Human Gene CCDC65 (uc001rso.3)
  Description: Homo sapiens coiled-coil domain containing 65 (CCDC65), mRNA.
RefSeq Summary (NM_033124): This gene encodes a sperm tail protein that is highly expressed in adult testis, spermatocytes and spermatids. The protein plays a critical role in the assembly of the nexin-dynein regulatory complex. Mutations in this gene result in primary ciliary dyskinesia. [provided by RefSeq, Nov 2013].
Transcript (Including UTRs)
   Position: hg19 chr12:49,297,893-49,315,359 Size: 17,467 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr12:49,298,120-49,315,226 Size: 17,107 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:49,297,893-49,315,359)mRNA (may differ from genome)Protein (484 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CCD65_HUMAN
DESCRIPTION: RecName: Full=Coiled-coil domain-containing protein 65; AltName: Full=Testis development protein NYD-SP28;
TISSUE SPECIFICITY: Highly expressed in adult testis, in spermatocytes and spermatids. Also observed in spermatogonia. Not detected in Leydig cells, nor in fetal testis (at protein level).
SEQUENCE CAUTION: Sequence=BAC05324.1; Type=Erroneous initiation;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: CCDC65
Diseases sorted by gene-association score: ciliary dyskinesia, primary, 27* (519), primary ciliary dyskinesia 27: ccdc65-related primary ciliary dyskinesia* (100), primary ciliary dyskinesia (10), kartagener syndrome (3)
* = Manually curated disease association

-  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: 26.09 RPKM in Testis
Total median expression: 72.93 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 -82.50227-0.363 Picture PostScript Text
3' UTR -24.90133-0.187 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:
PF14772 - Sperm tail

ModBase Predicted Comparative 3D Structure on Q8IXS2
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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 BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function

Biological Process:
GO:0003352 regulation of cilium movement
GO:0060271 cilium assembly

Cellular Component:
GO:0005575 cellular_component
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0031514 motile cilium
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  AK302082 - Homo sapiens cDNA FLJ51378 complete cds, highly similar to Homo sapiens NYD-SP28 protein (NYD-SP28), mRNA.
AK093051 - Homo sapiens cDNA FLJ35732 fis, clone TESTI2003141.
AX747886 - Sequence 1411 from Patent EP1308459.
AF382188 - Homo sapiens NYD-SP28 mRNA, complete cds.
AK314623 - Homo sapiens cDNA, FLJ95464, highly similar to Homo sapiens NYD-SP28 protein (NYD-SP28), mRNA.
BC039317 - Homo sapiens coiled-coil domain containing 65, mRNA (cDNA clone MGC:41762 IMAGE:5271866), complete cds.
JD137062 - Sequence 118086 from Patent EP1572962.
JD298207 - Sequence 279231 from Patent EP1572962.
JD237153 - Sequence 218177 from Patent EP1572962.
KJ895091 - Synthetic construct Homo sapiens clone ccsbBroadEn_04485 CCDC65 gene, encodes complete protein.
AK098529 - Homo sapiens cDNA FLJ25663 fis, clone TST01640.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NJG5, B2RBE2, CCD65_HUMAN, NM_033124, NP_149115, Q8IXS2, Q8N7G4, Q8NA91, Q96JA0
UCSC ID: uc001rso.3
RefSeq Accession: NM_033124
Protein: Q8IXS2 (aka CCD65_HUMAN)
CCDS: CCDS8772.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CCDC65:
pcd (Primary Ciliary Dyskinesia)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_033124.4
exon count: 8CDS single in 3' UTR: no RNA size: 1832
ORF size: 1455CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3065.00frame shift in genome: no % Coverage: 99.07
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.