RAT1/YOR048C Summary Help

Standard Name RAT1 1
Systematic Name YOR048C
Alias HKE1 , TAP1 , XRN2
Feature Type ORF, Verified
Description Nuclear 5' to 3' single-stranded RNA exonuclease; involved in RNA metabolism, including rRNA and snRNA processing as well as poly (A+) dependent and independent mRNA transcription termination; required for cotranscriptional pre-rRNA cleavage (1, 2, 3, 4, 5 and see Summary Paragraph)
Name Description Ribonucleic Acid Trafficking 1
Chromosomal Location
ChrXV:421650 to 418630 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: 17.1 cM
Gene Ontology Annotations All RAT1 GO evidence and references
  View Computational GO annotations for RAT1
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 3 genes
Classical genetics
Large-scale survey
reduction of function
75 total interaction(s) for 47 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 30
  • Affinity Capture-RNA: 1
  • Affinity Capture-Western: 4
  • Biochemical Activity: 1
  • Reconstituted Complex: 1

Genetic Interactions
  • Dosage Growth Defect: 1
  • Dosage Rescue: 2
  • Negative Genetic: 1
  • Phenotypic Enhancement: 11
  • Phenotypic Suppression: 5
  • Synthetic Growth Defect: 6
  • Synthetic Lethality: 3
  • Synthetic Rescue: 9

Expression Summary
Length (a.a.) 1,006
Molecular Weight (Da) 115,933
Isoelectric Point (pI) 6.8
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrXV:421650 to 418630 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: 17.1 cM
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..3021 421650..418630 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000005574

RAT1 encodes a nuclear 5'-3' exoribonuclease involved in rRNA processing (1, 6, 7).

RAT1 has been identified in several different screens, including a screen for temperature-sensitive mutations that cause defects in mRNA export (RAT1, (1)), mutations that activate Pol III transcription of a tRNA with a mutated promoter (TAP1,(7)), and mutations that are synthetically lethal with swi4 mutations (RSF11, (8)). The connection between these different genetic screens and RAT1 function has not yet been made.

Rat1p is 39% identical to the cytoplasmic Kem1p/Xrn1p exonuclease (1, 6, 7). Only dominant alleles of RAT1 were found in a screen for suppressors that rescued the viability of a kem1 ski2 double mutant strain; Ski2p is a putative RNA helicase (2). These dominant alleles of RAT1 mislocalized Rat1p to the cytoplasm. Overexpression of wildtype KEM1 does not suppress rat1-1 mutations; however, if Kem1p is targeted to the nucleus, it can substitute for Rat1p function, suggesting that Rat1p and Kem1p are functionally redundant proteins performing roles in separate cellular compartments (2). The rat1-1 allele exhibits temperature-sensitive defects in the formation of the 5' end of 5.8s rRNA, implicating Rat1p in processing of rRNA (1, 9). It was later shown that Rat1p and Kem1p are involved in processing pre-rRNA spacer fragments and snoRNAs as well (10).

Last updated: 2000-04-12 Contact SGD

References cited on this page View Complete Literature Guide for RAT1
1) Amberg DC, et al.  (1992) Isolation and characterization of RAT1: an essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA. Genes Dev 6(7):1173-89
2) Johnson AW  (1997) Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively. Mol Cell Biol 17(10):6122-30
3) Kim M, et al.  (2004) The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432(7016):517-22
4) Ghazal G, et al.  (2009) Yeast RNase III triggers polyadenylation-independent transcription termination. Mol Cell 36(1):99-109
5) Axt K, et al.  (2014) Kinetic Analysis Demonstrates a Requirement for the Rat1 Exonuclease in Cotranscriptional Pre-rRNA Cleavage. PLoS One 9(2):e85703
6) Kenna M, et al.  (1993) An essential yeast gene with homology to the exonuclease-encoding XRN1/KEM1 gene also encodes a protein with exoribonuclease activity. Mol Cell Biol 13(1):341-50
7) Di Segni G, et al.  (1993) TAP1, a yeast gene that activates the expression of a tRNA gene with a defective internal promoter. Mol Cell Biol 13(6):3424-33
8) Toone WM, et al.  (1995) Rme1, a negative regulator of meiosis, is also a positive activator of G1 cyclin gene expression. EMBO J 14(23):5824-32
9) Henry Y, et al.  (1994) The 5' end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. EMBO J 13(10):2452-63
10) Petfalski E, et al.  (1998) Processing of the precursors to small nucleolar RNAs and rRNAs requires common components. Mol Cell Biol 18(3):1181-9