Human Gene CNOT4 (ENST00000541284.6_10) from GENCODE V47lift37

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Description: CCR4-NOT transcription complex subunit 4, transcript variant 10 (from RefSeq NM_001393373.1)
Gencode Transcript: ENST00000541284.6_10
Gencode Gene: ENSG00000080802.21_14
Transcript (Including UTRs)
Position: hg19 chr7:135,046,547-135,194,850 Size: 148,304 Total Exon Count: 12 Strand: -
Coding Region
Position: hg19 chr7:135,047,637-135,123,079 Size: 75,443 Coding Exon Count: 11

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr7:135,046,547-135,194,850)			mRNA (may differ from genome)		Protein (713 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	ExonPrimer	GeneCards	HGNC
Malacards	MGI	PubMed	Reactome	UniProtKB	Wikipedia

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 D001564 Benzo(a)pyrene D004997 Ethinyl Estradiol D013629 Tamoxifen D013749 Tetrachlorodibenzodioxin C035207 4-amino-2,6-dinitrotoluene D004390 Chlorpyrifos D011345 Fenofibrate D005557 Formaldehyde D058185 Magnetite Nanoparticles D004113 Succimer more ... click here to view the complete list

Common Gene Haplotype Alleles


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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

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-98.30	306	-0.321	Picture	PostScript	Text
3' UTR	-232.50	1090	-0.213	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

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF14570 - RING/Ubox like zinc-binding domain
PF14608 - RNA-binding, Nab2-type zinc finger

SCOP Domains:
54928 - RNA-binding domain, RBD
57850 - RING/U-box
57903 - FYVE/PHD zinc finger
90229 - CCCH zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1E4U - NMR MuPIT

1UR6 - NMR

ModBase Predicted Comparative 3D Structure on O95628


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

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


	AK074493 - Homo sapiens cDNA FLJ90012 fis, clone HEMBA1000462, highly similar to CCR4-NOT transcription complex subunit 4 (EC 6.3.2.-). 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. 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. AK074671 - Homo sapiens cDNA FLJ90190 fis, clone MAMMA1001094, highly similar to Human potential transcriptional repressor NOT4Hp (NOT4H) mRNA. AF091094 - Homo sapiens clone 243 unknown mRNA, complete sequence. JD229685 - Sequence 210709 from Patent EP1572962. JD431703 - Sequence 412727 from Patent EP1572962. JD133925 - Sequence 114949 from Patent EP1572962. JD503219 - Sequence 484243 from Patent EP1572962. JD280104 - Sequence 261128 from Patent EP1572962. JD236962 - Sequence 217986 from Patent EP1572962. JD562700 - Sequence 543724 from Patent EP1572962. JD187997 - Sequence 169021 from Patent EP1572962. JD301223 - Sequence 282247 from Patent EP1572962. JD365345 - Sequence 346369 from Patent EP1572962. JD392068 - Sequence 373092 from Patent EP1572962. JD359106 - Sequence 340130 from Patent EP1572962. JD205387 - Sequence 186411 from Patent EP1572962. 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. KJ897255 - Synthetic construct Homo sapiens clone ccsbBroadEn_06649 CNOT4 gene, encodes complete protein.

Biochemical and Signaling Pathways


	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: B7Z6I4, CNOT4_HUMAN, E7ET38, ENST00000541284.1, ENST00000541284.2, ENST00000541284.3, ENST00000541284.4, ENST00000541284.5, F8VQP3, NM_001393373, NOT4, O95339, O95627, O95628, Q8IYM7, Q8NCL0, Q9NPQ1, Q9NZN6, uc324swq.1, uc324swq.2 UCSC ID: ENST00000541284.6_10 RefSeq Accession: NM_001190850.2 Protein: O95628 (aka CNOT4_HUMAN or CNO4_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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