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Aliases for CNOT9 Gene

Aliases for CNOT9 Gene

  • CCR4-NOT Transcription Complex Subunit 9 2 3 4 5
  • 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 RQCD1 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 Deadenylation-dependent mRNA decay and Gene Expression.

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.

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
GH02G218566 1.8 FANTOM5 ENCODE dbSUPER 25.3 +0.7 743 4.7 MLX CREB3L1 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC CNOT9 PLCD4 BCS1L USP37 SLC23A3 NHEJ1 AAMP ZNF142 RNF25 CNPPD1
GH02G218470 1.2 FANTOM5 Ensembl ENCODE 26.7 -97.1 -97094 1.9 CTCF RFX1 MXI1 EP300 RAD21 SMC3 CREB1 HMBOX1 FOS ETV6 CNOT9 MIR26B TMBIM1 PNKD AAMP USP37 RN7SKP38 VIL1
GH02G218443 1.1 ENCODE 26.3 -122.7 -122740 4.1 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF143 CNOT9 PLCD4 RETREG2 USP37 VIL1 RN7SKP38
GH02G219368 1.2 Ensembl ENCODE 20.5 +800.7 800731 2.4 FOXA2 FEZF1 ZNF2 GATA2 ZNF416 KLF7 YY2 REST TSHZ1 ZNF488 RNF25 CNOT9 STK36 ANKZF1 ENSG00000269068 RESP18 ASIC4 TMEM198 PTPRN SPEG
GH02G219520 1.8 FANTOM5 Ensembl ENCODE dbSUPER 13.6 +953.5 953450 3.5 HDGF PKNOX1 ATF1 ARNT ETS1 TCF12 GTF3C2 ZNF766 GLIS2 ELK1 ASIC4 CNOT9 NHEJ1 USP37 SLC23A3 BCS1L ANKZF1 ENSG00000272644 LOC105373885 TMEM198
- 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 MLX CREB3L1 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC

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-RCD1_HUMAN
    Recommended name:
    Cell differentiation protein RCD1 homolog
    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

Protein Domains for CNOT9 Gene

Graphical View of Domain Structure for InterPro Entry

Q92600

UniProtKB/Swiss-Prot:

RCD1_HUMAN :
  • Belongs to the RCD1 family.
Family:
  • Belongs to the RCD1 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.

Gene Ontology (GO) - Molecular Function for CNOT9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18180299
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

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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 IBA,ISS --
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

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: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 --
GO:0006417 regulation of translation IEA --
genes like me logo Genes that share ontologies with CNOT9: view

No data available for SIGNOR curated interactions for CNOT9 Gene

Transcripts for CNOT9 Gene

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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-RCD1_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 35
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RQCD1 35 34
  • 99.55 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RQCD1 34 35
  • 95.21 (n)
cow
(Bos Taurus)
Mammalia RQCD1 34 35
  • 94.76 (n)
rat
(Rattus norvegicus)
Mammalia Rqcd1 34
  • 92.98 (n)
mouse
(Mus musculus)
Mammalia Rqcd1 34 35
  • 92.2 (n)
Cnot9 16
platypus
(Ornithorhynchus anatinus)
Mammalia RQCD1 35
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves RQCD1 34 35
  • 83.19 (n)
lizard
(Anolis carolinensis)
Reptilia RQCD1 35
  • 99 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rqcd1 34
  • 79.38 (n)
MGC76003 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.13761 34
zebrafish
(Danio rerio)
Actinopterygii rqcd1 34 35
  • 75.79 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1813 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012050 34
  • 67.73 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rcd-1 34 35
  • 66.79 (n)
Rcd-1r 35
  • 59 (a)
OneToMany
CG2053 35
  • 37 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ntl-9 34 35
  • 64.38 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL194W 34
  • 59.6 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CAF40 34 35 37
  • 56.26 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E13267g 34
  • 55.56 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G20800 34
  • 59.75 (n)
soybean
(Glycine max)
eudicotyledons Gma.4905 34
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.4960 34
rice
(Oryza sativa)
Liliopsida Os04g0613400 34
  • 64.1 (n)
wheat
(Triticum aestivum)
Liliopsida Ta.6222 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 91 (a)
OneToMany
CSA.8006 35
  • 86 (a)
OneToMany
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rcd1 34
  • 62.08 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU07071 34
  • 60.89 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3625 34
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 H.H. (J. Biol. Chem. 2008) 3 4 22 64
  2. Novel factor highly conserved among eukaryotes controls sexual development in fission yeast. (PMID: 9447985) Okazaki N. … Okayama H. (Mol. Cell. Biol. 1998) 2 3 4 64
  3. BioID-based Identification of Skp Cullin F-box (SCF)I^-TrCP1/2 E3 Ligase Substrates. (PMID: 25900982) Coyaud E. … Raught B. (Mol. Cell Proteomics 2015) 3 64
  4. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3 64
  5. RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-I_B pathway. (PMID: 26170170) Murakawa Y. … Landthaler M. (Nat Commun 2015) 3 64

Products for CNOT9 Gene

Sources for CNOT9 Gene

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