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RAI1 decapping nuclease [ Saccharomyces cerevisiae S288C ]

Gene ID: 852646, updated on 29-Jun-2024

Summary

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Gene symbol
RAI1
Gene description
decapping nuclease
Primary source
FungiDB:YGL246C
Locus tag
YGL246C
See related
SGD:S000003215; AllianceGenome:SGD:S000003215; VEuPathDB:YGL246C
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Saccharomyces cerevisiae S288C (strain: S288C)
Lineage
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary
Enables RNA pyrophosphohydrolase activity; enzyme regulator activity; and phosphodiesterase decapping endonuclease activity. Involved in RNA metabolic process. Located in cytosol and nucleus. Orthologous to human DXO (decapping exoribonuclease). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See RAI1 in Genome Data Viewer
Location:
chromosome: VII
Exon count:
1
Sequence:
Chromosome: VII; NC_001139.9 (37617..38780, complement)

Chromosome VII - NC_001139.9Genomic Context describing neighboring genes Neighboring gene 3',5'-cyclic-nucleotide phosphodiesterase PDE1 Neighboring gene Brr6p Neighboring gene glutamate--tRNA ligase GUS1 Neighboring gene Rtf1p

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_001139.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. "NAD-capQ" detection and quantitation of NAD caps. Grudzien-Nogalska E, et al. RNA, 2018 Oct. PMID 30045887, Free PMC Article
  2. Dismantling promoter-driven RNA polymerase II transcription complexes in vitro by the termination factor Rat1. Pearson EL, et al. J Biol Chem, 2013 Jul 5. PMID 23689372, Free PMC Article
  3. Dxo1 is a new type of eukaryotic enzyme with both decapping and 5'-3' exoribonuclease activity. Chang JH, et al. Nat Struct Mol Biol, 2012 Oct. PMID 22961381, Free PMC Article
  4. Torpedo nuclease Rat1 is insufficient to terminate RNA polymerase II in vitro. Dengl S, et al. J Biol Chem, 2009 Aug 7. PMID 19535338, Free PMC Article
  5. Transcription termination complex, Rtt103-Rai1-Rat1, regulates sub-telomeric transcripts in Saccharomyces cerevisiae. Ramalingam K, et al. RNA Biol, 2023 Jan. PMID 36974034, Free PMC Article

See all (63) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Transcription termination complex, Rtt103-Rai1-Rat1, regulates sub-telomeric transcripts in Saccharomyces cerevisiae.
    Title: Transcription termination complex, Rtt103-Rai1-Rat1, regulates sub-telomeric transcripts in Saccharomyces cerevisiae.
  2. Results identified Rai1, in regulating early transcription elongation genome-wide and a novel role for the histone modifier, Bre1, in regulating Pol II dynamics at polyA sites.
    Title: Subgenic Pol II interactomes identify region-specific transcription elongation regulators.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by SGD

Function Evidence Code Pubs
enables RNA NAD+-cap (NAD+-forming) hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables enzyme regulator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables mRNA 5'-diphosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables mRNA 5'-diphosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphodiesterase decapping endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphodiesterase decapping endonuclease activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription termination IEA
Inferred from Electronic Annotation
more info
  
involved_in NAD-cap decapping IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within NAD-cap decapping IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in deadenylation-independent decapping of nuclear-transcribed mRNA IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nuclear polyadenylation-dependent rRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nuclear-transcribed mRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nuclear-transcribed mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in rRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in termination of RNA polymerase II transcription, poly(A)-coupled IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
decapping nuclease
NP_011268.1
  • Nuclear decapping endonuclease; targets mRNAs with unmethylated 7-methylguanosine cap structures and 5'-triphosphates; binds to and stabilizes the exoribonuclease Rat1p; required for pre-rRNA processing; involved in an early step of decapping non-canonical nicotinamide adenine dinucleotide (NAD) capped nuclear mRNAs (NAD-RNAs), part of ncRNA surveillance; relocalizes to the cytosol in response to hypoxia; homologous to human DOM3Z

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_001139.9 Reference assembly

    Range
    37617..38780 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001181112.1 → NP_011268.1  TPA: decapping nuclease [Saccharomyces cerevisiae S288C]

    See identical proteins and their annotated locations for NP_011268.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    D6VV89, P53063
    UniProtKB/TrEMBL
    A0A8H4FBG1, A6ZTU5, B3LHT8, B5VI97, C7GNZ2, C8Z812, N1P5F9
    Conserved Domains (1) summary
    pfam08652
    Location:222 → 289
    RAI1; RAI1 like PD-(D/E)XK nuclease
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P53063.3

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