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, O... See more...

Aliases for CNOT9 Gene

Aliases for CNOT9 Gene

  • CCR4-NOT Transcription Complex Subunit 9 2 3 4 5
  • RCD1 2 3 4
  • Cell Differentiation Protein RQCD1 Homolog 3 4
  • Cancer/Testis Antigen 129 2 3
  • CAF40 2 3
  • CT129 2 3
  • RQCD1 3 4
  • Rcd1 (Required For Cell Differentiation, S.Pombe) Homolog 1 2
  • RCD1 Required For Cell Differentiation1 Homolog (S. Pombe) 2
  • RCD1 Required For Cell Differentiation1 Homolog 3
  • Cell Differentiation Protein RCD1 Homolog 3
  • Protein Involved In Sexual Development 3
  • RCD-1 3
  • CNOT9 5
  • RCD1+ 2
  • Rcd-1 4

External Ids for CNOT9 Gene

Previous HGNC Symbols for CNOT9 Gene

  • RQCD1

Summaries for CNOT9 Gene

Entrez Gene Summary for CNOT9 Gene

  • 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]

GeneCards Summary for CNOT9 Gene

CNOT9 (CCR4-NOT Transcription Complex Subunit 9) is a Protein Coding gene. Diseases associated with CNOT9 include Bladder Adenocarcinoma. Among its related pathways are Deadenylation-dependent mRNA decay and Gene Expression.

UniProtKB/Swiss-Prot Summary for CNOT9 Gene

  • 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 initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Involved in down-regulation of MYB- and JUN-dependent transcription. May play a role in cell differentiation (By similarity). Can bind oligonucleotides, such as poly-G, poly-C or poly-T (in vitro), but the physiological relevance of this is not certain. Does not bind poly-A. Enhances ligand-dependent transcriptional activity of nuclear hormone receptors, including RARA, expect ESR1-mediated transcription that is not only slightly increased, if at all.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CNOT9 Gene

Genomics for CNOT9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CNOT9 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CNOT9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CNOT9

Genomic Locations for CNOT9 Gene

Genomic Locations for CNOT9 Gene
chr2:218,568,578-218,597,080
(GRCh38/hg38)
Size:
28,503 bases
Orientation:
Plus strand
chr2:219,433,303-219,461,803
(GRCh37/hg19)
Size:
28,501 bases
Orientation:
Plus strand

Genomic View for CNOT9 Gene

Genes around CNOT9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CNOT9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CNOT9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CNOT9 Gene

Proteins for CNOT9 Gene

  • Protein details for CNOT9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92600-CNOT9_HUMAN
    Recommended name:
    CCR4-NOT transcription complex subunit 9
    Protein Accession:
    Q92600
    Secondary Accessions:
    • B2RPI0
    • B5MDQ4
    • B7Z1E5
    • Q96IX4

    Protein attributes for CNOT9 Gene

    Size:
    299 amino acids
    Molecular mass:
    33631 Da
    Quaternary structure:
    • Homodimer. Component of the CCR4-NOT complex; distinct complexes seem to exist that differ in the participation of probably mutually exclusive catalytic subunits. Interacts with MYB, ATF2, RARA, RARB, RARG, RXRA, RXRB and RXRG. Identified in a complex with ATF2 bound to target DNA (By similarity). Interacts with NANOS2 (By similarity). Directly interacts with ZNF335.
    SequenceCaution:
    • Sequence=AAH07102.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CNOT9 Gene

    Alternative splice isoforms for CNOT9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CNOT9 Gene

Post-translational modifications for CNOT9 Gene

  • Ubiquitination at Lys222 and Lys281
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CNOT9 Gene

Domains & Families for CNOT9 Gene

Gene Families for CNOT9 Gene

Protein Domains for CNOT9 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CNOT9 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ58752, highly similar to Homo sapiens RCD1 required for cell differentiation 1 homolog (RQCD1), mRNA (B7Z1E5_HUMAN)
  • RQCD1 protein (D5MQE1_HUMAN)
  • CCR4-NOT transcription complex subunit 9 (RCD1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q92600

