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

Last Reviewed on: 2009-09-01    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
5'-deoxyribose-5-phosphate lyase activity	IMP: Inferred from Mutant Phenotype Assigned on 2009-06-09 IDA: Inferred from Direct Assay Assigned on 2008-06-25	Gellon L, et al.  (2008) Intrinsic 5'-deoxyribose-5-phosphate lyase activity in Saccharomyces cerevisiae Trf4 protein with a possible role in base excision DNA repair. DNA Repair (Amst) 7(2):187-98	SGD
polynucleotide adenylyltransferase activity	IMP: Inferred from Mutant Phenotype Assigned on 2006-09-22 IDA: Inferred from Direct Assay Assigned on 2009-06-03	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
	IDA: Inferred from Direct Assay Assigned on 2009-08-18	LaCava J, et al.  (2005) RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121(5):713-24	SGD
	ISS: Inferred from Sequence or structural Similarity with SGD:PAP1 Assigned on 2006-09-22 IMP: Inferred from Mutant Phenotype Assigned on 2005-06-10	Vanacova S, et al.  (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3(6):e189	SGD
	IGI: Inferred from Genetic Interaction with SGD:RRP6 Assigned on 2006-01-20 IDA: Inferred from Direct Assay Assigned on 2006-01-20	Houseley J and Tollervey D  (2006) Yeast Trf5p is a nuclear poly(A) polymerase. EMBO Rep 7(2):205-11	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2005-11-08 IDA: Inferred from Direct Assay Assigned on 2005-11-08	Haracska L, et al.  (2005) Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit poly(A) RNA polymerase activity but no DNA polymerase activity. Mol Cell Biol 25(22):10183-9	SGD
	IDA: Inferred from Direct Assay Assigned on 2005-04-14	Saitoh S, et al.  (2002) Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA. Cell 109(5):563-73	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
base-excision repair	IGI: Inferred from Genetic Interaction with SGD:NTG1, SGD:OGG1, SGD:RAD27, SGD:NTG2 Assigned on 2009-06-09 IMP: Inferred from Mutant Phenotype Assigned on 2009-06-09	Gellon L, et al.  (2008) Intrinsic 5'-deoxyribose-5-phosphate lyase activity in Saccharomyces cerevisiae Trf4 protein with a possible role in base excision DNA repair. DNA Repair (Amst) 7(2):187-98	SGD
histone mRNA catabolic process	IGI: Inferred from Genetic Interaction with SGD:TRF5 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
ncRNA polyadenylation	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-18	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
	IGI: Inferred from Genetic Interaction with SGD:RRP6 Assigned on 2009-08-18	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
	IGI: Inferred from Genetic Interaction with SGD:RRP6 Assigned on 2006-09-25	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
	IDA: Inferred from Direct Assay Assigned on 2009-08-18	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:RRP6, SGD:GCD10 Assigned on 2009-08-18	Kadaba S, et al.  (2004) Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae. Genes Dev 18(11):1227-40	SGD
	IGI: Inferred from Genetic Interaction with SGD:RRP6 Assigned on 2009-08-18	Houseley J and Tollervey D  (2006) Yeast Trf5p is a nuclear poly(A) polymerase. EMBO Rep 7(2):205-11	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-08-18 IDA: Inferred from Direct Assay Assigned on 2009-08-18	Vanacova S, et al.  (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3(6):e189	SGD
nuclear mRNA surveillance of mRNA 3'-end processing	IGI: Inferred from Genetic Interaction with SGD:HPR1, SGD:MFT1, SGD:SUB2 Assigned on 2009-08-31	Rougemaille M, et al.  (2007) Dissecting mechanisms of nuclear mRNA surveillance in THO/sub2 complex mutants. EMBO J 26(9):2317-26	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:RRP6 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
	IMP: Inferred from Mutant Phenotype Assigned on 2009-09-01	Milligan L, et al.  (2008) A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts. Mol Cell Biol 28(17):5446-57	SGD
nuclear polyadenylation-dependent mRNA catabolic process	IGI: Inferred from Genetic Interaction with SGD:RRP6 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 rRNA 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
	IGI: Inferred from Genetic Interaction with SGD:TRF5 Assigned on 2009-08-31 IMP: Inferred from Mutant Phenotype 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: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	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 snoRNA catabolic process	IGI: Inferred from Genetic Interaction with SGD:TRF5 Assigned on 2009-08-31 IMP: Inferred from Mutant Phenotype 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:RRP6 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
	IMP: Inferred from Mutant Phenotype 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
nuclear polyadenylation-dependent tRNA 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
	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
	IMP: Inferred from Mutant Phenotype 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
	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
polyadenylation-dependent mRNA catabolic process	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
polyadenylation-dependent snoRNA 3'-end processing	IGI: Inferred from Genetic Interaction with SGD:RRP6 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
snoRNA polyadenylation	IGI: Inferred from Genetic Interaction with SGD:RRP6 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
tRNA modification	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-23	Dickinson H, et al.  (2012) The TRAMP complex shows tRNA editing activity in S. cerevisiae. Mol Biol Evol 29(5):1451-9	SGD
U4 snRNA 3'-end processing	IGI: Inferred from Genetic Interaction with SGD:RRP6 Assigned on 2009-05-14 IMP: Inferred from Mutant Phenotype Assigned on 2009-05-14	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

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
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 2001-01-18	Walowsky C, et al.  (1999) The topoisomerase-related function gene TRF4 affects cellular sensitivity to the antitumor agent camptothecin. J Biol Chem 274(11):7302-8	SGD
TRAMP complex	IDA: Inferred from Direct Assay Assigned on 2009-06-03	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
	IDA: Inferred from Direct Assay Assigned on 2005-06-21	LaCava J, et al.  (2005) RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121(5):713-24	SGD
	IDA: Inferred from Direct Assay Assigned on 2005-06-21	Vanacova S, et al.  (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3(6):e189	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 PAP2

** 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
metal ion binding	IEA: Inferred from Electronic Annotation with EBI:KW-0479 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
nucleotidyltransferase activity	IEA: Inferred from Electronic Annotation with EBI:IPR002934 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-0548 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
transferase activity	IEA: Inferred from Electronic Annotation with EBI:KW-0808 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
cell cycle	IEA: Inferred from Electronic Annotation with EBI:KW-0131 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
cell division	IEA: Inferred from Electronic Annotation with EBI:KW-0132 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
mitosis	IEA: Inferred from Electronic Annotation with EBI:KW-0498 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
nucleus	IEA: Inferred from Electronic Annotation with EBI:SL-0191 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-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)).