# HISTORY
24 Mar 2016: Updated by: TOUCHUP-v1.15
14 Mar 2016: Updated by: TOUCHUP-v1.12

# molecular_function
20121212: Eukaryota_PTN000074206 has function polynucleotide adenylyltransferase activity (GO:0004652) 

# cellular_component
20121212: Eukaryota_PTN000074206 is found in nucleus (GO:0005634) 
20121212: Euteleostomi_PTN000074212 is found in cytoplasm (GO:0005737) 

# biological_process
20121212: Eukaryota_PTN000074206 participates in mRNA polyadenylation (GO:0006378) 

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

# NOTES
MOLECULAR FUNCTION
- added polynucleotide adenylyltransferase activity to the LUCA of the entire tree -- Eukaryota_PTN000074206
-- based on these proteins either having been annotated (PAINT wants to assign to Opisthokonta_PTN000074208), and I looked at the papers for the Arabidopsis proteins (i.e. http://www.arabidopsis.org/servlets/TairObject?type=locus&name=At2g25850) which show direct evidence for this protein having poly(A) polymerase activity.
CELLULAR COMPONENT
- added nucleus to the LUCA of the entire tree -- Eukaryota_PTN000074206
-- based on these proteins either having been annotated (PAINT wants to assign to Opisthokonta_PTN000074208), and I looked at the papers for the Arabidopsis proteins (i.e. http://www.arabidopsis.org/servlets/TairObject?type=locus&name=At2g25850) which show direct evidence for this protein in the nucleus.
-- all of these species shown in the tree are Eukaryotic, there are no archaea or bacteria, so they all have nuclei!
- added cytoplasm to a small clade -- Euteleostomi_PTN000074212
-- there are special poly(A) polymerases are also found in the cyotplasm and the nucleus in the mammals.  There is a duplication event at root_PTN000074211, which is right before I have added this to the clade I chose.
BIOLOGICAL FUNCTION
- added mRNA polyadenylation to Eukaryota_PTN000074206
-- based on the same reasons above.  mRNA processing is a parent to mRNA polyadenylation, as are RNA polyadenylation, gene expression, and mRNA 3'-end processing.
- added mRNA splicing, via splicosome to root_PTN000074217
-- based on the annotation of the HUMAN_PAPOLA to the term.  I went back to the last duplication, which was as far as I was comfortable spreading/PAINTing this annotation.
- added termination of RNA Polymerase II transcription to same root_PTN000074217
-- based on the annotation of the HUMAN_PAPOLA to the term.  I again went only to the most recent duplication event.
NOTES
- I decided not to PAINT mRNA splicing, via splicosome and termination of RNA Polymerase II transcription further to Euteleostomi_PTN000074212 b/c I don't really know what the differnce is between the major clade  (that has no annotations) and the subclade that has annotations (i.e. mouse, human & bovine).  There are too many duplications in the branch for me to be comfortable PAINTing terms to the major clade.

# 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).