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Aliases for CCDC39 Gene

Aliases for CCDC39 Gene

  • Coiled-Coil Domain Containing 39 2 3 5
  • Coiled-Coil Domain-Containing Protein 39 3
  • CILD14 3
  • FAP59 3

External Ids for CCDC39 Gene

Previous GeneCards Identifiers for CCDC39 Gene

  • GC03M181815
  • GC03M180320
  • GC03M177736

Summaries for CCDC39 Gene

Entrez Gene Summary for CCDC39 Gene

  • The protein encoded by this gene is involved in the motility of cilia and flagella. The encoded protein is essential for the assembly of dynein regulatory and inner dynein arm complexes, which regulate ciliary beat. Defects in this gene are a cause of primary ciliary dyskinesia type 14 (CILD14). [provided by RefSeq, Jul 2011]

GeneCards Summary for CCDC39 Gene

CCDC39 (Coiled-Coil Domain Containing 39) is a Protein Coding gene. Diseases associated with CCDC39 include Ciliary Dyskinesia, Primary, 14 and Primary Ciliary Dyskinesia. GO annotations related to this gene include nucleotide binding.

UniProtKB/Swiss-Prot for CCDC39 Gene

  • Required for assembly of dynein regulatory complex (DRC) and inner dynein arm (IDA) complexes, which are responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella (PubMed:21131972). Probably acts together with CCDC40 to form a molecular ruler that determines the 96 nanometer (nm) repeat length and arrangements of components in cilia and flagella (By similarity). Not required for outer dynein arm complexes assembly (PubMed:21131972).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CCDC39 Gene

Genomics for CCDC39 Gene

Regulatory Elements for CCDC39 Gene

Enhancers for CCDC39 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F180718 1.7 VISTA 10.6 +151.6 151601 1.5 MAFF MAFK CCDC39-AS1 CCDC39 LOC647253 RN7SL229P
GH03F180870 0.7 ENCODE 8.2 -0.4 -437 2.6 CBX3 ZNF680 L3MBTL2 MAX UBTF ZNF316 NFE2 EMSY E2F6 MGA CCDC39 LOC647253 RPL32P10
GH03F180910 1.1 ENCODE 4.1 -41.8 -41764 3.8 HDGF PKNOX1 WRNIP1 SIN3A ARID4B DMAP1 ZNF48 YY1 GLIS2 ZNF143 DNAJC19 LOC647253 CCDC39 RPL32P10 GC03P180962
GH03F180708 0.4 ENCODE 10.8 +162.9 162878 0.2 MAFK CCDC39-AS1 CCDC39 RN7SL229P
GH03F180706 0.4 FANTOM5 10.8 +164.8 164776 0.3 NR2F2 CCDC39-AS1 CCDC39 RN7SL229P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CCDC39 on UCSC Golden Path with GeneCards custom track

Promoters for CCDC39 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001486597 804 800 CBX3 ZNF680 L3MBTL2 UBTF E2F6 MGA

Genomic Location for CCDC39 Gene

Chromosome:
3
Start:
180,602,858 bp from pter
End:
180,871,005 bp from pter
Size:
268,148 bases
Orientation:
Minus strand

Genomic View for CCDC39 Gene

Genes around CCDC39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCDC39 Gene

Proteins for CCDC39 Gene

  • Protein details for CCDC39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UFE4-CCD39_HUMAN
    Recommended name:
    Coiled-coil domain-containing protein 39
    Protein Accession:
    Q9UFE4
    Secondary Accessions:
    • B4E2H1

    Protein attributes for CCDC39 Gene

    Size:
    941 amino acids
    Molecular mass:
    109901 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CCDC39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CCDC39 Gene

Post-translational modifications for CCDC39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CCDC39 Gene

No data available for DME Specific Peptides for CCDC39 Gene

Domains & Families for CCDC39 Gene

Protein Domains for CCDC39 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CCDC39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UFE4

UniProtKB/Swiss-Prot:

