Human Gene CNOT6L (ENST00000504123.7_10) from GENCODE V47lift37
  Description: CCR4-NOT transcription complex subunit 6 like, transcript variant 2 (from RefSeq NM_144571.3)
Gencode Transcript: ENST00000504123.7_10
Gencode Gene: ENSG00000138767.14_16
Transcript (Including UTRs)
   Position: hg19 chr4:78,634,541-78,740,522 Size: 105,982 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr4:78,641,585-78,740,462 Size: 98,878 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:78,634,541-78,740,522)mRNA (may differ from genome)Protein (555 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CNO6L_HUMAN
DESCRIPTION: RecName: Full=CCR4-NOT transcription complex subunit 6-like; EC=3.1.-.-; AltName: Full=Carbon catabolite repressor protein 4 homolog B;
FUNCTION: Plays a role in the deadenylation of mRNAs in the cytoplasm. Has 3'-5' poly(A) exoribonuclease activity for synthetic poly(A) RNA substrate. May be involved in the deadenylation-dependent degradation of mRNAs through the 3'-UTR AU-rich element-mediated mechanism. Involved in deadenylation- dependent degradation of CDKN1B mRNA.
COFACTOR: Magnesium.
SUBUNIT: Component of the CCR4-NOT complex at least composed of CNOT1, CNOT2, CNOT3, CNOT8, CNOT9, CNOT10 and TNKS1BP1. Interacts with NANOS2 (By similarity).
INTERACTION: Q13112:CHAF1B; NbExp=2; IntAct=EBI-1046635, EBI-1052944; O75175:CNOT3; NbExp=2; IntAct=EBI-1046635, EBI-743073; P50616:TOB1; NbExp=3; IntAct=EBI-1046635, EBI-723281;
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Highly expressed in placenta, skeletal muscle, pancreas, testis and leukocytes. Weakly expressed in heart, spleen and thymus.
MISCELLANEOUS: Depletion of CNOT6L causes cell growth defect.
SIMILARITY: Belongs to the CCR4/nocturin family.
SIMILARITY: Contains 4 LRR (leucine-rich) repeats.

-  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: 8.69 RPKM in Spleen
Total median expression: 239.43 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.1060-0.335 Picture PostScript Text
3' UTR -1716.407044-0.244 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
IPR005135 - Endo/exonuclease/phosphatase
IPR001611 - Leu-rich_rpt

Pfam Domains:
PF03372 - Endonuclease/Exonuclease/phosphatase family
PF13855 - Leucine rich repeat

SCOP Domains:
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1
56219 - DNase I-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3NGN - X-ray MuPIT 3NGO - X-ray MuPIT 3NGQ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96LI5
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004518 nuclease activity
GO:0004527 exonuclease activity
GO:0004535 poly(A)-specific ribonuclease activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006397 mRNA processing
GO:0006417 regulation of translation
GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
GO:0008284 positive regulation of cell proliferation
GO:0010606 positive regulation of cytoplasmic mRNA processing body assembly
GO:0031047 gene silencing by RNA
GO:0061157 mRNA destabilization
GO:0090305 nucleic acid phosphodiester bond hydrolysis
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030014 CCR4-NOT complex


