| Name | CCR4-NOT transcription complex subunit 9 |
| Description | This gene encodes a member of the highly conserved RCD1 protein family. The encoded protein is a transcriptional cofactor and a core protein of the CCR4-NOT complex. It may be involved in signal transduction as well as retinoic acid-regulated cell differentiation and development. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Oct 2012] |
| Summary |
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n CNOT9 is a conserved, non‐catalytic subunit of the CCR4–NOT complex that plays a central role in post‐transcriptional gene regulation. Structural and biochemical studies have shown that CNOT9 interacts directly with a central domain of the scaffold protein CNOT1, thereby creating binding surfaces for key regulatory factors. In particular, CNOT9 binds conserved tryptophan motifs within miRNA effector proteins (such as GW182/TNRC6) to mediate miRNA‐dependent translational repression and mRNA decay."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " Furthermore, CNOT9 (also known as hRcd1 or Caf40) has been implicated in additional gene regulatory functions, including the repression of promoter activity and TTP‐dependent recruitment of the deadenylase machinery to AU‐rich mRNAs."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": " Collectively, these findings suggest that CNOT9 functions as an adaptor that links RNA recognition by specific binding proteins to the assembly and activation of the catalytic deadenylation module of the CCR4–NOT complex, thereby coordinating translational repression and mRNA degradation.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Hansruedi Mathys, Jérôme Basquin, Sevim Ozgur, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Structural and biochemical insights to the role of the CCR4-NOT complex and DDX6 ATPase in microRNA repression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2014.03.036"}], "href": "https://doi.org/10.1016/j.molcel.2014.03.036"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24768538"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24768538"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Ying Chen, Andreas Boland, Duygu Kuzuoğlu-Öztürk, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2014.03.034"}], "href": "https://doi.org/10.1016/j.molcel.2014.03.034"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24768540"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24768540"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "D Bulbrook, H Brazier, P Mahajan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Tryptophan-Mediated Interactions between Tristetraprolin and the CNOT9 Subunit Are Required for CCR4-NOT Deadenylase Complex Recruitment."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Mol Biol (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jmb.2017.12.018"}], "href": "https://doi.org/10.1016/j.jmb.2017.12.018"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29291391"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29291391"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Carin G M Zwartjes, Sandrine Jayne, Debbie L C van den Berg, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Repression of promoter activity by CNOT2, a subunit of the transcription regulatory Ccr4-not complex."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M311747200"}], "href": "https://doi.org/10.1074/jbc.M311747200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "14707134"}], "href": "https://pubmed.ncbi.nlm.nih.gov/14707134"}]}]}]}
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| NCBI Gene ID | 9125 |
| API | |
| Download Associations | |
| Predicted Functions |
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| Co-expressed Genes |
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| Expression in Tissues and Cell Lines |
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CNOT9 has 2,168 functional associations with biological entities spanning 6 categories (chemical, disease, phenotype or trait, functional term, phrase or reference, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 44 datasets.
Click the + buttons to view associations for CNOT9 from the datasets below.
If available, associations are ranked by standardized value
| Dataset | Summary | |
|---|---|---|
| Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles | tissue samples with high or low expression of CNOT9 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset. | |
| Carcinogenome Chemical Perturbation Carcinogenicity Signatures | small molecule perturbations changing expression of CNOT9 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset. | |
| CCLE Cell Line Proteomics | Cell lines associated with CNOT9 protein from the CCLE Cell Line Proteomics dataset. | |
| ChEA Transcription Factor Targets 2022 | transcription factors binding the promoter of CNOT9 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset. | |
| ClinVar Gene-Phenotype Associations 2025 | phenotypes associated with CNOT9 gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset. | |
| CM4AI KOLF21J CRISPRi Gene Perturbation Atlas | gene perturbations changing expression of CNOT9 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset. | |
| CM4AI U2OS Cell Map Protein Localization Assemblies | assemblies containing CNOT9 protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset. | |
| COMPARTMENTS Curated Protein Localization Evidence Scores 2025 | cellular components containing CNOT9 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset. | |
| COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 | cellular components co-occuring with CNOT9 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset. | |
| DepMap CRISPR Gene Dependency | cell lines with fitness changed by CNOT9 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset. | |
| DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 | diseases co-occuring with CNOT9 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset. | |
| DisGeNET Gene-Disease Associations | diseases associated with CNOT9 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset. | |
| DisGeNET Gene-Phenotype Associations | phenotypes associated with CNOT9 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset. | |
| GO Biological Process Annotations 2023 | biological processes involving CNOT9 gene from the curated GO Biological Process Annotations 2023 dataset. | |
| GO Biological Process Annotations 2025 | biological processes involving CNOT9 gene from the curated GO Biological Process Annotations2025 dataset. | |
| GO Cellular Component Annotations 2023 | cellular components containing CNOT9 protein from the curated GO Cellular Component Annotations 2023 dataset. | |
| GO Cellular Component Annotations 2025 | cellular components containing CNOT9 protein from the curated GO Cellular Component Annotations 2025 dataset. | |
| GO Molecular Function Annotations 2023 | molecular functions performed by CNOT9 gene from the curated GO Molecular Function Annotations 2023 dataset. | |
| GO Molecular Function Annotations 2025 | molecular functions performed by CNOT9 gene from the curated GO Molecular Function Annotations 2025 dataset. | |
| GTEx eQTL 2025 | SNPs regulating expression of CNOT9 gene from the GTEx eQTL 2025 dataset. | |
| GTEx Tissue Gene Expression Profiles 2023 | tissues with high or low expression of CNOT9 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset. | |
| GWAS Catalog SNP-Phenotype Associations 2025 | phenotypes associated with CNOT9 gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset. | |
| JASPAR Predicted Human Transcription Factor Targets 2025 | transcription factors regulating expression of CNOT9 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset. | |
| JASPAR Predicted Mouse Transcription Factor Targets 2025 | transcription factors regulating expression of CNOT9 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Mouse Transcription Factor Targets 2025 dataset. | |
| KEGG Pathways 2026 | pathways involving CNOT9 protein from the KEGG Pathways 2026 dataset. | |
| Kinase Library Tyrosine Kinome Atlas | kinases that phosphorylate CNOT9 protein from the Kinase Library Tyrosine Kinome Atlas dataset. | |
| LINCS L1000 CMAP Chemical Perturbation Consensus Signatures | small molecule perturbations changing expression of CNOT9 gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset. | |
| LINCS L1000 CMAP CRISPR Knockout Consensus Signatures | gene perturbations changing expression of CNOT9 gene from the LINCS L1000 CMAP CRISPR Knockout Consensus Signatures dataset. | |
| MGI Mouse Phenotype Associations 2023 | phenotypes of transgenic mice caused by CNOT9 gene mutations from the MGI Mouse Phenotype Associations 2023 dataset. | |
| NIBR DRUG-seq U2OS MoA Box Gene Expression Profiles | drug perturbations changing expression of CNOT9 gene from the NIBR DRUG-seq U2OS MoA Box dataset. | |
| PFOCR Pathway Figure Associations 2023 | pathways involving CNOT9 protein from the PFOCR Pathway Figure Associations 2023 dataset. | |
| PFOCR Pathway Figure Associations 2024 | pathways involving CNOT9 protein from the Wikipathways PFOCR 2024 dataset. | |
| Reactome Pathways 2024 | pathways involving CNOT9 protein from the Reactome Pathways 2024 dataset. | |
| Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures | gene perturbations changing expression of CNOT9 gene from the Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures dataset. | |
| Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures | gene perturbations changing expression of CNOT9 gene from the Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures dataset. | |
| Rummagene Transcription Factor Associations 2026 | transcription factors regulating expression of CNOT9 gene from the Rummagene Transcription Factor Associations 2026 dataset. | |
| RummaGEO Drug Perturbation Signatures | drug perturbations changing expression of CNOT9 gene from the RummaGEO Drug Perturbation Signatures dataset. | |
| RummaGEO Gene Perturbation Signatures | gene perturbations changing expression of CNOT9 gene from the RummaGEO Gene Perturbation Signatures dataset. | |
| Sci-Plex Drug Perturbation Signatures | drug perturbations changing expression of CNOT9 gene from the Sci-Plex Drug Perturbation Signatures dataset. | |
| Tahoe Therapeutics Tahoe 100M Perturbation Atlas | drug perturbations changing expression of CNOT9 gene from the Tahoe Therapeutics Tahoe 100M Perturbation Atlas dataset. | |
| TISSUES Curated Tissue Protein Expression Evidence Scores 2025 | tissues with high expression of CNOT9 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores 2025 dataset. | |
| TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 | tissues with high expression of CNOT9 protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 dataset. | |
| TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 | tissues co-occuring with CNOT9 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset. | |
| WikiPathways Pathways 2024 | pathways involving CNOT9 protein from the WikiPathways Pathways 2024 dataset. | |
