Human Gene CCDC50 (uc003fsv.3) Description and Page Index
  Description: Homo sapiens coiled-coil domain containing 50 (CCDC50), transcript variant 2, mRNA.
RefSeq Summary (NM_178335): This gene encodes a soluble, cytoplasmic, tyrosine-phosphorylated protein with multiple ubiquitin-interacting domains. Mutations in this gene cause nonsyndromic, postlingual, progressive sensorineural DFNA44 hearing loss. In mouse, the protein is expressed in the inner ear during development and postnatal maturation and associates with microtubule-based structures. This protein may also function as a negative regulator of NF-kB signaling and as an effector of epidermal growth factor (EGF)-mediated cell signaling. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008].
Transcript (Including UTRs)
   Position: hg19 chr3:191,046,874-191,116,459 Size: 69,586 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr3:191,047,464-191,109,549 Size: 62,086 Coding Exon Count: 12 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:191,046,874-191,116,459)mRNA (may differ from genome)Protein (482 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIOMIM
PubMedStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CCDC50
CDC HuGE Published Literature: CCDC50
Positive Disease Associations: Echocardiography
Related Studies:
  1. Echocardiography
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.

-  MalaCards Disease Associations
  MalaCards Gene Search: CCDC50
Diseases sorted by gene-association score: deafness, autosomal dominant 44* (987), dfna44 nonsyndromic hearing loss and deafness* (100), autosomal dominant non-syndromic sensorineural deafness type dfna* (70), chromosome 3q29 microdeletion syndrome (17), spastic paraplegia 14, autosomal recessive (13), deafness, autosomal dominant 10 (12), deafness, autosomal dominant 13 (8), autosomal dominant nonsyndromic deafness 12 (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.43 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 613.89 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -299.20590-0.507 Picture PostScript Text
3' UTR -1826.686910-0.264 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF15295 - Coiled-coil domain-containing protein 50 N-terminus

ModBase Predicted Comparative 3D Structure on Q8IVM0-2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AJ416916 - Homo sapiens mRNA for C3orf6 protein (C3ORF6 gene), short splice variant.
AJ557013 - Homo sapiens mRNA for C3orf6 protein (C3ORF6 gene), long splice variant.
BC065004 - Homo sapiens coiled-coil domain containing 50, mRNA (cDNA clone MGC:70346 IMAGE:6049272), complete cds.
KJ895670 - Synthetic construct Homo sapiens clone ccsbBroadEn_05064 CCDC50 gene, encodes complete protein.
HQ448050 - Synthetic construct Homo sapiens clone IMAGE:100071429; CCSB012307_01 coiled-coil domain containing 50 (CCDC50) gene, encodes complete protein.
JD397964 - Sequence 378988 from Patent EP1572962.
JD485499 - Sequence 466523 from Patent EP1572962.
JD396623 - Sequence 377647 from Patent EP1572962.
JD458727 - Sequence 439751 from Patent EP1572962.
CU687992 - Synthetic construct Homo sapiens gateway clone IMAGE:100021672 5' read CCDC50 mRNA.
JD426556 - Sequence 407580 from Patent EP1572962.
JD288455 - Sequence 269479 from Patent EP1572962.
AK092045 - Homo sapiens cDNA FLJ34726 fis, clone MESAN2006022.
AX747331 - Sequence 856 from Patent EP1308459.
JD267019 - Sequence 248043 from Patent EP1572962.
JD135057 - Sequence 116081 from Patent EP1572962.
JD285520 - Sequence 266544 from Patent EP1572962.
JD522072 - Sequence 503096 from Patent EP1572962.
JD560760 - Sequence 541784 from Patent EP1572962.
JD476856 - Sequence 457880 from Patent EP1572962.
JD312065 - Sequence 293089 from Patent EP1572962.
JD346555 - Sequence 327579 from Patent EP1572962.
AK093660 - Homo sapiens cDNA FLJ36341 fis, clone THYMU2006505.
AK055652 - Homo sapiens cDNA FLJ31090 fis, clone IMR321000102.
AL512753 - Homo sapiens mRNA; cDNA DKFZp667A116 (from clone DKFZp667A116).

-  Other Names for This Gene
  Alternate Gene Symbols: C3orf6, NM_178335, NP_848018, Q8IVM0-2
UCSC ID: uc003fsv.3
RefSeq Accession: NM_178335
Protein: Q8IVM0-2, splice isoform of Q8IVM0 CCDS: CCDS33912.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CCDC50:
deafness-overview (Hereditary Hearing Loss and Deafness Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178335.2
exon count: 12CDS single in 3' UTR: no RNA size: 8949
ORF size: 1449CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3089.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.