# HISTORY 25 Mar 2016: Updated by: TOUCHUP-v1.15 15 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function # cellular_component 20150813: root_PTN001765154 is found in precatalytic spliceosome (GO:0071011) 20150813: root_PTN001765154 is found in U12-type spliceosomal complex (GO:0005689) 20150813: root_PTN001765154 is found in U2 snRNP (GO:0005686) 20150813: root_PTN001765154 is found in U2-type spliceosomal complex (GO:0005684) 20150813: root_PTN001765154 is found in catalytic step 2 spliceosome (GO:0071013) 20150813: Ascomycota_PTN000505101 is NOT found in U12-type spliceosomal complex (GO:0005689) 20150813: Chromadorea_PTN000980147 is NOT found in U12-type spliceosomal complex (GO:0005689) 20150813: Dictyostelium discoideum_DDB_G0286297 is NOT found in U12-type spliceosomal complex (GO:0005689) 20150813: Excavarus_PTN001099210 is NOT found in U12-type spliceosomal complex (GO:0005689) 20150813: Alveolata_PTN000300176 is NOT found in U12-type spliceosomal complex (GO:0005689) 20150813: Ascomycota_PTN000300164 is NOT found in U12-type spliceosomal complex (GO:0005689) 20150813: Dictyostelium_PTN000980175 is NOT found in U12-type spliceosomal complex (GO:0005689) 20150813: Excavarus_PTN000980182 is NOT found in U12-type spliceosomal complex (GO:0005689) 20150813: Alveolata_PTN000505107 is NOT found in U12-type spliceosomal complex (GO:0005689) 20150813: Chromadorea_PTN001099180 is NOT found in U12-type spliceosomal complex (GO:0005689) # biological_process 20150813: root_PTN001765154 participates in mRNA splicing, via spliceosome (GO:0000398) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES This family contains two subunits of the Sf3b subcomplex, which is part of the U12 snRNP (Will et al. 2004, PMID:15146077; Turunen et al. 2013, PMID:23074130) as well as being part of the U2 snRNP (Turunen et al. 2013, PMID:23074130). In the MSA, there is clearly a shared core homology, as well as distinct differences between the subclades for each of the two subunits, which are joined by a duplication node at the root of the family. The two subclades are: - SF3B2 (vertebrates, aka sap145 in S. pombe, aka CUS1 in S. cerevisiae) - SF3B6 (vertebrates, aka sap14 in S. pombe) Note: If there is a homolog of SF3B6 in S. cerevisiae, it is missing from this tree. Note: There may be some issues regarding the usage of "SF3B14" name. The MGI page for SF3B6 gives Sf3b14 as an alias for SF3B6, and the SF3B6 subclade contains some sequences labeled as SF3B14 (e.g. Bos taurus SF3B14, Pan troglodytes H2QHI7, Macaca mulatta F7BUD8, and Gallus gallus E1BW94. However, Wang et al. 2005 (PMID:16314500) list S. cerevisiae RDS3 as the equivalent of SFB14B. ScRDS3 is present in PTHR13120 and the MSA there looks great. 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 and the U12-type terms to the root node 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).