RAT1 ssRNA exonuclease RAT1 [Saccharomyces cerevisiae S288C] - Gene

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, Dec 2024]
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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_001147.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001147.6

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
A termination-independent role of Rat1 in cotranscriptional splicing.
Title: A termination-independent role of Rat1 in cotranscriptional splicing.
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.
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.
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.
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.
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.
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.
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.
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.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

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 more info	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 more info	PubMed
located_in nucleus	HDA 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

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

NC_001147.6 Reference assembly

Range

418630..421650 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]