CCD39_HUMAN :
  • Belongs to the CCDC39 family.
Family:
  • Belongs to the CCDC39 family.
genes like me logo Genes that share domains with CCDC39: view

No data available for Gene Families for CCDC39 Gene

Function for CCDC39 Gene

Molecular function for CCDC39 Gene

UniProtKB/Swiss-Prot Function:
Required for assembly of dynein regulatory complex (DRC) and inner dynein arm (IDA) complexes, which are responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella (PubMed:21131972). Probably acts together with CCDC40 to form a molecular ruler that determines the 96 nanometer (nm) repeat length and arrangements of components in cilia and flagella (By similarity). Not required for outer dynein arm complexes assembly (PubMed:21131972).
genes like me logo Genes that share phenotypes with CCDC39: view

Human Phenotype Ontology for CCDC39 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CCDC39 Gene

MGI Knock Outs for CCDC39:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for CCDC39 Gene

Localization for CCDC39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCDC39 Gene

Cytoplasm, cytoskeleton, cilium axoneme. Note=CCDC40 is required for localization to axonemes. {ECO:0000269 PubMed:21131974}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CCDC39 gene
Compartment Confidence
cytoskeleton 5
nucleus 3
cytosol 2
extracellular 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for CCDC39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA --
GO:0005929 cilium IEA --
GO:0005930 axoneme IEA,IDA 21131972
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with CCDC39: view

Pathways & Interactions for CCDC39 Gene

SuperPathways for CCDC39 Gene

No Data Available

Interacting Proteins for CCDC39 Gene

Gene Ontology (GO) - Biological Process for CCDC39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001947 heart looping IMP 22693285
GO:0003341 cilium movement IEA,IMP 22499950
GO:0003356 regulation of cilium beat frequency IMP 23255504
GO:0007368 determination of left/right symmetry IEA --
GO:0007507 heart development IEA --
genes like me logo Genes that share ontologies with CCDC39: view

No data available for Pathways by source and SIGNOR curated interactions for CCDC39 Gene

Transcripts for CCDC39 Gene

mRNA/cDNA for CCDC39 Gene

Unigene Clusters for CCDC39 Gene

Coiled-coil domain containing 39:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC39 Gene

No ASD Table

Relevant External Links for CCDC39 Gene

GeneLoc Exon Structure for
CCDC39
ECgene alternative splicing isoforms for
CCDC39

Expression for CCDC39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CCDC39 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CCDC39 Gene

This gene is overexpressed in Stomach (60.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CCDC39 Gene



NURSA nuclear receptor signaling pathways regulating expression of CCDC39 Gene:

CCDC39

SOURCE GeneReport for Unigene cluster for CCDC39 Gene:

Hs.712820

mRNA Expression by UniProt/SwissProt for CCDC39 Gene:

Q9UFE4-CCD39_HUMAN
Tissue specificity: Mainly expressed in nasal brushings and, to a lesser extent, in lungs and testis.
genes like me logo Genes that share expression patterns with CCDC39: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for CCDC39 Gene

Orthologs for CCDC39 Gene

This gene was present in the common ancestor of animals.

Orthologs for CCDC39 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CCDC39 34 35
  • 99.57 (n)
dog
(Canis familiaris)
Mammalia CCDC39 34 35
  • 89.05 (n)
cow
(Bos Taurus)
Mammalia CCDC39 34 35
  • 89.01 (n)
rat
(Rattus norvegicus)
Mammalia Ccdc39 34
  • 80.15 (n)
mouse
(Mus musculus)
Mammalia Ccdc39 34 16 35
  • 79.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 77 (a)
OneToMany
-- 35
  • 72 (a)
OneToMany
-- 35
  • 69 (a)
OneToMany
-- 35
  • 69 (a)
OneToMany
-- 35
  • 60 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia CCDC39 35
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves CCDC39 34 35
  • 67.2 (n)
lizard
(Anolis carolinensis)
Reptilia CCDC39 35
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ccdc39 34
  • 63.24 (n)
zebrafish
(Danio rerio)
Actinopterygii ccdc39 34
  • 58.28 (n)
CCDC39 35
  • 49 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001293 34
  • 40.88 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG17387 34 35
  • 39.45 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 50 (a)
OneToOne
Species where no ortholog for CCDC39 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CCDC39 Gene

