Human Gene CNOT4 (ENST00000361528.8) from GENCODE V44
  Description: Homo sapiens CCR4-NOT transcription complex subunit 4 (CNOT4), transcript variant 1, mRNA. (from RefSeq NM_013316)
RefSeq Summary (NM_013316): The protein encoded by this gene is a subunit of the CCR4-NOT complex, a global transcriptional regulator. The encoded protein interacts with CNOT1 and has E3 ubiquitin ligase activity. Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2010].
Gencode Transcript: ENST00000361528.8
Gencode Gene: ENSG00000080802.21
Transcript (Including UTRs)
   Position: hg38 chr7:135,362,885-135,510,091 Size: 147,207 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg38 chr7:135,362,885-135,438,331 Size: 75,447 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:135,362,885-135,510,091)mRNA (may differ from genome)Protein (639 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGImyGene2
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CNOT4_HUMAN
DESCRIPTION: RecName: Full=CCR4-NOT transcription complex subunit 4; EC=6.3.2.-; AltName: Full=CCR4-associated factor 4; AltName: Full=E3 ubiquitin-protein ligase CNOT4; AltName: Full=Potential transcriptional repressor NOT4Hp;
FUNCTION: Has E3 ubiquitin ligase activity. The CCR4-NOT complex functions as general transcription regulation complex.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Subunit of the CCR4-NOT core complex that contains CHAF1A, CHAF1B, CNOT1, CNOT2, CNOT3, CNOT4, CNOT6 and CNOT8. Binds CNOT1 via its C-terminus. Binds E2 ubiquitin ligases via its RING domain. Interacts (via RING domain) with UBE2D2.
SUBCELLULAR LOCATION: Cytoplasm (Probable). Nucleus (Probable).
PTM: Autoubiquitinated.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 1 C3H1-type zinc finger.
SIMILARITY: Contains 1 RING-type zinc finger.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SEQUENCE CAUTION: Sequence=AAC72963.1; Type=Frameshift; Positions=Several; Sequence=AAC72963.1; Type=Miscellaneous discrepancy; Note=Sequencing errors; Sequence=AAD00180.1; Type=Frameshift; Positions=358, 400; Sequence=BAC11125.1; 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: CNOT4
Diseases sorted by gene-association score: adenoiditis (11)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.01 RPKM in Testis
Total median expression: 183.62 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -88.80295-0.301 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom
IPR000571 - Znf_CCCH
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1E4U - NMR MuPIT 1UR6 - NMR


ModBase Predicted Comparative 3D Structure on O95628
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0016740 transferase 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:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
GO:0016567 protein ubiquitination
GO:0051865 protein autoubiquitination

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


-  Descriptions from all associated GenBank mRNAs
  AK074671 - Homo sapiens cDNA FLJ90190 fis, clone MAMMA1001094, highly similar to Human potential transcriptional repressor NOT4Hp (NOT4H) mRNA.
AK074493 - Homo sapiens cDNA FLJ90012 fis, clone HEMBA1000462, highly similar to CCR4-NOT transcription complex subunit 4 (EC 6.3.2.-).
AF091094 - Homo sapiens clone 243 unknown mRNA, complete sequence.
U71267 - Human potential transcriptional repressor NOT4Hp (NOT4H) mRNA, complete cds.
AK300365 - Homo sapiens cDNA FLJ61661 complete cds, highly similar to Rattus norvegicus CCR4-NOT transcription complex, subunit 4 (Cnot4), mRNA.
AK314540 - Homo sapiens cDNA, FLJ95362.
AB385213 - Synthetic construct DNA, clone: pF1KB9414, Homo sapiens CNOT4 gene for CCR4-NOT transcription complex subunit 4, complete cds, without stop codon, in Flexi system.
AF180475 - Homo sapiens Not4-Np (NOT4-N) mRNA, complete cds.
BC035590 - Homo sapiens CCR4-NOT transcription complex, subunit 4, mRNA (cDNA clone MGC:45148 IMAGE:5576434), complete cds.
AL389980 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 2005259.
U71268 - Human potential transcriptional repressor NOT4Hp (NOT4H) mRNA, complete cds.
KJ897255 - Synthetic construct Homo sapiens clone ccsbBroadEn_06649 CNOT4 gene, encodes complete protein.

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

Reactome (by CSHL, EBI, and GO)

Protein O95628 (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: CNOT4_HUMAN, ENST00000361528.1, ENST00000361528.2, ENST00000361528.3, ENST00000361528.4, ENST00000361528.5, ENST00000361528.6, ENST00000361528.7, NM_013316, NOT4, O95339, O95627, O95628, Q8IYM7, Q8NCL0, Q9NPQ1, Q9NZN6, uc003vss.1, uc003vss.2, uc003vss.3, uc003vss.4
UCSC ID: ENST00000361528.8
RefSeq Accession: NM_013316
Protein: O95628 (aka CNOT4_HUMAN or CNO4_HUMAN)
CCDS: CCDS43650.1, CCDS55164.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.