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Aliases for CNOT9 Gene

Aliases for CNOT9 Gene

  • CCR4-NOT Transcription Complex Subunit 9 2 3 5
  • Cell Differentiation Protein RQCD1 Homolog 3 4
  • Cancer/Testis Antigen 129 2 3
  • RCD-1 3 4
  • RQCD1 3 4
  • RCD1 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
  • CAF40 3
  • CT129 3

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. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Deadenylation-dependent mRNA decay.

UniProtKB/Swiss-Prot 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.

Additional gene information for CNOT9 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CNOT9 Gene

Genomics for CNOT9 Gene

Regulatory Elements for CNOT9 Gene

Enhancers for CNOT9 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02H218393 2.1 FANTOM5 Ensembl ENCODE dbSUPER 44.9 -167.6 -167569 14 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC SSRP1 CNOT9 AAMP USP37 STK36 ANKZF1 TNS1 BCS1L ENSG00000273466 NHEJ1 TMBIM1
GH02H218908 2 FANTOM5 Ensembl ENCODE dbSUPER 34.9 +341.0 341024 2 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZBTB7B CNOT9 STK36 ZNF142 USP37 AAMP OBSL1 NHEJ1 CDK5R2 ENSG00000235024 ENSG00000269068
GH02H218566 1.8 FANTOM5 ENCODE dbSUPER 25.3 +0.7 743 4 HDGF PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B AAMP CNOT9 USP37 PLCD4 BCS1L NHEJ1 CNPPD1 SLC23A3 ZNF142 RNF25
GH02H218710 1.4 ENCODE dbSUPER 27 +142.6 142637 2 HDGF FOXA2 PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B AAMP CNOT9 STK36 DES ANKZF1 LINC00608 ENSG00000234638 RNF25 STK11IP TNS1
GH02H218658 1.1 ENCODE 33.6 +91.0 91013 2 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 ZNF143 SP3 CNOT9 USP37 AAMP NHEJ1 STK11IP PLCD4 RNF25 STK36 BCS1L ZNF142
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CNOT9 on UCSC Golden Path with GeneCards custom track

Promoters for CNOT9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000130427 325 3001 HDGF PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B

Genomic Location for CNOT9 Gene

Chromosome:
2
Start:
218,568,575 bp from pter
End:
218,597,080 bp from pter
Size:
28,506 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=Translation N-terminally shortened.; 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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CNOT9 Gene

Domains & Families for CNOT9 Gene

Gene Families for CNOT9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for CNOT9 Gene

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

Clone Products

  • Applied Biological Materials Clones for CNOT9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
cytosol 5
nucleus 4
extracellular 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for CNOT9 Gene

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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CNOT9 Gene

Pathways & Interactions for CNOT9 Gene

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

Gene Ontology (GO) - Biological Process for CNOT9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IBA --
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006402 mRNA catabolic process IEA --
genes like me logo Genes that share ontologies with CNOT9: view

No data available for SIGNOR curated interactions for CNOT9 Gene

Drugs & Compounds for CNOT9 Gene

No Compound Related Data Available

Transcripts for CNOT9 Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CNOT9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

No ASD Table

Relevant External Links for CNOT9 Gene

GeneLoc Exon Structure for
CNOT9
ECgene alternative splicing isoforms for
CNOT9

Expression for CNOT9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of CNOT9 Gene:

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(4.5)
genes like me logo Genes that share expression patterns with CNOT9: view

Primer Products

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 34
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RQCD1 33 34
  • 99.55 (n)
dog
(Canis familiaris)
Mammalia RQCD1 33 34
  • 95.21 (n)
cow
(Bos Taurus)
Mammalia RQCD1 33 34
  • 94.76 (n)
rat
(Rattus norvegicus)
Mammalia Rqcd1 33
  • 92.98 (n)
mouse
(Mus musculus)
Mammalia Rqcd1 33 34
  • 92.2 (n)
Cnot9 16
platypus
(Ornithorhynchus anatinus)
Mammalia RQCD1 34
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves RQCD1 33 34
  • 83.19 (n)
lizard
(Anolis carolinensis)
Reptilia RQCD1 34
  • 99 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rqcd1 33
  • 79.38 (n)
MGC76003 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.13761 33
zebrafish
(Danio rerio)
Actinopterygii rqcd1 33 34
  • 75.79 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1813 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012050 33
  • 67.73 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rcd-1 33 34
  • 66.79 (n)
Rcd-1r 34
  • 59 (a)
OneToMany
CG2053 34
  • 37 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ntl-9 33 34
  • 64.38 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL194W 33
  • 59.6 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CAF40 33 34 36
  • 56.26 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E13267g 33
  • 55.56 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G20800 33
  • 59.75 (n)
soybean
(Glycine max)
eudicotyledons Gma.4905 33
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.4960 33
rice
(Oryza sativa)
Liliopsida Os04g0613400 33
  • 64.1 (n)
wheat
(Triticum aestivum)
Liliopsida Ta.6222 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 91 (a)
OneToMany
CSA.8006 34
  • 86 (a)
OneToMany
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rcd1 33
  • 62.08 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU07071 33
  • 60.89 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3625 33
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)

Paralogs for CNOT9 Gene

No data available for Paralogs for CNOT9 Gene

Variants for CNOT9 Gene

Sequence variations from dbSNP and Humsavar for CNOT9 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000079946 -- 218,569,737(+) ATGCA(C/G)TTTGT intron-variant, upstream-variant-2KB
rs1000113410 -- 218,577,300(+) TGGGG(A/C/G)TGAAA intron-variant
rs1000463999 -- 218,567,935(+) AAGGG(A/G)CCAGG intron-variant, upstream-variant-2KB
rs1000540838 -- 218,573,394(+) CCAGC(A/G)CTATT intron-variant, utr-variant-5-prime
rs1000552143 -- 218,572,667(+) GCCAT(A/G)GGTAT intron-variant, upstream-variant-2KB

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)

Relevant External Links for CNOT9 Gene

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

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

Disorders for CNOT9 Gene

Relevant External Links for CNOT9

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CNOT9

No disorders were found for CNOT9 Gene.

No data available for MalaCards , 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 22 60
  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 3 4 60
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  4. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. (PMID: 27173435) Boldt K … UK10K Rare Diseases Group (Nature communications 2016) 3 60
  5. A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. (PMID: 26673895) Kırlı K … Görlich D (eLife 2015) 3 60

Products for CNOT9 Gene

Sources for CNOT9 Gene

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