-  Descriptions from all associated GenBank mRNAs
  LF383985 - JP 2014500723-A/191488: Polycomb-Associated Non-Coding RNAs.
AL133112 - Homo sapiens mRNA; cDNA DKFZp434K098 (from clone DKFZp434K098); partial cds.
AK027214 - Homo sapiens cDNA: FLJ23561 fis, clone LNG09974.
AK303417 - Homo sapiens cDNA FLJ58660 complete cds, highly similar to Mus musculus CCR4-NOT transcription complex, subunit 6-like (Cnot6l), transcript variant 1, mRNA.
BC152816 - Synthetic construct Homo sapiens clone IMAGE:100016034, MGC:184142 CCR4-NOT transcription complex, subunit 6-like (CNOT6L) mRNA, encodes complete protein.
MA619562 - JP 2018138019-A/191488: Polycomb-Associated Non-Coding RNAs.
AK124855 - Homo sapiens cDNA FLJ42865 fis, clone BRHIP2018712.
LF359037 - JP 2014500723-A/166540: Polycomb-Associated Non-Coding RNAs.
LF359038 - JP 2014500723-A/166541: Polycomb-Associated Non-Coding RNAs.
LF359039 - JP 2014500723-A/166542: Polycomb-Associated Non-Coding RNAs.
LF359040 - JP 2014500723-A/166543: Polycomb-Associated Non-Coding RNAs.
LF359041 - JP 2014500723-A/166544: Polycomb-Associated Non-Coding RNAs.
JD280875 - Sequence 261899 from Patent EP1572962.
JD301052 - Sequence 282076 from Patent EP1572962.
JD312965 - Sequence 293989 from Patent EP1572962.
JD220676 - Sequence 201700 from Patent EP1572962.
JD377857 - Sequence 358881 from Patent EP1572962.
JD285086 - Sequence 266110 from Patent EP1572962.
JD494906 - Sequence 475930 from Patent EP1572962.
JD062496 - Sequence 43520 from Patent EP1572962.
JD544793 - Sequence 525817 from Patent EP1572962.
JD442025 - Sequence 423049 from Patent EP1572962.
JD074309 - Sequence 55333 from Patent EP1572962.
JD332653 - Sequence 313677 from Patent EP1572962.
JD494172 - Sequence 475196 from Patent EP1572962.
JD114531 - Sequence 95555 from Patent EP1572962.
JD350155 - Sequence 331179 from Patent EP1572962.
JD091220 - Sequence 72244 from Patent EP1572962.
JD475351 - Sequence 456375 from Patent EP1572962.
MA594614 - JP 2018138019-A/166540: Polycomb-Associated Non-Coding RNAs.
MA594615 - JP 2018138019-A/166541: Polycomb-Associated Non-Coding RNAs.
MA594616 - JP 2018138019-A/166542: Polycomb-Associated Non-Coding RNAs.
MA594617 - JP 2018138019-A/166543: Polycomb-Associated Non-Coding RNAs.
MA594618 - JP 2018138019-A/166544: Polycomb-Associated Non-Coding RNAs.
AK058188 - Homo sapiens cDNA FLJ25459 fis, clone TST09038.
JD086066 - Sequence 67090 from Patent EP1572962.
JD103213 - Sequence 84237 from Patent EP1572962.
LF359042 - JP 2014500723-A/166545: Polycomb-Associated Non-Coding RNAs.
JD316058 - Sequence 297082 from Patent EP1572962.
JD491307 - Sequence 472331 from Patent EP1572962.
JD168742 - Sequence 149766 from Patent EP1572962.
LF359044 - JP 2014500723-A/166547: Polycomb-Associated Non-Coding RNAs.
JD250837 - Sequence 231861 from Patent EP1572962.
AK304397 - Homo sapiens cDNA FLJ57444 complete cds, highly similar to Mus musculus CCR4-NOT transcription complex, subunit 6-like (Cnot6l), transcript variant 1, mRNA.
LF359048 - JP 2014500723-A/166551: Polycomb-Associated Non-Coding RNAs.
LF359050 - JP 2014500723-A/166553: Polycomb-Associated Non-Coding RNAs.
DQ592832 - Homo sapiens piRNA piR-59944, complete sequence.
LF359054 - JP 2014500723-A/166557: Polycomb-Associated Non-Coding RNAs.
JD424361 - Sequence 405385 from Patent EP1572962.
MA594619 - JP 2018138019-A/166545: Polycomb-Associated Non-Coding RNAs.
MA594621 - JP 2018138019-A/166547: Polycomb-Associated Non-Coding RNAs.
MA594625 - JP 2018138019-A/166551: Polycomb-Associated Non-Coding RNAs.
MA594627 - JP 2018138019-A/166553: Polycomb-Associated Non-Coding RNAs.
MA594631 - JP 2018138019-A/166557: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96LI5 (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: CCR4B , CNO6L_HUMAN, ENST00000504123.1, ENST00000504123.2, ENST00000504123.3, ENST00000504123.4, ENST00000504123.5, ENST00000504123.6, NM_144571, Q96LI5, Q9UF92, uc322ycb.1, uc322ycb.2
UCSC ID: ENST00000504123.7_10
RefSeq Accession: NM_144571.3
Protein: Q96LI5 (aka CNO6L_HUMAN)

-  Gene Model Information
  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.