Human Gene CNOT10 (uc003cfe.2)
  Description: Homo sapiens CCR4-NOT transcription complex, subunit 10 (CNOT10), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:32,726,637-32,815,367 Size: 88,731 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr3:32,726,953-32,815,103 Size: 88,151 Coding Exon Count: 18 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:32,726,637-32,815,367)mRNA (may differ from genome)Protein (717 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIPubMedReactome
UniProtKBBioGrid CRISPR DB

-  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           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: 18.59 RPKM in Testis
Total median expression: 252.42 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 -163.00316-0.516 Picture PostScript Text
3' UTR -57.42264-0.217 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:
PF13176 - Tetratricopeptide repeat
PF13181 - Tetratricopeptide repeat

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like

ModBase Predicted Comparative 3D Structure on Q9H9A5-3
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK023227 - Homo sapiens cDNA FLJ13165 fis, clone NT2RP3003686.
AK022952 - Homo sapiens cDNA FLJ12890 fis, clone NT2RP2004124.
LF384602 - JP 2014500723-A/192105: Polycomb-Associated Non-Coding RNAs.
AK309670 - Homo sapiens cDNA, FLJ99711.
BC006382 - Homo sapiens cDNA clone IMAGE:4099860, containing frame-shift errors.
BC002931 - Homo sapiens CCR4-NOT transcription complex, subunit 10, mRNA (cDNA clone MGC:11369 IMAGE:3955575), complete cds.
BC002928 - Homo sapiens CCR4-NOT transcription complex, subunit 10, mRNA (cDNA clone MGC:11357 IMAGE:3954507), complete cds.
AK297085 - Homo sapiens cDNA FLJ60672 complete cds, highly similar to Homo sapiens CCR4-NOT transcription complex, subunit 10 (CNOT10), mRNA.
AK298693 - Homo sapiens cDNA FLJ61333 complete cds, highly similar to Homo sapiens CCR4-NOT transcription complex, subunit 10 (CNOT10), mRNA.
AK022576 - Homo sapiens cDNA FLJ12514 fis, clone NT2RM2001768.
EU831581 - Synthetic construct Homo sapiens clone HAIB:100066610; DKFZo004H1218 CCR4-NOT transcription complex, subunit 10 protein (CNOT10) gene, encodes complete protein.
DQ892895 - Synthetic construct clone IMAGE:100005525; FLH191782.01X; RZPDo839G1177D CCR4-NOT transcription complex, subunit 10 (CNOT10) gene, encodes complete protein.
DQ896143 - Synthetic construct Homo sapiens clone IMAGE:100010603; FLH191778.01L; RZPDo839G1167D CCR4-NOT transcription complex, subunit 10 (CNOT10) gene, encodes complete protein.
KJ906105 - Synthetic construct Homo sapiens clone ccsbBroadEn_15775 CNOT10 gene, encodes complete protein.
EU831494 - Synthetic construct Homo sapiens clone HAIB:100066523; DKFZo008H1217 CCR4-NOT transcription complex, subunit 10 protein (CNOT10) gene, encodes complete protein.
KJ898568 - Synthetic construct Homo sapiens clone ccsbBroadEn_07962 CNOT10 gene, encodes complete protein.
AK302196 - Homo sapiens cDNA FLJ56488 complete cds, highly similar to Homo sapiens CCR4-NOT transcription complex, subunit 10 (CNOT10), mRNA.
AK027026 - Homo sapiens cDNA: FLJ23373 fis, clone HEP16118.
AK021695 - Homo sapiens cDNA FLJ11633 fis, clone HEMBA1004274.
MA620179 - JP 2018138019-A/192105: Polycomb-Associated Non-Coding RNAs.
JD278645 - Sequence 259669 from Patent EP1572962.
JD406216 - Sequence 387240 from Patent EP1572962.
JD041655 - Sequence 22679 from Patent EP1572962.
JD436566 - Sequence 417590 from Patent EP1572962.
CU678298 - Synthetic construct Homo sapiens gateway clone IMAGE:100017480 5' read CNOT10 mRNA.
CU678296 - Synthetic construct Homo sapiens gateway clone IMAGE:100017782 5' read CNOT10 mRNA.
DQ597677 - Homo sapiens piRNA piR-35743, complete sequence.
AL117639 - Homo sapiens mRNA; cDNA DKFZp434K115 (from clone DKFZp434K115).
JD023765 - Sequence 4789 from Patent EP1572962.
JD029483 - Sequence 10507 from Patent EP1572962.
JD456362 - Sequence 437386 from Patent EP1572962.
JD180431 - Sequence 161455 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03018 - RNA degradation

Reactome (by CSHL, EBI, and GO)

Protein Q9H9A5 (Reactome details) participates in the following event(s):

R-HSA-6798044 BTG2 binds CCR4-NOT complex
R-HSA-429955 CCR4-NOT complex deadenylates mRNA
R-HSA-6804115 TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
R-HSA-6791312 TP53 Regulates Transcription of Cell Cycle Genes
R-HSA-429947 Deadenylation of mRNA
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-212436 Generic Transcription Pathway
R-HSA-8953854 Metabolism of RNA
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001256741, NP_001243670, Q9H9A5-3, uc003cfe.1
UCSC ID: uc003cfe.2
RefSeq Accession: NM_001256741
Protein: Q9H9A5-3, splice isoform of Q9H9A5 CCDS: CCDS2655.1, CCDS58821.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001256741.1
exon count: 18CDS single in 3' UTR: no RNA size: 2748
ORF size: 2154CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 4442.00frame 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.