# HISTORY
07 May 2016: Updated by: TOUCHUP-v1.18
14 Mar 2016: Updated by: TOUCHUP-v1.14
24 Mar 2016: Updated by: TOUCHUP-v1.15

# molecular_function
20140903: node_PTN000116297 has function peptidyl-prolyl cis-trans isomerase activity (GO:0003755) 
20140903: Eukaryota_PTN000116300 has function ubiquitin-ubiquitin ligase activity (GO:0034450) 

# cellular_component
20140903: Bilateria_PTN000869907 is found in mitochondrion (GO:0005739) 
20140903: Theria <Mammalia>_PTN000117183 is found in mitochondrial matrix (GO:0005759) 
20140903: Eukaryota_PTN000116300 is found in nucleus (GO:0005634) 

# biological_process
20140904: Theria <Mammalia>_PTN000117183 participates in apoptotic mitochondrial changes (GO:0008637) 
20140904: Theria <Mammalia>_PTN000117183 participates in regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445) 
20140904: Eumetazoa_PTN000869969 participates in regulation of apoptotic process (GO:0042981) 
20140903: Eukaryota_PTN000116300 participates in protein polyubiquitination (GO:0000209) 

# WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED

# NOTES
- Propagated "regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)" to the node containing SCHPO_rct1 since those proteins have the RRM motif.
- Did not propagate any splicosome term (CC or BP) because those are based on two HTP studies from fly and human.
Sourceforge item created: https://sourceforge.net/p/geneontology/ontology-requests/11123/
Disputes
- PINC	protein	P45877	GO:0007165	TAS	ECO:0000304	PMID:1652374	 (Dispute ID: 1333)
DELETED 2014-09-08

# 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).