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RAT1 ssRNA exonuclease RAT1 [ Saccharomyces cerevisiae S288C ]

Gene ID: 854213, updated on 4-Jan-2025

Summary

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Official Symbol
RAT1
Official Full Name
ssRNA exonuclease RAT1
Primary source
SGD:S000005574
Locus tag
YOR048C
See related
AllianceGenome:SGD:S000005574; FungiDB:YOR048C; VEuPathDB:YOR048C
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Saccharomyces cerevisiae S288C (strain: S288C)
Lineage
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as
HKE1; TAP1; XRN2
Summary
Enables 5'-3' RNA exonuclease activity. Involved in RNA metabolic process and negative regulation of transcription elongation by RNA polymerase II. Acts upstream of or within mRNA splicing, via spliceosome. Located in nucleus. Human ortholog(s) of this gene implicated in adenoid cystic carcinoma and lung cancer. Orthologous to human XRN2 (5'-3' exoribonuclease 2). [provided by Alliance of Genome Resources, Jan 2025]
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Genomic context

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See RAT1 in Genome Data Viewer
Location:
chromosome: XV
Exon count:
1
Sequence:
Chromosome: XV; NC_001147.6 (418630..421650, complement)

Chromosome XV - NC_001147.6Genomic Context describing neighboring genes Neighboring gene ATP-dependent RNA helicase DBP5 Neighboring gene Std1p Neighboring gene phospholipid-translocating ATPase RSB1 Neighboring gene Ett1p

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_001147.6

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Isolation and characterization of RAT1: an essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA. Amberg DC, et al. Genes Dev, 1992 Jul. PMID 1628825
  2. The 5' end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. Henry Y, et al. EMBO J, 1994 May 15. PMID 7515008, Free PMC Article
  3. 5'-exonuclease-2 of Saccharomyces cerevisiae. Purification and features of ribonuclease activity with comparison to 5'-exonuclease-1. Stevens A, et al. J Biol Chem, 1995 Jul 7. PMID 7608167
  4. Kinetic analysis demonstrates a requirement for the Rat1 exonuclease in cotranscriptional pre-rRNA cleavage. Axt K, et al. PLoS One, 2014. PMID 24498264, Free PMC Article
  5. An essential yeast gene with homology to the exonuclease-encoding XRN1/KEM1 gene also encodes a protein with exoribonuclease activity. Kenna M, et al. Mol Cell Biol, 1993 Jan. PMID 8417335, Free PMC Article

See all (130) 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. A termination-independent role of Rat1 in cotranscriptional splicing.
    Title: A termination-independent role of Rat1 in cotranscriptional splicing.
  3. Results indicate that multiple mechanistic features contribute to 5'-3' exoribonuclease Rat1-mediated termination of RNA polymerase II (RNAPII).
    Title: Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1.
  4. Data indicate that Rat1 exonuclease (Rat1) acts catalytically in 5.8S and 25S rRNA processing but binds to the pre-rRNA prior to these activities.
    Title: Kinetic analysis demonstrates a requirement for the Rat1 exonuclease in cotranscriptional pre-rRNA cleavage.
  5. Degradation of the nascent transcript allows Rat1 to pursue Pol II in a guided fashion and arrive at the site of RNA exit from Pol II.
    Title: Dismantling promoter-driven RNA polymerase II transcription complexes in vitro by the termination factor Rat1.
  6. Rat1 exonuclease pre-rRNA folding and 5.8S rRNA maturation are regulated by a cluster of ribosome synthesis factors
    Title: A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease.
  7. data suggest that Rat1p serves to terminate RNAPII molecules engaged in the production of uncapped RNA, regardless of their position on the gene locus.
    Title: The yeast 5'-3' exonuclease Rat1p functions during transcription elongation by RNA polymerase II.
  8. Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1.
    Title: Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1.
  9. the activity of Rat1 is also required for efficient termination by RNA polymerase I (Pol I) on the rDNA
    Title: Efficient termination of transcription by RNA polymerase I requires the 5' exonuclease Rat1 in yeast.
  10. results suggest a unified allosteric/torpedo model in which Rat1 is not a dedicated termination factor, but is an integrated component of the cleavage/polyadenylation apparatus
    Title: The role of Rat1 in coupling mRNA 3'-end processing to transcription termination: implications for a unified allosteric-torpedo model.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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 5'-3' RNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5'-3' RNA exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 5'-3' RNA exonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables exonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables mRNA binding HDA PubMed 
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA-templated transcription termination IEA
Inferred from Electronic Annotation
more info
  
involved_in NAD-cap decapping IDA
Inferred from Direct Assay
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 mRNA processing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription elongation by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in negative regulation of transcription elongation by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nuclear mRNA surveillance IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in nuclear mRNA surveillance 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 nucleobase-containing compound metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in rRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in rRNA processing IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in rRNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in sno(s)RNA processing IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in sno(s)RNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in termination of RNA polymerase II transcription, exosome-dependent IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in termination of RNA polymerase II transcription, exosome-dependent IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in termination of RNA polymerase II transcription, poly(A)-coupled IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in mitochondrion HDA PubMed 
located_in nucleus HDA 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
  

General protein information

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Preferred Names
ssRNA exonuclease RAT1
NP_014691.1
  • Nuclear 5' to 3' single-stranded RNA exonuclease; involved in RNA metabolism, including rRNA and snoRNA processing, as well as poly (A+) dependent and independent mRNA transcription termination; required for cotranscriptional pre-rRNA cleavage; displaces Cdk1p from elongating transcripts, especially as RNAPII reaches the poly(A) site, negatively regulates phosphorylation of the CTD of RNAPII, and inhibits RNAPII transcriptional elongation

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_001147.6 Reference assembly

    Range
    418630..421650 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001183467.1 → NP_014691.1  TPA: ssRNA exonuclease RAT1 [Saccharomyces cerevisiae S288C]

    See identical proteins and their annotated locations for NP_014691.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    D6W2B4, Q02792
    UniProtKB/TrEMBL
    N1NWV4
    Conserved Domains (1) summary
    COG5049
    Location:1 → 1006
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q02792.3

Gene LinkOut

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