UniProtKB/Swiss-Prot:

CNOT9_HUMAN :
  • Belongs to the CNOT9 family.
Family:
  • Belongs to the CNOT9 family.
genes like me logo Genes that share domains with CNOT9: view

Function for CNOT9 Gene

Molecular function for CNOT9 Gene

UniProtKB/Swiss-Prot 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 initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Involved in down-regulation of MYB- and JUN-dependent transcription. May play a role in cell differentiation (By similarity). Can bind oligonucleotides, such as poly-G, poly-C or poly-T (in vitro), but the physiological relevance of this is not certain. Does not bind poly-A. Enhances ligand-dependent transcriptional activity of nuclear hormone receptors, including RARA, expect ESR1-mediated transcription that is not only slightly increased, if at all.

Phenotypes From GWAS Catalog for CNOT9 Gene

Gene Ontology (GO) - Molecular Function for CNOT9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005154 epidermal growth factor receptor binding IPI 20878056
GO:0005515 protein binding IPI 18180299
GO:0019900 kinase binding IPI 20878056
GO:0019904 protein domain specific binding IPI 24768540
GO:0042803 protein homodimerization activity IDA 24768540
genes like me logo Genes that share ontologies with CNOT9: view
genes like me logo Genes that share phenotypes with CNOT9: view

Animal Models for CNOT9 Gene

MGI Knock Outs for CNOT9:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNOT9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CNOT9 Gene

Localization for CNOT9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CNOT9 Gene

Nucleus. Cytoplasm, P-body. Note=NANOS2 promotes its localization to P-body. {ECO:0000250 UniProtKB:Q9JKY0}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CNOT9 gene
Compartment Confidence
nucleus 4
cytosol 4
extracellular 2
mitochondrion 2
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytoplasmic bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CNOT9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body ISS --
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with CNOT9: view

Pathways & Interactions for CNOT9 Gene

genes like me logo Genes that share pathways with CNOT9: view

SIGNOR curated interactions for CNOT9 Gene

Activates:

Gene Ontology (GO) - Biological Process for CNOT9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening TAS --
GO:0006402 mRNA catabolic process IEA --
GO:0006417 regulation of translation IEA --
GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest TAS --
GO:0007548 sex differentiation TAS --
genes like me logo Genes that share ontologies with CNOT9: view

Drugs & Compounds for CNOT9 Gene

No Compound Related Data Available

Transcripts for CNOT9 Gene

mRNA/cDNA for CNOT9 Gene

3 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNOT9

Alternative Splicing Database (ASD) splice patterns (SP) for CNOT9 Gene

No ASD Table

Relevant External Links for CNOT9 Gene

GeneLoc Exon Structure for
CNOT9

Expression for CNOT9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CNOT9

mRNA Expression by UniProt/SwissProt for CNOT9 Gene:

Q92600-CNOT9_HUMAN
Tissue specificity: Detected in spleen, thymus, prostate, testis, ovary and intestine.

Evidence on tissue expression from TISSUES for CNOT9 Gene

  • Nervous system(4.6)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with CNOT9: view

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CNOT9 Gene

Orthologs for CNOT9 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CNOT9 Gene

