# HISTORY 24 Mar 2016: Updated by: TOUCHUP-v1.15 14 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function 20110117: Eukaryota_PTN000139030 has function single-stranded DNA binding (GO:0003697) 20140521: Opisthokonta_PTN001345267 has function gamma-tubulin binding (GO:0043015) # cellular_component 20140521: Eukaryota_PTN000139030 is found in nucleus (GO:0005634) 20140521: Opisthokonta_PTN001345267 is found in centrosome (GO:0005813) # biological_process 20140521: Eukaryota_PTN000139030 participates in regulation of transcription, DNA-templated (GO:0006355) 20140521: Opisthokonta_PTN001345267 participates in double-strand break repair via homologous recombination (GO:0000724) 20140521: Opisthokonta_PTN001345267 participates in chromosome organization (GO:0051276) 20140521: Opisthokonta_PTN001345267 participates in centrosome duplication (GO:0051298) 20110117: Mammalia_PTN000139037 participates in regulation of cell proliferation (GO:0042127) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED ## Annotations that have been removed. 20140521: Opisthokonta_PTN001345267 to cytokinesis (GO:0000910) is an excluded term and not to be used for annotation # NOTES . Phylogeny Present in eukaryotes excepting yeasts, but including Dicty and plants. Conservation is quite good across mammals (AN7) so most annotations are propagated to that node. MF - Propagated single-stranded DNA binding to AN0 because the InterPro domain has that annotation, probably indicating that the DNA binding site is conserved across the entire family. - Propagate transcription factor activity to AN7 after discussion with GOA. - Propagated gamma tubulin binding to AN7. - Do not propagate histone acetyl transferase activity because there is conflicting data. CC -Propagate centrosome and nucleus in mammals (AN7). -Do not propagate A. thaliana mitochondria (HTP experiment). -Do not propagate BRCA2-MAGE-D1 complex: not convinced this is a real complex (PMID: 15930293). -Do not propagate cytoplasm (HTP experiment). BP - Propagate double-strand break repair via homologous recombination (annotations in mouse and human). - Propagate regulation of cell proliferation to cover cell proliferation of specific cell types, and other developmental processes. - Propagate centrosome duplication to AN7. =Questions for MOD curators= ==Molecular Function== ===Human (P51587)=== *'''Question:''' Can it be confirmed that PMID: 9619837 shows that BRCA2 has transcription factor activity? I cannot see that. (emailed Rachael Jan 17, 2011 -PG) **'''Curator answer:''' Yes, there doesn't appear to be experimental evidence for the transcription activator activity, it's more of a TAS. However, in PMID:9126734 there is evidence for this term, so I have updated the annotation to this paper. I have also added annotations to BRCA2 for histone acetyltransferase activity from PMID: 9619837, as these were missing. - Rachael (GOA) Jan 18, 2011 *'''Question:''' Centrosome duplication annotation IDA from PMID: 17286961: Should this not be an IMP? (" GFP�CLS prevents endogenous BRCA2 from localizing to the centrosome (middle panel).") Would you be comfortable propagating this information? **'''Curator answer:''' So the CLS (centrosome localisation signal) of BRCA2 is preventing endogenous BRCA2 from localising to the centrosome thus causing abnormal centrosome duplication, so in this case the GFP-CLS is acting as an inhibitor of BRCA2, so I have updated the annotation to IMP. **'''Curator answer:''' They do a co-IP on Page 37, it says: "We thus performed a co-precipitation analysis that showed that BRCA2 associates with gamma-tubulin. BRCA2 was immunoprecipitated from HeLa cells, and analysis of anti-BRCA2 immunoprecipitates with anti-gamma-tubulin demonstrated the presence of gamma-tubulin in the immunoprecipitated complexes (Fig. 2C, left panel). In reciprocal experiments, a similar immunoblot analysis of anti-gamma-tubulin immunoprecipitates for the presence of BRCA2 confirmed the interaction of the two proteins...These results indicate that there is a specific direct or indirect interaction between gamma-tubulin and BRCA2." ===Rat (O35923)=== *'''Question:''' Response to estrogen stimulus: Can this be confirmed? (PMID: 14583453). It seems like the gene is a target of the estrogen response, not a mediator. **'''Curator answer:'''The definitions of the 'response to' terms are far broader in scope than a role of mediation. The annotation will remain as is. *'''Question:''' Idem for Response to nutrients. **'''Curator answer:'''The annotation will remain as is. =Questions for ontology developers= * '''Question''': BRCA2-MAGE-D1 complex ; GO:0033593: Is this a real complex? If so, why is MAGE-D2 protein not annotated? (SF# 3220799) **'''Curator answer:''' PG 20 Jan 2011 MSL, 26 Aug 2011: Updated with revised questions and answers from wiki HM. updated on May 21 2014 # REFERENCE Annotation inferences using phylogenetic trees The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).