This page displays GO annotations in different sections according to the annotation method used to add that annotation to SGD.

Last Reviewed on: 2009-09-15    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
3'-5'-exoribonuclease activity	IDA: Inferred from Direct Assay Assigned on 2009-02-11	Burkard KT and Butler JS  (2000) A nuclear 3'-5' exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p. Mol Cell Biol 20(2):604-16	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Callahan KP and Butler JS  (2008) Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p. Nucleic Acids Res 36(21):6645-55	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-10-03	Allmang C, et al.  (1999) Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J 18(19):5399-410	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-02-11	Briggs MW, et al.  (1998) Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3' end formation. J Biol Chem 273(21):13255-63	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-10-03	Allmang C, et al.  (1999) The yeast exosome and human PM-Scl are related complexes of 3' --> 5' exonucleases. Genes Dev 13(16):2148-58	SGD
histone mRNA catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Reis CC and Campbell JL  (2007) Contribution of Trf4/5 and the nuclear exosome to genome stability through regulation of histone mRNA levels in Saccharomyces cerevisiae. Genetics 175(3):993-1010	SGD
nuclear polyadenylation-dependent antisense transcript catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Camblong J, et al.  (2007) Antisense RNA Stabilization Induces Transcriptional Gene Silencing via Histone Deacetylation in S. cerevisiae. Cell 131(4):706-17	SGD
nuclear polyadenylation-dependent CUT catabolic process	IGI: Inferred from Genetic Interaction with SGD:PAP2 Assigned on 2009-08-31 IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Wyers F, et al.  (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121(5):725-37	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Arigo JT, et al.  (2006) Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol Cell 23(6):841-51	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Houseley J, et al.  (2007) Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control. EMBO J 26(24):4996-5006	SGD
nuclear polyadenylation-dependent mRNA catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Egecioglu DE, et al.  (2006) Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA 12(1):26-32	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Roth KM, et al.  (2009) Regulation of NAB2 mRNA 3'-end formation requires the core exosome and the Trf4p component of the TRAMP complex. RNA 15(6):1045-58	SGD
nuclear polyadenylation-dependent rRNA catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Callahan KP and Butler JS  (2008) Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p. Nucleic Acids Res 36(21):6645-55	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Kadaba S, et al.  (2006) Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA. RNA 12(3):508-21	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Kuai L, et al.  (2004) Polyadenylation of rRNA in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 101(23):8581-6	SGD
	IGI: Inferred from Genetic Interaction with SGD:SDA1 Assigned on 2009-08-31	Dez C, et al.  (2006) Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae. EMBO J 25(7):1534-46	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Fang F, et al.  (2004) 5-fluorouracil enhances exosome-dependent accumulation of polyadenylated rRNAs. Mol Cell Biol 24(24):10766-76	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Houseley J, et al.  (2007) Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control. EMBO J 26(24):4996-5006	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Allmang C, et al.  (1999) The yeast exosome and human PM-Scl are related complexes of 3' --> 5' exonucleases. Genes Dev 13(16):2148-58	SGD
nuclear polyadenylation-dependent snoRNA catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Egecioglu DE, et al.  (2006) Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA 12(1):26-32	SGD
nuclear polyadenylation-dependent snRNA catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Kadaba S, et al.  (2006) Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA. RNA 12(3):508-21	SGD
nuclear polyadenylation-dependent tRNA catabolic process	IGI: Inferred from Genetic Interaction with SGD:PAP2 Assigned on 2009-08-31	Copela LA, et al.  (2008) Competition between the Rex1 exonuclease and the La protein affects both Trf4p-mediated RNA quality control and pre-tRNA maturation. RNA 14(6):1214-27	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-08-31	Vanacova S, et al.  (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3(6):e189	SGD
nuclear retention of pre-mRNA at the site of transcription	IGI: Inferred from Genetic Interaction with SGD:HPR1, SGD:MFT1, SGD:SUB2 Assigned on 2009-09-10	Rougemaille M, et al.  (2007) Dissecting mechanisms of nuclear mRNA surveillance in THO/sub2 complex mutants. EMBO J 26(9):2317-26	SGD
nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription	IGI: Inferred from Genetic Interaction with SGD:RIP1, SGD:NUP159, SGD:PAP1 Assigned on 2009-08-31	Hilleren P, et al.  (2001) Quality control of mRNA 3'-end processing is linked to the nuclear exosome. Nature 413(6855):538-42	SGD
	IGI: Inferred from Genetic Interaction with SGD:MFT1, SGD:HPR1, SGD:RNA15, SGD:RNA14 Assigned on 2009-08-31	Libri D, et al.  (2002) Interactions between mRNA export commitment, 3'-end quality control, and nuclear degradation. Mol Cell Biol 22(23):8254-66	SGD
polyadenylation-dependent snoRNA 3'-end processing	IMP: Inferred from Mutant Phenotype Assigned on 2009-09-01	Egecioglu DE, et al.  (2006) Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA 12(1):26-32	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	van Hoof A, et al.  (2000) Yeast exosome mutants accumulate 3'-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol Cell Biol 20(2):441-52	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Grzechnik P and Kufel J  (2008) Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast. Mol Cell 32(2):247-58	SGD
posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery	IMP: Inferred from Mutant Phenotype Assigned on 2009-09-14	Vodala S, et al.  (2008) The nuclear exosome and adenylation regulate posttranscriptional tethering of yeast GAL genes to the nuclear periphery. Mol Cell 31(1):104-13	SGD
U1 snRNA 3'-end processing	IGI: Inferred from Genetic Interaction with SGD:RNT1 Assigned on 2008-10-03 IMP: Inferred from Mutant Phenotype Assigned on 2008-10-03	Allmang C, et al.  (1999) Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J 18(19):5399-410	SGD
U4 snRNA 3'-end processing	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Egecioglu DE, et al.  (2006) Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA 12(1):26-32	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-10-06	van Hoof A, et al.  (2000) Yeast exosome mutants accumulate 3'-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol Cell Biol 20(2):441-52	SGD
	IGI: Inferred from Genetic Interaction with SGD:RNT1 Assigned on 2008-10-03 IMP: Inferred from Mutant Phenotype Assigned on 2008-10-03	Allmang C, et al.  (1999) Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J 18(19):5399-410	SGD
	IGI: Inferred from Genetic Interaction with SGD:REX2 Assigned on 2008-06-10	van Hoof A, et al.  (2000) Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNase MRP and RNase P RNAs in yeast. EMBO J 19(6):1357-65	SGD
U5 snRNA 3'-end processing	IGI: Inferred from Genetic Interaction with SGD:RNT1 Assigned on 2008-10-03 IMP: Inferred from Mutant Phenotype Assigned on 2008-10-03	Allmang C, et al.  (1999) Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J 18(19):5399-410	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
nuclear exosome (RNase complex)	IDA: Inferred from Direct Assay Assigned on 2009-09-10	Synowsky SA, et al.  (2009) Comparative multiplexed mass spectrometric analyses of endogenously expressed yeast nuclear and cytoplasmic exosomes. J Mol Biol 385(4):1300-13	SGD
	IDA: Inferred from Direct Assay Assigned on 2001-01-18	Allmang C, et al.  (1999) The yeast exosome and human PM-Scl are related complexes of 3' --> 5' exonucleases. Genes Dev 13(16):2148-58	SGD
nucleolus	IDA: Inferred from Direct Assay Assigned on 2009-08-24	Dez C, et al.  (2006) Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae. EMBO J 25(7):1534-46	SGD
nucleus	IDA: Inferred from Direct Assay Assigned on 2009-02-11	Burkard KT and Butler JS  (2000) A nuclear 3'-5' exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p. Mol Cell Biol 20(2):604-16	SGD

