# HISTORY
26 Mar 2016: Updated by: TOUCHUP-v1.15
16 Mar 2016: Updated by: TOUCHUP-v1.14

# molecular_function
20151025: Eukaryota_PTN000478524 has function transcription corepressor activity (GO:0003714) 

# cellular_component
20151025: Eukaryota_PTN000478524 is found in nucleus (GO:0005634) 

# biological_process
# PRUNED

26 Mar 2016: Opisthokonta_PTN001082521 has been pruned from tree

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

# NOTES
16 Mar 2016: Opisthokonta_PTN001082521 has been pruned from tree
Comment on tree
---------------
In the MSA, the entire Opisthokonts_PTN001082521 node looks like it does not belong in this tree. Both Sc NUP42 & NUP159, which are well characterized components of the nuclear pore complex, are part of this node.
In addition, the presence of Nup42 and Nup159 in a with SCAI, but not with NUPL2 or NUP214 suggests a misplacement within this tree.  In Hoelz et al.'s 2011 article on The Structure of the Nuclear Pore Complex for Annual Reviews in Biochemistry, their table indicates that Sc Nup42 is the equivalent of human CG1 while Sc Nup159 is the equivalent of human Nup214. Thus, this tree contains two yeast genes that are not thought to be co-equivalents to a single mammalian gene (SCAI), and it does not contain sequences for either of the appropriate mammalian equivalents for NUP42 (equivalent to mammalian NUPL2, aka CG1) or NUP159 (equivalent to mammalian NUP214). In the Mouse Genome Database, the name CG1 is associated with Nupl2, while in UniProt the name CG1 is listed as a gene name for three genes (KTN1, MAMD1, and NUPL2), none of which are SCAI.
Comment on Annotation propagations
-------------------------------
After pruning the Opisthokonts_PTN001082521 node, the rest of the MSA looks good. Only two proteins, mouse Scai and Human SCAI have experimental annotations, all of which are from a single paper, PMID:19350017. I went ahead and propagated the annotations related to regulation of transcription, but not the more downstream ones related to effects of which genes are regulated, e.g. "negative regulation of cell migration".

# 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).