Human Gene CCDC83 (uc001pbh.1)
  Description: Homo sapiens coiled-coil domain containing 83 (CCDC83), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr11:85,566,144-85,631,051 Size: 64,908 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr11:85,576,167-85,630,553 Size: 54,387 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:85,566,144-85,631,051)mRNA (may differ from genome)Protein (413 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CCD83_HUMAN
DESCRIPTION: RecName: Full=Coiled-coil domain-containing protein 83;
SEQUENCE CAUTION: Sequence=BAC04154.1; Type=Frameshift; Positions=225;

-  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


-  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: 19.40 RPKM in Testis
Total median expression: 19.44 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 -216.14512-0.422 Picture PostScript Text
3' UTR -117.00498-0.235 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
  InterPro Domains: Graphical view of domain structure
IPR026702 - CCDC83

ModBase Predicted Comparative 3D Structure on Q8IWF9
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  AK124113 - Homo sapiens cDNA FLJ42119 fis, clone TESTI2005739, weakly similar to Drosophila melanogaster Rho-kinase (Rhk) mRNA.
AK314036 - Homo sapiens cDNA, FLJ94696.
BC040280 - Homo sapiens coiled-coil domain containing 83, mRNA (cDNA clone MGC:34732 IMAGE:5166625), complete cds.
CU691846 - Synthetic construct Homo sapiens gateway clone IMAGE:100019286 5' read CCDC83 mRNA.
HQ447277 - Synthetic construct Homo sapiens clone IMAGE:100070587; CCSB009372_01 coiled-coil domain containing 83 (CCDC83) gene, encodes complete protein.
KJ904016 - Synthetic construct Homo sapiens clone ccsbBroadEn_13410 CCDC83 gene, encodes complete protein.
AK093405 - Homo sapiens cDNA FLJ36086 fis, clone TESTI2020176.
AX748105 - Sequence 1630 from Patent EP1308459.
AY251167 - Homo sapiens HSD9 mRNA, complete cds.
JD486424 - Sequence 467448 from Patent EP1572962.
JD263102 - Sequence 244126 from Patent EP1572962.
JD289453 - Sequence 270477 from Patent EP1572962.
JD454900 - Sequence 435924 from Patent EP1572962.
JD225799 - Sequence 206823 from Patent EP1572962.
JD243426 - Sequence 224450 from Patent EP1572962.
JD309939 - Sequence 290963 from Patent EP1572962.
JD244486 - Sequence 225510 from Patent EP1572962.
JD499372 - Sequence 480396 from Patent EP1572962.
JD552444 - Sequence 533468 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RA49, BC040280, CCD83_HUMAN, HSD9, NM_173556, NP_775827, Q6X7T2, Q6ZVT5, Q8IWF9, Q8N9Y1
UCSC ID: uc001pbh.1
RefSeq Accession: NM_173556
Protein: Q8IWF9 (aka CCD83_HUMAN)
CCDS: CCDS66196.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC040280.1
exon count: 11CDS single in 3' UTR: no RNA size: 2035
ORF size: 1242CDS single in intron: no Alignment % ID: 99.90
txCdsPredict score: 2507.00frame shift in genome: no % Coverage: 94.84
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.