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

Last Reviewed on: 2007-10-29    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
ATP-dependent 5'-3' DNA helicase activity	IDA: Inferred from Direct Assay Assigned on 2007-10-12	Sung P, et al.  (1987) RAD3 protein of Saccharomyces cerevisiae is a DNA helicase. Proc Natl Acad Sci U S A 84(24):8951-5	SGD
contributes_to core RNA polymerase binding transcription factor activity	IC: Inferred By Curator from holo TFIIH complex Assigned on 2011-12-19	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
damaged DNA binding	IDA: Inferred from Direct Assay Assigned on 2007-10-18	Sung P, et al.  (1994) Negative superhelicity promotes ATP-dependent binding of yeast RAD3 protein to ultraviolet-damaged DNA. J Biol Chem 269(11):8303-8	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
nucleotide-excision repair, DNA incision	IDA: Inferred from Direct Assay Assigned on 2007-10-24	Sung P, et al.  (1996) Reconstitution of TFIIH and requirement of its DNA helicase subunits, Rad3 and Rad25, in the incision step of nucleotide excision repair. J Biol Chem 271(18):10821-6	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 2010-05-19	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
regulation of mitotic recombination	IMP: Inferred from Mutant Phenotype Assigned on 2007-10-16	Lee BS, et al.  (2000) Nucleotide excision repair/TFIIH helicases RAD3 and SSL2 inhibit short-sequence recombination and Ty1 retrotransposition by similar mechanisms. Mol Cell Biol 20(7):2436-45	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2007-10-16	Maines S, et al.  (1998) Novel mutations in the RAD3 and SSL1 genes perturb genome stability by stimulating recombination between short repeats in Saccharomyces cerevisiae. Genetics 150(3):963-76	SGD
regulation of transposition, RNA-mediated	IMP: Inferred from Mutant Phenotype Assigned on 2008-02-13	Lee BS, et al.  (2000) Nucleotide excision repair/TFIIH helicases RAD3 and SSL2 inhibit short-sequence recombination and Ty1 retrotransposition by similar mechanisms. Mol Cell Biol 20(7):2436-45	SGD
transcription from RNA polymerase II promoter	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
core TFIIH complex	IDA: Inferred from Direct Assay Assigned on 2007-11-18	Takagi Y, et al.  (2003) Revised subunit structure of yeast transcription factor IIH (TFIIH) and reconciliation with human TFIIH. J Biol Chem 278(45):43897-900	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-06-01	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
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
nucleotide-excision repair factor 3 complex	IDA: Inferred from Direct Assay Assigned on 2010-06-01	Habraken Y, et al.  (1996) Transcription factor TFIIH and DNA endonuclease Rad2 constitute yeast nucleotide excision repair factor 3: implications for nucleotide excision repair and Cockayne syndrome. Proc Natl Acad Sci U S A 93(20):10718-22	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 RAD3

** 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
4 iron, 4 sulfur cluster binding	IEA: Inferred from Electronic Annotation with EBI:KW-0004 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
ATP binding	IEA: Inferred from Electronic Annotation with EBI:IPR010614, EBI:IPR002464, EBI:IPR001945, EBI:IPR006555 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
ATP-dependent DNA helicase activity	IEA: Inferred from Electronic Annotation with EBI:IPR010614, EBI:IPR001945, EBI:IPR006554 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
ATP-dependent helicase activity	IEA: Inferred from Electronic Annotation with EBI:IPR002464, EBI:IPR006555 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
DNA binding	IEA: Inferred from Electronic Annotation with EBI:IPR010614, EBI:IPR001945 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-0238 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
helicase activity	IEA: Inferred from Electronic Annotation with EBI:KW-0347 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
hydrolase activity, acting on acid anhydrides	IEA: Inferred from Electronic Annotation with EBI:IPR014013 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	IEA: Inferred from Electronic Annotation with EBI:IPR001945, EBI:IPR006554, EBI:IPR006555 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
iron-sulfur cluster binding	IEA: Inferred from Electronic Annotation with EBI:KW-0411 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
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
nucleic acid binding	IEA: Inferred from Electronic Annotation with EBI:IPR002464, EBI:IPR006555 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: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

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
DNA repair	IEA: Inferred from Electronic Annotation with EBI:KW-0234 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
nucleobase-containing compound metabolic process	IEA: Inferred from Electronic Annotation with EBI:IPR006555 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
nucleotide-excision repair	IEA: Inferred from Electronic Annotation with EBI:IPR001945 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
response to DNA damage stimulus	IEA: Inferred from Electronic Annotation with EBI:KW-0227 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:IPR001945, EBI:IPR010643 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: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)).