Human Gene C9orf106 (uc004bxs.2)
  Description: Homo sapiens chromosome 9 open reading frame 106 (C9orf106), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:132,083,295-132,084,882 Size: 1,588 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr9:132,084,093-132,084,791 Size: 699 Coding Exon Count: 1 

Page IndexSequence and LinksPrimersGenetic AssociationsGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:132,083,295-132,084,882)mRNA (may differ from genome)Protein (232 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCHPRDLynxMGIPubMedUniProtKB

-  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): C9orf106
CDC HuGE Published Literature: C9orf106
Positive Disease Associations: Antidepressive Agents , Erythrocyte Count , Iron , Myocardial Infarction , Triglycerides
Related Studies:
  1. Antidepressive Agents
    S L Clark et al. Psychological medicine 2012, Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D., Psychological medicine. [PubMed 22041458]
    Although our findings require replication and functional validation, this study demonstrates the potential of GWAS to discover genes and pathways that could mediate adverse effects of antidepressant medication.
  2. Erythrocyte Count
    , , . [PubMed 0]
  3. Erythrocyte Count
    , , . [PubMed 0]
           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: 0.62 RPKM in Cervix - Endocervix
Total median expression: 8.11 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 -13.2053-0.249 Picture PostScript Text
3' UTR -26.4491-0.291 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
  ModBase Predicted Comparative 3D Structure on A2RU00
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding


-  Descriptions from all associated GenBank mRNAs
  AK092588 - Homo sapiens cDNA FLJ35269 fis, clone PROST2005466.
AX747616 - Sequence 1141 from Patent EP1308459.
BC132699 - Homo sapiens chromosome 9 open reading frame 106, mRNA (cDNA clone MGC:164330 IMAGE:40146721), complete cds.
BC132701 - Homo sapiens chromosome 9 open reading frame 106, mRNA (cDNA clone MGC:164332 IMAGE:40146723), complete cds.
JD038543 - Sequence 19567 from Patent EP1572962.
HQ258482 - Synthetic construct Homo sapiens clone IMAGE:100073144 Unknown protein gene, encodes complete protein.
KJ900758 - Synthetic construct Homo sapiens clone ccsbBroadEn_10152 C9orf106 gene, encodes complete protein.
JD270390 - Sequence 251414 from Patent EP1572962.
JD544560 - Sequence 525584 from Patent EP1572962.
JD221727 - Sequence 202751 from Patent EP1572962.
JD303888 - Sequence 284912 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A2RU00, A2RU00_HUMAN, NM_001012715, NP_001012733
UCSC ID: uc004bxs.2
RefSeq Accession: NM_001012715
Protein: A2RU00

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001012715.3
exon count: 2CDS single in 3' UTR: no RNA size: 843
ORF size: 699CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1172.00frame 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.