# HISTORY 24 Mar 2016: Updated by: TOUCHUP-v1.15 14 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function # cellular_component 20150708: Eukaryota_PTN000133809 is found in U4/U6 x U5 tri-snRNP complex (GO:0046540) 20150708: Eukaryota_PTN000133809 is found in catalytic step 2 spliceosome (GO:0071013) 20150708: Eukaryota_PTN000133873 is found in catalytic step 1 spliceosome (GO:0071012) 20150708: Eukaryota_PTN000133873 is found in prespliceosome (GO:0071010) 20150708: Eukaryota_PTN000133873 is found in post-mRNA release spliceosomal complex (GO:0071014) 20150708: Eukaryota_PTN000133873 is found in Prp19 complex (GO:0000974) 20150708: Eukaryota_PTN000133873 is found in catalytic step 2 spliceosome (GO:0071013) 20150707: Eukaryota_PTN000133724 is found in Prp19 complex (GO:0000974) 20150707: Eukaryota_PTN000133724 is found in prespliceosome (GO:0071010) 20150707: Eukaryota_PTN000133724 is found in catalytic step 2 spliceosome (GO:0071013) 20150707: Eukaryota_PTN000133724 is found in post-mRNA release spliceosomal complex (GO:0071014) 20150707: Eukaryota_PTN000133724 is found in catalytic step 1 spliceosome (GO:0071012) 20150707: Eukaryota_PTN000133724 is found in precatalytic spliceosome (GO:0071011) # biological_process 20150708: root_PTN000133723 participates in mRNA splicing, via spliceosome (GO:0000398) 20150708: Eukaryota_PTN000133809 participates in spliceosomal tri-snRNP complex assembly (GO:0000244) 20150708: Viridiplantae_PTN000133864 participates in positive regulation of primary miRNA processing (GO:2000636) 20150708: Viridiplantae_PTN000133864 participates in RNA-directed DNA methylation (GO:0080188) 20150708: Viridiplantae_PTN000133864 participates in positive regulation of miRNA metabolic process (GO:2000630) 20150708: Eukaryota_PTN000133873 participates in generation of catalytic spliceosome for first transesterification step (GO:0000349) 20150707: Eukaryota_PTN000133724 participates in spliceosomal complex assembly (GO:0000245) # PRUNED 24 Mar 2016: Eukaryota_PTN001343311 has been pruned from tree # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES 14 Mar 2016: Eukaryota_PTN001343311 has been pruned from tree - Eukaryota_PTN000133809 - Sc PRP6, PRPF6, At STA1 = PRP6 subunit of U4/U6xU5 tri-snRNP - Eukaryota_PTN000133873 - Sc SYF1, XAB2 = Prp19 complex component of spliceosome - Eukaryota_PTN001343311 - At HCF107 ** very small subclade, does not look good in MSA => PRUNED - Eukaryota_PTN000133724 - ScCLF1, CRNKL1 = Prp19 complex component of spliceosome PRP6 subclade ------------ This is a subunit of the U5 snRNP, and thus also of the U4/U6 x U5 tri-snRNP. - In human, PRPF6 has also been shown to be a transcription coactivator of the androgen receptor. However, there isn't any corroborating evidence to know how conserved this is or how high up to propagate it, and it clearly shouldn't go to the top of this subclade since yeast don't have androgen receptors. - The MF term for "RNA binding" was shown to be with the MALAT1 nrRNA, not with a spliceosomal RNA (PMID:20797886). However, in PMID:10788320, they find that human PRPF6 does not bind to the U5 snRNA. Therefore, I have not propagated this MF term to the top of this subclade since it isn't associated with what seems to be the ancestral function in U4/U6xU5 tri-snRNP assembly. - There is some conflicting evidence about whether PRP6 is part of the U4/U6 snRNP and/or the U5 snRNP as well as being a part of the U4/U6xU5 snRNP that is required for its assembly. In S. cerevisiae there are reports that PRP6 both is (PMID:2147224) and is not (PMID:8479905) a part of the U4/U6 snRNP. For human PRPF6, there is evidence that it is part of U5 snRNP as well as the U4/U6xU5 tri-snRNP, and that it is not found in the U4/U6 snRNP. Of the snRNP terms, I have propagated only the one for the tri-snRNP. SYF1/XAB2 subclade ----------------- This is a subunit of the Prp19 complex which becomes part of the spliceosome. - There is an annotation for human XAB2 for involvement in transcription-coupled nucleotide excision repair. However, there is no corroboration in other species and the possibility that it is a downstream effect of defects in splicing, which is also coupled to transcription. HCF107 subclade -------------- There are only 12 sequences present in this subclade. Its alignment with the rest of the sequences in the MSA does not look good. In addition, the functional characterization of A. thaliana HCF107 does not suggest involvement in spliceosomal splicing. Therefore, I have pruned it. CLF1/CRNKL1 subclade ------------------- This is a subunit of the Prp19 complex which becomes part of the spliceosome. This protein may have some additional roles as well, but I don't see enough evidence, or in more than a single species to feel confident that I can propagate these possible additional roles: - DNA replication - PMID:11973290 has evidence for Sc CLF1 playing a role in DNA replication and binding to origin recognition complexes. A subsequent paper, PMID:15023545, provides evidence via two-hybrid that CLF1 interacts with CSM1 which may be involved in premeiotic DNA replication. However, I don't see any corroboration in other species. - localization to centrosome & centrosome duplication - PMID:20818332 indicates that Dm crn localizes to centrosomes and may be linked to a pathway required for centrosome duplication or segregation. Again, I don't see any corroboration in other species. # 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).