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	IMP: Inferred from Mutant Phenotype Assigned on 2007-03-09 IDA: Inferred from Direct Assay Assigned on 2007-03-09	Dziembowski A, et al.  (2007) A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat Struct Mol Biol 14(1):15-22	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-02-03 IDA: Inferred from Direct Assay Assigned on 2009-02-03	Schneider C, et al.  (2007) The exosome subunit Rrp44 plays a direct role in RNA substrate recognition. Mol Cell 27(2):324-31	SGD
endoribonuclease activity	IMP: Inferred from Mutant Phenotype Assigned on 2009-02-04 IDA: Inferred from Direct Assay Assigned on 2009-02-04	Schneider C, et al.  (2009) The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome. Nucleic Acids Res 37(4):1127-40	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-02-04 IDA: Inferred from Direct Assay Assigned on 2009-02-04	Lebreton A, et al.  (2008) Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature 456(7224):993-6	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-02-04	Schaeffer D, et al.  (2009) The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nat Struct Mol Biol 16(1):56-62	SGD
tRNA binding	IMP: Inferred from Mutant Phenotype Assigned on 2009-02-03 IDA: Inferred from Direct Assay Assigned on 2009-02-03	Schneider C, et al.  (2007) The exosome subunit Rrp44 plays a direct role in RNA substrate recognition. Mol Cell 27(2):324-31	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 2008-09-22	Mitchell P, et al.  (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Cell 91(4):457-66	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
ncRNA 3'-end processing	IMP: Inferred from Mutant Phenotype Assigned on 2008-12-01	Grosshans H, et al.  (2001) Biogenesis of the signal recognition particle (SRP) involves import of SRP proteins into the nucleolus, assembly with the SRP-RNA, and Xpo1p-mediated export. J Cell Biol 153(4):745-62	SGD
nonfunctional rRNA decay	IMP: Inferred from Mutant Phenotype Assigned on 2009-09-10	Cole SE, et al.  (2009) A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay. Mol Cell 34(4):440-50	SGD
nuclear mRNA surveillance	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31	Bousquet-Antonelli C, et al.  (2000) Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102(6):765-75	SGD
nuclear polyadenylation-dependent CUT catabolic process	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
nuclear polyadenylation-dependent mRNA catabolic process	IC: Inferred By Curator from nuclear exosome (RNase complex) Assigned on 2009-09-15	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 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
nuclear polyadenylation-dependent tRNA catabolic process	IDA: Inferred from Direct Assay Assigned on 2009-08-31	LaCava J, et al.  (2005) RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121(5):713-24	SGD
	IGI: Inferred from Genetic Interaction with SGD:GCD10 Assigned on 2009-08-31	Kadaba S, et al.  (2004) Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae. Genes Dev 18(11):1227-40	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
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-31 IDA: Inferred from Direct Assay Assigned on 2009-08-31	Schneider C, et al.  (2007) The exosome subunit Rrp44 plays a direct role in RNA substrate recognition. Mol Cell 27(2):324-31	SGD
nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	IC: Inferred By Curator from cytoplasmic exosome (RNase complex) Assigned on 2009-03-13	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-transcribed mRNA catabolic process, non-stop decay	IC: Inferred By Curator from cytoplasmic exosome (RNase complex) Assigned on 2009-03-13	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
polyadenylation-dependent snoRNA 3'-end processing	IC: Inferred By Curator from nuclear exosome (RNase complex) Assigned on 2009-09-10	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
rRNA catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-18	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
cytoplasmic 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
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 2009-01-29	Shiomi T, et al.  (1998) Human dis3p, which binds to either GTP- or GDP-Ran, complements Saccharomyces cerevisiae dis3. J Biochem (Tokyo) 123(5):883-90	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.

Cellular Component

High-throughput Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
mitochondrion	IDA: Inferred from Direct Assay Assigned on 2006-12-12	Reinders J, et al.  (2006) Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J Proteome Res 5(7):1543-54	SGD
	IDA: Inferred from Direct Assay Assigned on 2004-09-28	Sickmann A, et al.  (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100(23):13207-12	SGD
nucleolus	IDA: Inferred from Direct Assay Assigned on 2012-12-12	Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76	SGD
nucleus	IDA: Inferred from Direct Assay Assigned on 2012-12-12	Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76	SGD

** 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
endonuclease activity	IEA: Inferred from Electronic Annotation with EBI:KW-0255 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
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
ribonuclease activity	IEA: Inferred from Electronic Annotation with EBI:IPR001900 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:IPR003029, EBI:IPR001900 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	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
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
cytoplasm	IEA: Inferred from Electronic Annotation with EBI:SL-0086 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
	IEA: Inferred from Electronic Annotation with EBI:KW-0963 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
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
mitochondrion	IEA: Inferred from Electronic Annotation with EBI:SL-0173 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
	IEA: Inferred from Electronic Annotation with EBI:KW-0496 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
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)).