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

Last Reviewed on: 2011-12-15    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
contributes_to core RNA polymerase binding transcription factor activity	IC: Inferred By Curator from holo TFIIH complex Assigned on 2011-12-15	Yang C, et al.  (2010) Improved methods for expression and purification of Saccharomyces cerevisiae TFIIF and TFIIH; Identification of a functional Escherichia coli promoter and internal translation initiation within the N-terminal coding region of the TFIIF TFG1 subunit. Protein Expr Purif 70(2):172-178	SGD
NOT cyclin-dependent protein kinase activating kinase activity	IMP: Inferred from Mutant Phenotype Assigned on 2005-11-02 IDA: Inferred from Direct Assay Assigned on 2005-11-02	Cismowski MJ, et al.  (1995) KIN28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol Cell Biol 15(6):2983-92	SGD
RNA polymerase II carboxy-terminal domain kinase activity	IDA: Inferred from Direct Assay Assigned on 2005-11-02	Cismowski MJ, et al.  (1995) KIN28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol Cell Biol 15(6):2983-92	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-02-07 IDA: Inferred from Direct Assay Assigned on 2011-02-07	Hengartner CJ, et al.  (1998) Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases. Mol Cell 2(1):43-53	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
7-methylguanosine mRNA capping	IMP: Inferred from Mutant Phenotype Assigned on 2012-12-10	Chymkowitch P, et al.  (2012) Cdc28 kinase activity regulates the basal transcription machinery at a subset of genes. Proc Natl Acad Sci U S A 109(26):10450-5	SGD
phosphorylation of RNA polymerase II C-terminal domain	IDA: Inferred from Direct Assay Assigned on 2010-05-19	Kim M, et al.  (2009) Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7. J Biol Chem 284(39):26421-6	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-06-01	Keogh MC, et al.  (2002) Kin28 is found within TFIIH and a Kin28-Ccl1-Tfb3 trimer complex with differential sensitivities to T-loop phosphorylation. Mol Cell Biol 22(5):1288-97	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-06-01	Cismowski MJ, et al.  (1995) KIN28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol Cell Biol 15(6):2983-92	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-02-07 IDA: Inferred from Direct Assay Assigned on 2011-02-07	Hengartner CJ, et al.  (1998) Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases. Mol Cell 2(1):43-53	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-05-19	Akhtar MS, et al.  (2009) TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II. Mol Cell 34(3):387-93	SGD
phosphorylation of RNA polymerase II C-terminal domain involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex	IMP: Inferred from Mutant Phenotype Assigned on 2013-02-18 IPI: Inferred from Physical Interaction with SGD:PTA1 Assigned on 2013-02-18	Rodriguez CR, et al.  (2000) Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II. Mol Cell Biol 20(1):104-12	SGD
phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex	IMP: Inferred from Mutant Phenotype Assigned on 2013-02-15	Rodriguez CR, et al.  (2000) Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II. Mol Cell Biol 20(1):104-12	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2013-02-15	Hong SW, et al.  (2009) Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A 106(34):14276-80	SGD
positive regulation of transcription from RNA polymerase II promoter	IDA: Inferred from Direct Assay Assigned on 2011-02-07	Liu Y, et al.  (2004) Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex. Mol Cell Biol 24(4):1721-35	SGD
transcription from RNA polymerase I promoter	IMP: Inferred from Mutant Phenotype Assigned on 2011-12-19	Iben S, et al.  (2002) TFIIH plays an essential role in RNA polymerase I transcription. Cell 109(3):297-306	SGD
transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2010-06-01	Valay JG, et al.  (1995) The KIN28 gene is required both for RNA polymerase II mediated transcription and phosphorylation of the Rpb1p CTD. J Mol Biol 249(3):535-44	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-06-01	Cismowski MJ, et al.  (1995) KIN28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol Cell Biol 15(6):2983-92	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-05-19	Yang C, et al.  (2010) Improved methods for expression and purification of Saccharomyces cerevisiae TFIIF and TFIIH; Identification of a functional Escherichia coli promoter and internal translation initiation within the N-terminal coding region of the TFIIF TFG1 subunit. Protein Expr Purif 70(2):172-178	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
holo TFIIH complex	IDA: Inferred from Direct Assay Assigned on 2009-10-22	Yang C, et al.  (2010) Improved methods for expression and purification of Saccharomyces cerevisiae TFIIF and TFIIH; Identification of a functional Escherichia coli promoter and internal translation initiation within the N-terminal coding region of the TFIIF TFG1 subunit. Protein Expr Purif 70(2):172-178	SGD
TFIIK complex	IDA: Inferred from Direct Assay Assigned on 2010-06-01	Keogh MC, et al.  (2002) Kin28 is found within TFIIH and a Kin28-Ccl1-Tfb3 trimer complex with differential sensitivities to T-loop phosphorylation. Mol Cell Biol 22(5):1288-97	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-11-03	Yang C, et al.  (2010) Improved methods for expression and purification of Saccharomyces cerevisiae TFIIF and TFIIH; Identification of a functional Escherichia coli promoter and internal translation initiation within the N-terminal coding region of the TFIIF TFG1 subunit. Protein Expr Purif 70(2):172-178	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.

Molecular Function | Biological Process

High-throughput Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
protein kinase activity	IDA: Inferred from Direct Assay Assigned on 2012-05-04	Ptacek J, et al.  (2005) Global analysis of protein phosphorylation in yeast. Nature 438(7068):679-84	SGD

High-throughput Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
protein phosphorylation	IDA: Inferred from Direct Assay Assigned on 2012-05-04	Ptacek J, et al.  (2005) Global analysis of protein phosphorylation in yeast. Nature 438(7068):679-84	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
ATP binding	IEA: Inferred from Electronic Annotation with EBI:IPR017441, EBI:IPR000719, EBI:IPR002290 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-0067 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
kinase activity	IEA: Inferred from Electronic Annotation with EBI:KW-0418 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
nucleotide binding	IEA: Inferred from Electronic Annotation with EBI:KW-0547 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 kinase activity	IEA: Inferred from Electronic Annotation with EBI:IPR000719, EBI:IPR002290 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
protein serine/threonine kinase activity	IEA: Inferred from Electronic Annotation with EBI:IPR008271 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-0723 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
RNA polymerase II carboxy-terminal domain kinase activity	IEA: Inferred from Electronic Annotation with IUBMB:2.7.11.23 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	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
transferase activity, transferring phosphorus-containing groups	IEA: Inferred from Electronic Annotation with EBI:IPR011009 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro

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
phosphorylation	IEA: Inferred from Electronic Annotation with EBI:KW-0418 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 phosphorylation	IEA: Inferred from Electronic Annotation with EBI:IPR000719, EBI:IPR002290, EBI:IPR008271 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
regulation of transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:KW-0805 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:KW-0804 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)).