ENSEMBL:
Gene Tree for CCDC39 (if available)
TreeFam:
Gene Tree for CCDC39 (if available)

Paralogs for CCDC39 Gene

No data available for Paralogs for CCDC39 Gene

Variants for CCDC39 Gene

Sequence variations from dbSNP and Humsavar for CCDC39 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs397515392 Pathogenic 180,661,860(-) AAGAA(C/G)TATAT splice-donor-variant
rs587778820 Pathogenic 180,619,334(-) CTAGA(-/A)GAACA reference, frameshift-variant
rs587778821 Pathogenic 180,616,873(-) ACTAA(GTA/T)AAGAA intron-variant, reference, frameshift-variant
rs587778822 Pathogenic 180,651,496(-) TACAA(-/A)CAAAA reference, frameshift-variant
rs756235547 Pathogenic 180,659,582(+) CTAAC(C/T)GTCAA splice-acceptor-variant

Structural Variations from Database of Genomic Variants (DGV) for CCDC39 Gene

Variant ID Type Subtype PubMed ID
nsv509869 OTHER sequence alteration 20534489
nsv472530 CNV novel sequence insertion 20440878
esv2484281 CNV deletion 19546169
esv2244500 CNV deletion 18987734

Variation tolerance for CCDC39 Gene

Residual Variation Intolerance Score: 84.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.71; 73.14% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CCDC39 Gene

Human Gene Mutation Database (HGMD)
CCDC39
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCDC39

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCDC39 Gene

Disorders for CCDC39 Gene

MalaCards: The human disease database

(9) MalaCards diseases for CCDC39 Gene - From: OMIM, ClinVar, GeneTests, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CCD39_HUMAN
  • Ciliary dyskinesia, primary, 14 (CILD14) [MIM:613807]: A disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. {ECO:0000269 PubMed:21131972, ECO:0000269 PubMed:22693285, ECO:0000269 PubMed:23255504, ECO:0000269 PubMed:25186273}. Note=The disease is caused by mutations affecting the gene represented in this entry. The disease is characterized by primary ciliary dyskinesia with inner dynein arm (IDA) defects and axonemal dizorganisation: defects in CCDC39 and CCDC40 constitute the major cause of this phenotype. {ECO:0000269 PubMed:22693285, ECO:0000269 PubMed:23255504}.

Relevant External Links for CCDC39

Genetic Association Database (GAD)
CCDC39
Human Genome Epidemiology (HuGE) Navigator
CCDC39
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CCDC39
genes like me logo Genes that share disorders with CCDC39: view

No data available for Genatlas for CCDC39 Gene

Publications for CCDC39 Gene

  1. CCDC39 is required for assembly of inner dynein arms and the dynein regulatory complex and for normal ciliary motility in humans and dogs. (PMID: 21131972) Merveille A.C. … Amselem S. (Nat. Genet. 2011) 2 3 4 64
  2. Mutations in CCDC39 and CCDC40 are the major cause of primary ciliary dyskinesia with axonemal disorganization and absent inner dynein arms. (PMID: 23255504) Antony D. … Mitchison H.M. (Hum. Mutat. 2013) 3 4 64
  3. Delineation of CCDC39/CCDC40 mutation spectrum and associated phenotypes in primary ciliary dyskinesia. (PMID: 22693285) Blanchon S. … Amselem S. (J. Med. Genet. 2012) 3 4 64
  4. The coiled-coil domain containing protein CCDC40 is essential for motile cilia function and left-right axis formation. (PMID: 21131974) Becker-Heck A. … Burdine R.D. (Nat. Genet. 2011) 3 4 64
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64

Products for CCDC39 Gene

Sources for CCDC39 Gene

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