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

# molecular_function
20150807: Eukaryota_PTN000425278 contributes to function pre-mRNA 5'-splice site binding (GO:0030627) 

# cellular_component
20150807: Eukaryota_PTN000425278 is found in U1 snRNP (GO:0005685) 
20150807: Eukaryota_PTN000425278 is found in U2-type prespliceosome (GO:0071004) 
20150807: Eukaryota_PTN000425278 is found in commitment complex (GO:0000243) 

# biological_process
20150807: Eukaryota_PTN000425278 participates in mRNA 5'-splice site recognition (GO:0000395) 
# PRUNED

07 May 2016: Eukaryota_PTN000425344 has been pruned from tree

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

# NOTES
26 Mar 2016: Eukaryota_PTN000425344 has been pruned from tree
16 Mar 2016: Eukaryota_PTN000425344 has been pruned from tree
This family contains PRP39 subunit of the U1 snRNP, encoded by the PRPF39 gene in vertebrates and the PRP39 gene in S. cerevisiae. In yeast there is a duplication producing the PRP42 gene, which is also experimentally characterized has being a part of the U1 snRNP.
The U1 snRNP is one the first snRNP to assemble onto the pre-mRNA, recognizing the 5' splice site   (Wahl et al. 2009 PMID:19239890).
Comment on tree
--------------
This family has a duplication node at the root (PTN000425277) under which are two nodes:
- Eukaryota_PTN000425278 - contains PRP42 & PRP39, both of which are part of the U1 snRNP
- Eukaryota_PTN000425344 - contains S. cerevisiae VPS62 and TDA6
-- S. cerevisiae VPS62 has been characterized by two studies SGD classifies as HTP, though they both look solid;
It has been identified as involved in vacuolar protein sorting in a mutant screen (Bonangelino et al. 2002,
PMID:12134085) and as part of the membrane proteome of purified vacuoles (Wiederhold et al. 2009,
PMID:19001347)
-- TDA6 is a paralog of VPS62 that arose from the whole genome duplication (Byrne and Wolfe 2005,
PMID: 16169922)
The MSA looks good in each subclade, but not across the entire duplication node, so I have pruned the TDA6 subclade as it doesn't seem like it belongs in a family named for pre-mRNA processing.

# 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).