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    Cnot6 CCR4-NOT transcription complex, subunit 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 287249, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Cnot6provided by RGD
    Official Full Name
    CCR4-NOT transcription complex, subunit 6provided by RGD
    Primary source
    RGD:1310783
    See related
    EnsemblRapid:ENSRNOG00000054891 AllianceGenome:RGD:1310783
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    CCR4; RGD1310783
    Summary
    Predicted to enable nuclear receptor coactivator activity and poly(A)-specific ribonuclease activity. Predicted to be involved in negative regulation of gene expression; positive regulation of cell population proliferation; and positive regulation of cytoplasmic mRNA processing body assembly. Predicted to be located in cytoplasm and nucleus. Predicted to be part of CCR4-NOT complex. Orthologous to human CNOT6 (CCR4-NOT transcription complex subunit 6). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 393.8), Spleen (RPKM 218.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Cnot6 in Genome Data Viewer
    Location:
    10q21
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (34479892..34532166, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (33978785..34031025, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (35144291..35195126, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene Fms related receptor tyrosine kinase 4 Neighboring gene secretoglobin, family 3A, member 1 Neighboring gene CCR4-NOT transcription complex, subunit 6 like 2 Neighboring gene uncharacterized LOC120095087 Neighboring gene uncharacterized LOC120095088 Neighboring gene glutamine-fructose-6-phosphate transaminase 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. CCR4, a 3'-5' poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase. Chen J, et al. EMBO J, 2002 Mar 15. PMID 11889047, Free PMC Article
    2. The Ccr4a (CNOT6) and Ccr4b (CNOT6L) deadenylase subunits of the human Ccr4-Not complex contribute to the prevention of cell death and senescence. Mittal S, et al. Mol Biol Cell, 2011 Mar 15. PMID 21233283, Free PMC Article
    3. CCR4-NOT deadenylates mRNA associated with RNA-induced silencing complexes in human cells. Piao X, et al. Mol Cell Biol, 2010 Mar. PMID 20065043, Free PMC Article
    4. UNR, a new partner of poly(A)-binding protein, plays a key role in translationally coupled mRNA turnover mediated by the c-fos major coding-region determinant. Chang TC, et al. Genes Dev, 2004 Aug 15. PMID 15314026, Free PMC Article
    5. Components of the CCR4-NOT complex function as nuclear hormone receptor coactivators via association with the NRC-interacting Factor NIF-1. Garapaty S, et al. J Biol Chem, 2008 Mar 14. PMID 18180299

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables 3'-5'-RNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA exonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA exonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclear receptor coactivator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclear receptor coactivator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nuclear receptor coactivator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables poly(A)-specific ribonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(A)-specific ribonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables poly(A)-specific ribonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in miRNA-mediated gene silencing by mRNA destabilization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in miRNA-mediated gene silencing by mRNA destabilization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in miRNA-mediated gene silencing by mRNA destabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, no-go decay IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, no-go decay ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, no-go decay ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in nuclear-transcribed mRNA poly(A) tail shortening IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear-transcribed mRNA poly(A) tail shortening ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear-transcribed mRNA poly(A) tail shortening ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cytoplasmic mRNA processing body assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of cytoplasmic mRNA processing body assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of CCR4-NOT complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of CCR4-NOT complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of CCR4-NOT complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    CCR4-NOT transcription complex subunit 6
    Names
    carbon catabolite repressor protein 4 homolog
    cytoplasmic deadenylase
    NP_001380807.1
    XP_038941302.1
    XP_038941304.1
    XP_063124645.1
    XP_063124646.1
    XP_063124647.1
    XP_063124648.1
    XP_063124650.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001393878.1 → NP_001380807.1  CCR4-NOT transcription complex subunit 6

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/Swiss-Prot
      Q6AXU9
      UniProtKB/TrEMBL
      A0A0G2K816
      Related
      ENSRNOP00000074431.2, ENSRNOT00000084509.3
      Conserved Domains (3) summary
      cd10313
      Location:191 → 540
      Deadenylase_CCR4a; C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6
      COG4886
      Location:52 → 159
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:53 → 75
      LRR_1; leucine-rich repeat [structural motif]

    RNA

    1. NR_172026.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      34479892..34532166 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063268576.1 → XP_063124646.1  CCR4-NOT transcription complex subunit 6 isoform X2

      UniProtKB/TrEMBL
      A0A0G2KA59, A6HDX6

    2. XM_063268577.1 → XP_063124647.1  CCR4-NOT transcription complex subunit 6 isoform X2

      UniProtKB/TrEMBL
      A0A0G2KA59, A6HDX6

    3. XM_063268575.1 → XP_063124645.1  CCR4-NOT transcription complex subunit 6 isoform X1

      UniProtKB/Swiss-Prot
      Q6AXU9
      UniProtKB/TrEMBL
      A0A0G2K816

    4. XM_039085376.1 → XP_038941304.1  CCR4-NOT transcription complex subunit 6 isoform X2

      UniProtKB/TrEMBL
      A0A0G2KA59, A6HDX6
      Conserved Domains (3) summary
      COG4886
      Location:52 → 158
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:53 → 75
      LRR_1; leucine-rich repeat [structural motif]
      cl00490
      Location:186 → 535
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    5. XM_039085374.1 → XP_038941302.1  CCR4-NOT transcription complex subunit 6 isoform X1

      UniProtKB/Swiss-Prot
      Q6AXU9
      UniProtKB/TrEMBL
      A0A0G2K816
      Conserved Domains (3) summary
      cd10313
      Location:191 → 540
      Deadenylase_CCR4a; C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6
      COG4886
      Location:52 → 159
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:53 → 75
      LRR_1; leucine-rich repeat [structural motif]

    6. XM_063268578.1 → XP_063124648.1  CCR4-NOT transcription complex subunit 6 isoform X3

      UniProtKB/TrEMBL
      A6HDX8

    7. XM_063268580.1 → XP_063124650.1  CCR4-NOT transcription complex subunit 6 isoform X3

      UniProtKB/TrEMBL
      A6HDX8
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6AXU9.1 GenPept UniProtKB/Swiss-Prot:Q6AXU9

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