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

Last Reviewed on: 2012-07-03    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
molecular_function unknown	ND: No Biological Data Available Assigned on 2012-06-29	SGD  (2002) Use of the ND evidence code for Gene Ontology (GO) terms in SGD ()	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
cytoplasm-associated proteasomal ubiquitin-dependent protein catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2011-02-15	Metzger MB, et al.  (2008) Degradation of a Cytosolic Protein Requires Endoplasmic Reticulum-associated Degradation Machinery. J Biol Chem 283(47):32302-16	SGD
ER-associated misfolded protein catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2012-06-22	Ye Y, et al.  (2001) The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature 414(6864):652-6	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2012-06-22	Jarosch E, et al.  (2002) Protein dislocation from the ER requires polyubiquitination and the AAA-ATPase Cdc48. Nat Cell Biol 4(2):134-9	SGD
ER-associated protein catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2003-10-10	Bays NW, et al.  (2001) HRD4/NPL4 is required for the proteasomal processing of ubiquitinated ER proteins. Mol Biol Cell 12(12):4114-28	SGD
mitochondria-associated protein catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2011-02-23	Heo JM, et al.  (2010) A stress-responsive system for mitochondrial protein degradation. Mol Cell 40(3):465-80	SGD
mitotic spindle disassembly	IMP: Inferred from Mutant Phenotype Assigned on 2012-06-27	Cao K, et al.  (2003) The AAA-ATPase Cdc48/p97 regulates spindle disassembly at the end of mitosis. Cell 115(3):355-67	SGD
positive regulation of protein localization to nucleus	IMP: Inferred from Mutant Phenotype Assigned on 2012-06-26	Rape M, et al.  (2001) Mobilization of processed, membrane-tethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone. Cell 107(5):667-77	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2012-06-26	Hitchcock AL, et al.  (2001) The conserved npl4 protein complex mediates proteasome-dependent membrane-bound transcription factor activation. Mol Biol Cell 12(10):3226-41	SGD
proteasomal ubiquitin-dependent protein catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2012-06-29	Barbin L, et al.  (2010) The Cdc48-Ufd1-Npl4 complex is central in ubiquitin-proteasome triggered catabolite degradation of fructose-1,6-bisphosphatase. Biochem Biophys Res Commun 394(2):335-41	SGD
retrograde protein transport, ER to cytosol	IMP: Inferred from Mutant Phenotype Assigned on 2012-06-22	Ye Y, et al.  (2001) The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature 414(6864):652-6	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
Cdc48p-Npl4p-Ufd1p AAA ATPase complex	IDA: Inferred from Direct Assay Assigned on 2012-06-26	Rape M, et al.  (2001) Mobilization of processed, membrane-tethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone. Cell 107(5):667-77	SGD
	IDA: Inferred from Direct Assay Assigned on 2012-06-26	Hitchcock AL, et al.  (2001) The conserved npl4 protein complex mediates proteasome-dependent membrane-bound transcription factor activation. Mol Biol Cell 12(10):3226-41	SGD
Cdc48p-Npl4p-Vms1p AAA ATPase complex	IDA: Inferred from Direct Assay Assigned on 2012-07-03	Heo JM, et al.  (2010) A stress-responsive system for mitochondrial protein degradation. Mol Cell 40(3):465-80	SGD
Doa10p ubiquitin ligase complex	IDA: Inferred from Direct Assay Assigned on 2008-02-06	Carvalho P, et al.  (2006) Distinct ubiquitin-ligase complexes define convergent pathways for the degradation of ER proteins. Cell 126(2):361-73	SGD
nuclear outer membrane-endoplasmic reticulum membrane network	IDA: Inferred from Direct Assay Assigned on 2003-10-10	Hitchcock AL, et al.  (2001) The conserved npl4 protein complex mediates proteasome-dependent membrane-bound transcription factor activation. Mol Biol Cell 12(10):3226-41	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
cytoplasm	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
integral to membrane	ISM: Inferred from Sequence Model Assigned on 2011-05-31	De Hertogh B, et al.  (2002) Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae. Funct Integr Genomics 2(4-5):154-70	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.

Biological Process | Cellular Component

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
mRNA transport	IEA: Inferred from Electronic Annotation with EBI:KW-0509 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
protein transport	IEA: Inferred from Electronic Annotation with EBI:KW-0653 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
transport	IEA: Inferred from Electronic Annotation with EBI:KW-0813, EBI:KW-0811 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: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
endoplasmic reticulum	IEA: Inferred from Electronic Annotation with EBI:KW-0256 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
endoplasmic reticulum membrane	IEA: Inferred from Electronic Annotation with EBI:SL-0097 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
membrane	IEA: Inferred from Electronic Annotation with EBI:KW-0472 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
nuclear membrane	IEA: Inferred from Electronic Annotation with EBI:SL-0182 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
perinuclear region of cytoplasm	IEA: Inferred from Electronic Annotation with EBI:SL-0198 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

*** 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)).