CNOT3 (CCR4-NOT transcription complex subunit 3)

Gene

• Entrez ID: 4849
• Gene name: CCR4-NOT transcription complex subunit 3
• Gene symbol: CNOT3
• Synonyms: IDDSADF, LENG2, NOT3, NOT3H
• Chromosome: 19
• Chromosome location: 19q13.42

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs753475896	C>-,CC,CCC	Uncertain-significance, pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT051783	hsa-let-7c-5p	CLASH	23622248
MIRT039544	hsa-miR-652-3p	CLASH	23622248
MIRT038618	hsa-miR-185-3p	CLASH	23622248
MIRT900388	hsa-miR-1343	CLIP-seq
MIRT900389	hsa-miR-2115	CLIP-seq
MIRT900390	hsa-miR-3150a-3p	CLIP-seq
MIRT900391	hsa-miR-3175	CLIP-seq
MIRT900392	hsa-miR-3192	CLIP-seq
MIRT900393	hsa-miR-4313	CLIP-seq
MIRT900394	hsa-miR-4667-5p	CLIP-seq
MIRT900395	hsa-miR-4700-5p	CLIP-seq
MIRT900396	hsa-miR-4728-5p	CLIP-seq
MIRT900397	hsa-miR-4779	CLIP-seq
MIRT900398	hsa-miR-486-3p	CLIP-seq
MIRT900399	hsa-miR-516a-3p	CLIP-seq
MIRT900400	hsa-miR-765	CLIP-seq
MIRT900401	hsa-miR-939	CLIP-seq
MIRT900388	hsa-miR-1343	CLIP-seq
MIRT900389	hsa-miR-2115	CLIP-seq
MIRT900392	hsa-miR-3192	CLIP-seq
MIRT2202759	hsa-miR-4525	CLIP-seq
MIRT2202760	hsa-miR-4716-3p	CLIP-seq
MIRT900397	hsa-miR-4779	CLIP-seq
MIRT900398	hsa-miR-486-3p	CLIP-seq
MIRT900399	hsa-miR-516a-3p	CLIP-seq
MIRT900400	hsa-miR-765	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000289	Process	Nuclear-transcribed mRNA poly(A) tail shortening	IBA	21873635
GO:0000289	Process	Nuclear-transcribed mRNA poly(A) tail shortening	TAS
GO:0000932	Component	P-body	IBA	21873635
GO:0000932	Component	P-body	ISS
GO:0001829	Process	Trophectodermal cell differentiation	IEA
GO:0005515	Function	Protein binding	IPI	10637334, 12207886, 16189514, 16778766, 17452450, 18377426, 21981923, 21984185, 24736845, 26496610, 28514442, 31515488, 32296183, 32814053
GO:0005634	Component	Nucleus	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006355	Process	Regulation of transcription, DNA-templated	IEA
GO:0006417	Process	Regulation of translation	IEA
GO:0006977	Process	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	TAS
GO:0030014	Component	CCR4-NOT complex	IDA	19558367
GO:0030015	Component	CCR4-NOT core complex	IBA	21873635
GO:0031047	Process	Gene silencing by RNA	IEA
GO:0120162	Process	Positive regulation of cold-induced thermogenesis	ISS	28032897
GO:2000036	Process	Regulation of stem cell population maintenance	IBA	21873635
GO:2000036	Process	Regulation of stem cell population maintenance	IMP	22367759

Other IDs

• MIM: 604910
• HGNC: 7879
• e!Ensembl: ENSG00000088038

Protein

• UniProt ID: O75175
• Protein name: CCR4-NOT transcription complex subunit 3 (CCR4-associated factor 3) (Leukocyte receptor cluster member 2)
• Protein function: Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiati
• PDB: 4C0D, 4C0G, 5FU6, 5FU7, 9C3H, 9C3I
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04065	Not3	3 → 232	Not1 N-terminal domain, CCR4-Not complex component	Family
  PF04153	NOT2_3_5	620 → 747	NOT2 / NOT3 / NOT5 family	Family

• Sequence:

  MADKRKLQGEIDRCLKKVSEGVEQFEDIWQKLHNAANANQKEKYEADLKKEIKKLQRLRD
  QIKTWVASNEIKDKRQLIDNRKLIETQMERFKVVERETKTKAYSKEGLGLAQKVDPAQKE
  KEEVGQWLTNTIDTLNMQVDQFESEVESLSVQTRKKKGDKDKQDRIEGLKRHIEKHRYHV
  RMLETILRMLDNDSILVDAIRKIKDDVEYYVDSSQDPDFEENEFLYDDLDLEDIPQALVA
  TSPPSHSHMEDEIFNQSSSTPTSTTSSSPIPPSPANCTTENSEDDKKRGRSTDSEVSQSP
  AKNGSKPVHSNQHPQSPAVPPTYPSGPPPAASALSTTPGNNGVPAPAAPPSALGPKASPA
  PSHNSGTPAPYAQAVAPPAPSGPSTTQPRPPSVQPSGGGGGGSGGGGSSSSSNSSAGGGA
  GKQNGATSYSSVVADSPAEVALSSSGGNNASSQALGPPSGPHNPPPSTSKEPSAAAPTGA
  GGVAPGSGNNSGGPSLLVPLPVNPPSSPTPSFSDAKAAGALLNGPPQFSTAPEIKAPEPL
  SSLKSMAERAAISSGIEDPVPTLHLTERDIILSSTSAPPASAQPPLQLSEVNIPLSLGVC
  PLGPVPLTKEQLYQQAMEEAAWHHMPHPSDSERIRQYLPRNPCPTPPYHHQMPPPHSDTV
  EFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFE
  QGTYIYFDYEKWGQRKKEGFTFEYRYLEDRDLQ

• Sequence length: 753

Pathways

KEGG:

RNA degradation

Reactome:

Deadenylation of mRNA
TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Lymphoblastic leukemia	Precursor T-Cell Lymphoblastic Leukemia-Lymphoma, Precursor Cell Lymphoblastic Leukemia Lymphoma, Precursor T-cell acute lymphoblastic leukemia	rs387906351, rs104894562, rs398122513, rs398122840, rs398123063, rs1057524466, rs1064796115, rs1064795660, rs1064793129, rs1064796227, rs1567887558, rs1161194345, rs1597558200, rs1406320425, rs1597566470, rs1597566699, rs1597567692, rs1597567985, rs1438890364, rs1288977950, rs1597552140, rs1597566356, rs1597566726, rs1597568117, rs2069719445, rs2069729948, rs2070018439, rs745708044, rs1169577591	23263491, 30450575
Prostate cancer	Malignant neoplasm of prostate	rs121909139, rs121909140, rs121909141, rs121909142, rs121909143, rs606231169, rs606231170, rs137852584, rs137852578, rs137852580, rs137852581, rs137852582	29662167, 29610475

Unknown
Disease name	Disease term	dbSNP ID	References
Dysmorphic features	Dysmorphic features		26821858, 24267886, 27824329, 26637982, 11696541, 21897366, 23280189, 12215531, 17273961, 22495309, 10637334, 28263302, 20371351, 28135719
Prostatic neoplasms	Prostatic Neoplasms		29610475, 29662167