* Manually curated GO annotations reflect our best understanding of the basic molecular function, biological process, and cellular component for this gene product. Manually curated annotations are assigned by SGD curators based on published papers when available, or by curatorial statements if necessary. Curators periodically review all Manually curated GO annotations for accuracy and completeness. The "Last Reviewed on:" date at the top of this section indicates when these annotations were last reviewed.

There are no High-throughput annotations for RRP6

** GO annotations from High-throughput experiments are made based on a variety of large scale high-throughput experiments, including genome-wide experiments. Many of these annotations are made based on GO annotations (or mappings to GO annotations) assigned by the authors, rather than SGD curators. While SGD curators read these publications and often work closely with authors to incorporate the information, each individual annotation may not necessarily be reviewed by a curator. GO Annotations from high-throughput experiments will be assigned only when this type of data is available, and thus may not be assigned in all three aspects of the Gene Ontologies.

Molecular Function | Biological Process | Cellular Component

Computational Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
3'-5' exonuclease activity	IEA: Inferred from Electronic Annotation with EBI:IPR002562 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
catalytic activity	IEA: Inferred from Electronic Annotation with EBI:IPR010997 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
exonuclease activity	IEA: Inferred from Electronic Annotation with EBI:KW-0269 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
hydrolase activity	IEA: Inferred from Electronic Annotation with EBI:KW-0378 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
nuclease activity	IEA: Inferred from Electronic Annotation with EBI:KW-0540 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
nucleic acid binding	IEA: Inferred from Electronic Annotation with EBI:IPR012337, EBI:IPR002562, EBI:IPR002121 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
nucleotide binding	IEA: Inferred from Electronic Annotation with EBI:IPR010997 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
RNA binding	IEA: Inferred from Electronic Annotation with EBI:KW-0694 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
cellular metabolic process	IEA: Inferred from Electronic Annotation with EBI:IPR010997 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
nucleobase-containing compound metabolic process	IEA: Inferred from Electronic Annotation with EBI:IPR002562 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
RNA processing	IEA: Inferred from Electronic Annotation with EBI:IPR012588 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
rRNA processing	IEA: Inferred from Electronic Annotation with EBI:KW-0698 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

Computational Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
exosome (RNase complex)	IEA: Inferred from Electronic Annotation with EBI:KW-0271 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
intracellular	IEA: Inferred from Electronic Annotation with EBI:IPR002562, EBI:IPR002121 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
nuclear exosome (RNase complex)	IEA: Inferred from Electronic Annotation with EBI:IPR012588 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
nucleolus	IEA: Inferred from Electronic Annotation with EBI:SL-0188 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.	UniProtKB
nucleus	IEA: Inferred from Electronic Annotation with EBI:KW-0539 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

*** Computational GO Annotations are predictions. These annotations are NOT reviewed by a curator. Currently, all computational GO annotations for S. cerevisiae are assigned by an external source (for example, the Gene Ontology Annotation (GOA) project of the European Bioinformatics Institute (EBI)).