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

# molecular_function

# cellular_component
20150814: Eukaryota_PTN000357441 is found in U4 snRNP (GO:0005687) 
20150814: Eukaryota_PTN000357441 is found in spliceosomal tri-snRNP complex (GO:0097526) 
20150814: Eukaryota_PTN000357441 is found in U4atac snRNP (GO:0005690) 
20150814: Eukaryota_PTN000357441 is found in precatalytic spliceosome (GO:0071011) 
20150814: Alveolata_PTN000357495 is NOT found in U4atac snRNP (GO:0005690) 
20150814: Ascomycota_PTN000357483 is NOT found in U4atac snRNP (GO:0005690) 
20150814: Excavarus_PTN001016649 is NOT found in U4atac snRNP (GO:0005690) 
20150814: Dictyostelium_PTN001016642 is NOT found in U4atac snRNP (GO:0005690) 
20150814: Chromadorea_PTN001016611 is NOT found in U4atac snRNP (GO:0005690) 
20150814: node_PTN001016638 is NOT found in U4atac snRNP (GO:0005690) 

# biological_process
20150814: Eukaryota_PTN000357441 participates in mRNA splicing, via spliceosome (GO:0000398) 

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

# NOTES
This family contains PRP31 (PRPF31 in vertebrates) which binds the U4 snRNA and also the U4atac snRNA in species which possess the minor (U12-type) spliceosome.
It is believed that the last eukaryotic common ancestor (LECA) possessed both the major (U2-type) and minor (U12-type) spliceosomes and that the current diversity of organisms across multiple taxonomic groups which lack the minor U12-type has been generated by multiple loss events of the minor U12-type spliceosome (Lopez et al. 2008, PMID:18390578; Bartschat & Samuelsson 2010, PMID:20149226; Turunen et al. 2013, PMID:23074130; Irimia and Roy 2014, PMID:24890509).
Comment on annotation propagations:
-------------------------------
Based on the current views on the phylogeny of the major U2-type and minor U12-type spliceosomes, I have propagated both the U2-type (e.g. U4 terms) and the U12-type terms (e.g. U4atac terms) to the root node Eukaryota_PTN000250426 (ignoring the duplication node PTN000949721 that is the actual root of the tree).
Then, I have blocked propagation of the U12-type terms in multiple places based on the phylogenetic analysis in Bartschat & Samuelsson 2010 (PMID:20149226) and Turunen et al. 2013 (PMID:23074130) and the computational work of Lopez et al. 2008 (PMID:18390578) to determine the phylogenetic distribution of the major and minor spliceosomes.
- In some places, I have felt confident that I could place the block at the node representing an entire taxonomic group, e.g. Ascomycetes, Chromodorea (a group within Nemotoda), Alveolata (includes Plasmodium & Tetrahymena), Excavarus (includes Trichomonas, Trypanosoma, and Leishmania).
- In other places, such as the Basidiomycetes where there are members of this taxonomic group thought to still contain the minor U12-type, I have placed the block on the individual species currently represented in the tree if they are thought to have lost it.
- I have also blocked the U12-type terms in several individual species that appear to be the sole representative of their group included in the Panther Tree, e.g. Chlamydomonas reinhardtii (green algae), Entamoeba histolytica, and Thalassiosira pseudonana.

# 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).