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

Gene ID: 178184, updated on 2-Nov-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, Nov 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 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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of CCR4-NOT complex IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
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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