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    ccr-4 poly(A)-specific ribonuclease [ Caenorhabditis elegans ]

    Gene ID: 178184, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ccr-4
    Official Full Name
    poly(A)-specific ribonuclease
    Primary source
    WormBase:WBGene00000376
    Locus tag
    CELE_ZC518.3
    See related
    AllianceGenome:WB:WBGene00000376
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Caenorhabditis elegans (strain: Bristol N2)
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
    Summary
    Predicted to enable poly(A)-specific ribonuclease activity. Involved in nuclear-transcribed mRNA poly(A) tail shortening. Located in cytoplasm. Part of CCR4-NOT complex. Is expressed in several structures, including germ line; hypodermis; neurons; pharynx; and somatic cell. Orthologous to human CNOT6 (CCR4-NOT transcription complex subunit 6) and CNOT6L (CCR4-NOT transcription complex subunit 6 like). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See ccr-4 in Genome Data Viewer
    Location:
    chromosome: IV
    Exon count:
    11
    Sequence:
    Chromosome: IV; NC_003282.8 (12361542..12371852)

    Chromosome IV - NC_003282.8Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene Bestrophin homolog;Bestrophin homolog 22 Neighboring gene uncharacterized protein Neighboring gene Glutathione S-transferase Neighboring gene ncRNA Neighboring gene WD repeat-containing protein 46 Neighboring gene Protein atz-1 Neighboring gene ncRNA Neighboring gene pseudo

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003282.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. CCR4-NOT subunit CCF-1/CNOT7 promotes transcriptional activation to multiple stress responses in Caenorhabditis elegans. Tabarraei H, et al. Aging Cell, 2023 Apr. PMID 36797658, Free PMC Article
    2. Distinct Poly(A) nucleases have differential impact on sut-2 dependent tauopathy phenotypes. Kow RL, et al. Neurobiol Dis, 2021 Jan. PMID 33184027, Free PMC Article
    3. Increased sensitivity and accuracy of a single-stranded DNA splint-mediated ligation assay (sPAT) reveals poly(A) tail length dynamics of developmentally regulated mRNAs. Minasaki R, et al. RNA Biol, 2014. PMID 24526206, Free PMC Article
    4. Two conserved regulatory cytoplasmic poly(A) polymerases, GLD-4 and GLD-2, regulate meiotic progression in C. elegans. Schmid M, et al. Genes Dev, 2009 Apr 1. PMID 19339688, Free PMC Article
    5. Stage-specific combinations of opposing poly(A) modifying enzymes guide gene expression during early oogenesis. Nousch M, et al. Nucleic Acids Res, 2019 Nov 18. PMID 31511882, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CCR4-NOT subunit CCF-1/CNOT7 promotes transcriptional activation to multiple stress responses in Caenorhabditis elegans.
      Title: CCR4-NOT subunit CCF-1/CNOT7 promotes transcriptional activation to multiple stress responses in Caenorhabditis elegans.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by WormBase

    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 catalytic activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables endonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(A)-specific ribonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in nuclear-transcribed mRNA poly(A) tail shortening IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of CCR4-NOT complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    poly(A)-specific ribonuclease
    NP_001023607.1
    • Confirmed by transcript evidence
    NP_001129877.1
    • Confirmed by transcript evidence
    NP_001293990.1
    • Confirmed by transcript evidence
    NP_001379313.1
    • Confirmed by transcript evidence
    NP_502355.2
    • Confirmed by transcript evidence

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003282.8 Reference assembly

      Range
      12361542..12371852
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001028436.4 → NP_001023607.1  poly(A)-specific ribonuclease [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001023607.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      Q9U1P4
      Conserved Domains (3) summary
      cd09097
      Location:229 → 575
      Deadenylase_CCR4; C-terminal deadenylase domain of CCR4 and related domains
      COG4886
      Location:82 → 233
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:96 → 118
      LRR_RI; leucine-rich repeat [structural motif]

    2. NM_069954.6 → NP_502355.2  poly(A)-specific ribonuclease [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_502355.2

      Status: REVIEWED

      UniProtKB/TrEMBL
      G5EE09
      Conserved Domains (3) summary
      cd09097
      Location:222 → 568
      Deadenylase_CCR4; C-terminal deadenylase domain of CCR4 and related domains
      COG4886
      Location:75 → 226
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:68 → 88
      LRR_1; leucine-rich repeat [structural motif]

    3. NM_001392415.1 → NP_001379313.1  poly(A)-specific ribonuclease [Caenorhabditis elegans]

      Status: REVIEWED

      UniProtKB/TrEMBL
      Q8I4B4
      Conserved Domains (3) summary
      cd09097
      Location:213 → 559
      Deadenylase_CCR4; C-terminal deadenylase domain of CCR4 and related domains
      COG4886
      Location:66 → 217
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:80 → 102
      LRR_RI; leucine-rich repeat [structural motif]

    4. NM_001136405.2 → NP_001129877.1  poly(A)-specific ribonuclease [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001129877.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      B3GWC3
      Conserved Domains (1) summary
      cd09097
      Location:293 → 639
      Deadenylase_CCR4; C-terminal deadenylase domain of CCR4 and related domains

    5. NM_001307061.3 → NP_001293990.1  poly(A)-specific ribonuclease [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001293990.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A061AD13
      Conserved Domains (1) summary
      cd09097
      Location:16 → 362
      Deadenylase_CCR4; C-terminal deadenylase domain of CCR4 and related domains
    Nucleotide Protein
    Heading Accession and Version

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