# HISTORY 24 May 2016: Saved by krc using Paint 2.0-beta19 # molecular_function 20160524: node_PTN001400813 has function RNA binding (GO:0003723) # cellular_component 20160524: node_PTN001400813 is found in nuclear speck (GO:0016607) 20160524: node_PTN001400813 is found in precatalytic spliceosome (GO:0071011) # biological_process 20160524: node_PTN001400813 participates in regulation of RNA splicing (GO:0043484) 20160524: Euteleostomi_PTN000560557 participates in positive regulation of angiogenesis (GO:0045766) 20160524: Euteleostomi_PTN000560557 participates in vasculogenesis (GO:0001570) 20160524: node_PTN001400813 participates in mRNA processing (GO:0006397) 20160524: Euteleostomi_PTN000301887 participates in regulation of cell cycle (GO:0051726) # PRUNED 24 May 2016: Fungi_PTN001134849 has been pruned from tree # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES NOTE: Many long branch lengths and MSA looks terrible - Basic tree structure: ------------------ 9ZZZZ:PTN001896222 (dup node) - 9EUKA:PTN001896221 (1 NEMVE, 2 PHYPA) - 9EUKA:PTN001896225 -- 9EUKA:PTN001896226 *** 9ZZZZ:PTN001400813 (dup node) <= TOP NODE PROPAGATED TERMS TO --** PTN:000301884 ----* 9FUNG:PTN001134849 (Sc SQS1) ----* PTN000981281 ------ 9BILA:PTN000301885 (vert SON, EXP: mouse human) --** PTN:000560554 (vert AGGF1, EXP: human) --- PTN:001896280 (3 Dicty seqs) -- 9VIRI:PTN001896285 (plants) . NOTE on SQS1 ---- PMID:21318072: Phipps et al. review from 2011 indicates that the human homolog of yeast SQS1 is GPATCH2 (NP 060510), not SON, which is in the same branch with SQS1, or AGGF1, which is in the other main branch of this tree. GPATCH2 is in PTHR14195. => PRUNING 9FUNG:PTN001134849 (containing Sc SQS1) . COMMENTS on AGGF1 & SON ---- AGGF1 - appears to be a spliceosomal associated protein (Dmel: PMID:18981222; human: PMID:17332742 [not currently annotated] SON - involved in regulation of splicing of genes with weak splice sites (PMID:21504830) . COMMENTS on propagations 1. I have propagated most annotations to the duplication node containing both AGGF1 & SON since both appear to be involved in regulation of spliceosomal splicing. I'm not completely confident that the two nodes under the duplication node belong together, but I needed annotations from one branch to annotate the other one (e.g. RNA binding), so I chose this level. I didn't go higher as the very long branch lengths made me cautious about this tree. . 2. Within the SON and AGGF1 clades, I have propagated some more specific BP terms that appear to be downstream consequences of acting on splicing of a specific subset of genes. In the AGGF1 clade, there was evidence from both Drerio and human that this gene is involved in regulation of angiogenesis, so I selected the common node for the Eutheria (I think, 9EUTE). The SON node only had annotations for human, so I selected a node at the same level as in the AGGF1 clade. # 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).