Organism Taxonomy Gene Similarity Type Details
Oppossum
(Monodelphis domestica)
Mammalia RQCD1 31
  • 100 (a)
OneToOne
Chimpanzee
(Pan troglodytes)
Mammalia RQCD1 30 31
  • 99.55 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RQCD1 30 31
  • 95.21 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RQCD1 30 31
  • 94.76 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rqcd1 30
  • 92.98 (n)
Mouse
(Mus musculus)
Mammalia Rqcd1 30 31
  • 92.2 (n)
OneToOne
Cnot9 17
Platypus
(Ornithorhynchus anatinus)
Mammalia RQCD1 31
  • 69 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RQCD1 30 31
  • 83.19 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RQCD1 31
  • 99 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rqcd1 30
  • 79.38 (n)
MGC76003 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.13761 30
Zebrafish
(Danio rerio)
Actinopterygii rqcd1 30 31
  • 75.79 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1813 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012050 30
  • 67.73 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Rcd-1 30 31
  • 66.79 (n)
OneToMany
Rcd-1r 31
  • 59 (a)
OneToMany
CG2053 31
  • 37 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ntl-9 30 31
  • 64.38 (n)
OneToOne
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AEL194W 30
  • 59.6 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CAF40 30 31 33
  • 56.26 (n)
OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E13267g 30
  • 55.56 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT3G20800 30
  • 59.75 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.4960 30
Soybean
(Glycine max)
eudicotyledons Gma.4905 30
Rice
(Oryza sativa)
Liliopsida Os04g0613400 30
  • 64.1 (n)
Wheat
(Triticum aestivum)
Liliopsida Ta.6222 30
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 91 (a)
OneToMany
CSA.8006 31
  • 86 (a)
OneToMany
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rcd1 30
  • 62.08 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU07071 30
  • 60.89 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.3625 30
Species where no ortholog for CNOT9 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for CNOT9 Gene

ENSEMBL:
Gene Tree for CNOT9 (if available)
TreeFam:
Gene Tree for CNOT9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CNOT9: view image

Paralogs for CNOT9 Gene

No data available for Paralogs for CNOT9 Gene

Variants for CNOT9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CNOT9 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs1057519955 Likely Pathogenic: Malignant melanoma of skin 218,584,682(+) C/T MISSENSE_VARIANT
rs1057519956 Likely Pathogenic: Hepatocellular carcinoma; Transitional cell carcinoma of the bladder; Adenocarcinoma of stomach; Adenocarcinoma of prostate; Malignant melanoma of skin 218,583,025(+) T/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs1057519957 Likely Pathogenic: Hepatocellular carcinoma; Transitional cell carcinoma of the bladder; Adenocarcinoma of stomach; Adenocarcinoma of prostate; Malignant melanoma of skin 218,583,026(+) C/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs267599211 Likely Pathogenic: Malignant melanoma of skin 218,584,683(+) C/T MISSENSE_VARIANT
VAR_042429 - p.Ile143Thr

Additional dbSNP identifiers (rs#s) for CNOT9 Gene

Structural Variations from Database of Genomic Variants (DGV) for CNOT9 Gene

Variant ID Type Subtype PubMed ID
esv2721478 CNV deletion 23290073
nsv1123431 CNV deletion 24896259
nsv1131549 CNV deletion 24896259
nsv3168 CNV deletion 18451855

Variation tolerance for CNOT9 Gene

Residual Variation Intolerance Score: 32.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.15; 3.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CNOT9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CNOT9

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CNOT9 Gene

Disorders for CNOT9 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CNOT9 Gene - From: GeneCards

Disorder Aliases PubMed IDs
bladder adenocarcinoma
  • adenocarcinoma of bladder
- elite association - COSMIC cancer census association via MalaCards
Search CNOT9 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with CNOT9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CNOT9 Gene

Publications for CNOT9 Gene

  1. Components of the CCR4-NOT complex function as nuclear hormone receptor coactivators via association with the NRC-interacting Factor NIF-1. (PMID: 18180299) Garapaty S … Samuels HH (The Journal of biological chemistry 2008) 3 4 23
  2. Novel factor highly conserved among eukaryotes controls sexual development in fission yeast. (PMID: 9447985) Okazaki N … Okayama H (Molecular and cellular biology 1998) 2 4
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. (PMID: 31091453) Shami Shah A … Baskin JM (Cell reports 2019) 3
  5. A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape. (PMID: 30833792) Hubel P … Pichlmair A (Nature immunology 2019) 3

Products for CNOT9 Gene

Sources for CNOT9 Gene