Human Gene CCDC66 (uc003dhy.3)
  Description: Homo sapiens coiled-coil domain containing 66 (CCDC66), transcript variant 3, non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr3:56,591,184-56,655,848 Size: 64,665 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr3:56,627,543-56,655,646 Size: 28,104 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:56,591,184-56,655,848)mRNA (may differ from genome)Protein (584 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsH-INV
HGNCHPRDLynxMalacardsMGIneXtProt
PubMedTreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: CCD66_HUMAN
DESCRIPTION: RecName: Full=Coiled-coil domain-containing protein 66;
SEQUENCE CAUTION: Sequence=AAH47509.1; Type=Erroneous initiation; Sequence=AAI32828.2; Type=Erroneous initiation; Sequence=BAC04607.1; Type=Frameshift; Positions=214;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CCDC66
CDC HuGE Published Literature: CCDC66
Positive Disease Associations: Hip
Related Studies:
  1. Hip
    Douglas P Kiel et al. BMC medical genetics 2007, Genome-wide association with bone mass and geometry in the Framingham Heart Study., BMC medical genetics. [PubMed 17903296]
    The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.

-  MalaCards Disease Associations
  MalaCards Gene Search: CCDC66
Diseases sorted by gene-association score: leber congenital amaurosis 9 (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 9.12 RPKM in Testis
Total median expression: 192.16 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 -268.631160-0.232 Picture PostScript Text
3' UTR -26.40202-0.131 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:
PF15236 - Coiled-coil domain-containing protein 66

ModBase Predicted Comparative 3D Structure on A2RUB6
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0046548 retinal rod cell development
GO:0050908 detection of light stimulus involved in visual perception
GO:0060060 post-embryonic retina morphogenesis in camera-type eye


-  Descriptions from all associated GenBank mRNAs
  BC047509 - Homo sapiens coiled-coil domain containing 66, mRNA (cDNA clone MGC:48472 IMAGE:5276957), complete cds.
BC132827 - Homo sapiens coiled-coil domain containing 66, mRNA (cDNA clone MGC:164458 IMAGE:40146849), complete cds.
AL833326 - Homo sapiens mRNA; cDNA DKFZp686C0433 (from clone DKFZp686C0433).
AL832692 - Homo sapiens mRNA; cDNA DKFZp313G0734 (from clone DKFZp313G0734).
HQ258593 - Synthetic construct Homo sapiens clone IMAGE:100073129 Unknown protein gene, encodes complete protein.
KJ904153 - Synthetic construct Homo sapiens clone ccsbBroadEn_13547 CCDC66 gene, encodes complete protein.
KJ904154 - Synthetic construct Homo sapiens clone ccsbBroadEn_13548 CCDC66 gene, encodes complete protein.
AK125303 - Homo sapiens cDNA FLJ43313 fis, clone NT2RI2013357.
AK095688 - Homo sapiens cDNA FLJ38369 fis, clone FEBRA2001828.
HQ234309 - Homo sapiens clone CCDC66_E10-E4 CCDC66 mRNA, partial sequence.
JD348691 - Sequence 329715 from Patent EP1572962.
JD050629 - Sequence 31653 from Patent EP1572962.
JD363613 - Sequence 344637 from Patent EP1572962.
JD073491 - Sequence 54515 from Patent EP1572962.
JD248662 - Sequence 229686 from Patent EP1572962.
JD036738 - Sequence 17762 from Patent EP1572962.
JD375886 - Sequence 356910 from Patent EP1572962.
JD234456 - Sequence 215480 from Patent EP1572962.
JD284114 - Sequence 265138 from Patent EP1572962.
JD236966 - Sequence 217990 from Patent EP1572962.
AK096754 - Homo sapiens cDNA FLJ39435 fis, clone PROST2004727.
AL832556 - Homo sapiens mRNA; cDNA DKFZp547B2318 (from clone DKFZp547B2318).
JD090461 - Sequence 71485 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A2RUB6, B3KWL8, CCD66_HUMAN, NR_024460, Q4VC34, Q8N949
UCSC ID: uc003dhy.3
RefSeq Accession: NR_024460
Protein: A2RUB6 (aka CCD66_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NR_024460.1
exon count: 18CDS single in 3' UTR: no RNA size: 3133
ORF size: 1755CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2718.50frame shift in genome: no % Coverage: 99.49
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.