# HISTORY 08 Jun 2016: Saved by krc using Paint 2.0-beta19 07 Jun 2016: Saved by krc using Paint 2.0-beta19 # molecular_function 20160112: Eukaryota_PTN000573960 has function nuclear localization sequence binding (GO:0008139) 20160112: Eukaryota_PTN000573960 has function structural constituent of nuclear pore (GO:0017056) 20160112: Eukaryota_PTN000573960 has function nucleocytoplasmic transporter activity (GO:0005487) # cellular_component 20160607: Eukaryota_PTN000573960 is found in nuclear pore nuclear basket (GO:0044615) 20160607: Eukaryota_PTN000573960 is found in nuclear pore central transport channel (GO:0044613) 20160607: Bilateria_PTN000573963 is NOT found in nuclear pore nuclear basket (GO:0044615) 20160607: Bilateria_PTN000573963 is NOT found in nuclear pore central transport channel (GO:0044613) 20160608: Bilateria_PTN000573963 is found in nuclear pore (GO:0005643) # biological_process 20160608: Eukaryota_PTN000573960 participates in protein import into nucleus (GO:0006606) 20160608: Eukaryota_PTN000573960 participates in RNA export from nucleus (GO:0006405) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES This family contains nucleoporins of the nuclear pore complex. This tree looks kind of strange. - There are conserved residues dispersed throughout the MSA, but the overall all alignment doesn't look fantastic. - In the tree view there are lots of rather long branch lengths in several places. - I am also surprised to see some of these things in the same tree. While everything (easily identifiable) is part of the NPC, the tree includes proteins fthat are listed as being present in several different portions of the NBC according to the Hoelz et al. 2011 Annual Review of Biochemistry article titled The Structure of the Nuclear Pore Complex (PMID:21495847). The tree structure doesn't really seem to correspond well to how the characterized proteins are described in this review. From Hoelz et al. 2011: - vertebrate Nup153 & Sc Nup1 = nuclear basket - vertebrate Nup214 & Sc Nup159 = cytoplasmic filaments . Notes about the tree ============= - Sc NUP159 (homologous to vertebrate Nup214) - incorrectly placed in PTHR21243 instead of this tree - vertebrate Nup214 is closer to vertebrate POM121 in this tree, than to Dmel Nup214 - this tree contains some vertebrate POM121 sequences, while PTHR15566 contains some other POM121 like sequences -- Hoelz et al. 2011 (PMID:21495847) lists human POM121 as one of the POMs . Tree structure: 9EUKA:PTN000573960 (root) - PTN000573961 -- Fungi_PTN001505918 - Sc NUP1 -- Opisthokonta_PTN001142932 --- Eumetazoa_PTN001142933 ---- PTN000573962 (duplication node) ----- Bilateria_PTN000574046 - Nup153 (rat, mouse, human, D. melanogaster) ----- Bilateria_PTN000573963 ------ Chordata_PTN001505863 ------- Chordata_PTN001142939 -------- root_PTN001505883 (duplication node) --------- Euteleostomi_PTN000573965 - Pom121 (and related) --------- Euteleostomi_PTN000574008 - vertebrate Nup214 ------ Ecdysozoa_PTN000574037 - D. melanogaster Nup214 -- Magnoliophyta_PTN001505921 - several plant sequences . PAINT propagation rules are blocking me from doing what I really want ============================================= ** NOT annotations that I don't really want to make ------------------- - I blocked propagation of two CC terms at the node 9BILA:PTN000573963. I only want to block propagation of the two terms since I think they are too specific for the NUP214 section of the tree. However, I don't want to be generating NOT annotations to these two terms. I'd just like to not make positive annotations from this point on. In this case, the fact that the tree structure seems odd may be an issue because if I don't annotate to the root, there are sequences that won't get annotations I think are appropriate. - However, more generally, there are many times where the behavior I want is merely to stop propagation, not to generate NOT annotations. There are only a few specific occasions where I would really want to generate NOT annotations. . ** IBA Annotations blocked by more specific experimental annotations ------------------ - For example, MOUSE:NUP214 is already annotated to "mRNA export from nucleus (GO:0006406) by IMP. It is not receiving the more general annotation "RNA export from nucleus (GO:0006405)" by IBA. => I'd really like to have the more general term propagated even though there is more specific experimental evidence in order to indicate that I think the role of this gene is broader than the experimental annotation that has been made directly to that gene. # 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).