RPKM 3.1) and 5 other tissues See more
Orthologs
human all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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. A conditional knockout resource for the genome-wide study of mouse gene function. Skarnes WC, et al. Nature, 2011 Jun 15. PMID 21677750, Free PMC Article
  5. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. Diez-Roux G, et al. PLoS Biol, 2011 Jan 18. PMID 21267068, Free PMC Article

See all (14) 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

Go to the top of the page Help

Alleles

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

General gene information

Go to the top of the page Help

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 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
  
Component Evidence Code Pubs
located_in axoneme ISO
Inferred from Sequence Orthology
more info
  
located_in cell projection IEA
Inferred from Electronic Annotation
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 
is_active_in motile cilium IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
coiled-coil domain-containing protein 40

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous