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

# molecular_function

# cellular_component
20140923: root_PTN000326128 is found in small-subunit processome (GO:0032040) 
20140829: root_PTN000326128 is found in nucleolus (GO:0005730) 

# biological_process
20140829: root_PTN000326128 participates in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462) 

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

# NOTES
This family is comprised of two clades, UTP3 (aka SAS10) and NGDN (for neuroguidin, aka LCP5), both of which are subunits of the ribosomal Small Subunit Processome, also called the SSU Processome, a large complex which is involved in the initial cleavages of the primary rRNA transcript to separate the small ribosomal subunit (SSU) rRNA from the remainder of the transcript and the biogenesis of the small ribosomal subunit.
The SSU processome was originally identified and characterized from S. cerevisiae (Dragon et al. 2002, PMID:12068309; Gallagher et al. 2004, PMID:15489292; Bernstein et al. 2004, PMID:15590835; and reviewed in Phipps et al. 2011, PMID:21318072). As of September 2014, it has begun to be characterized experimentally from other species such as human (Turner et al. 2012, PMID:22418842; Sato et al. 2013, PMID:24219289; and Hu et al. 2011, PMID:21078665), zebrafish (Wilkins et al. 2013, PMID:24147052), and mouse (Gallenberger et al. 2011, PMID:21051332).
The UTP3 (aka SAS10) subunit is a confirmed subunit of the SSU processome, but is not classified as being part of a specific subcomplex (Phipps et al. 2011, PMID:21318072).
The NGDN (for neuroguidin, aka LCP5) subunit is a candidate subunit of the SSU processome (Phipps et al. 2011, PMID:21318072). However, the mutant phenotype analysis described in Wiederkehr et al. 1998 (PMID:9814757) is highly suggestive of its presence in the SSU processome as the LCP5 deletion mutant is defective in processing of the primary rRNA transcript at sites A0 and A2, a phenotype characteristic of defects in the SSU processome.
Feng et al. 2013 (PMID:24214024) performed an extensive computational analysis from 77 completely sequenced eukaryotic genomes, including representatives of the five eukaryotic supergroups: Opisthokonts, Amoebozoa, Plantae, Excavates, and Chromalveolates, and compared these to sequences from both prokaryotic and Archaeal species for all 51 confirmed and 26 likely SSU processome subunits in S. cerevisiae as indicated in Phipps et al. 2011 (PMID:21318072). In addition, Srivastava et al. have identified SSU processome subunits in the parasitic protist Entamoeba histolytica (PMID:24631428).
UTP3 (aka SAS10) is one of the 51 confirmed proteins of the S. cerevisiae SSU processome (Phipps et al. 2011, PMID:21318072)) and is highly conserved across the 77 eukaryotic species, as listed in Table 1 of Feng et al. 2013 (PMID:24214024).
NGDN (for neuroguidin, aka LCP5) is also found in the parasitic protist Entamoeba histolytica. However, a subunit corresponding to the UTP3 (aka SAS10) subunit was not identified in this species (Srivastava et al. 2014, PMID:24631428).
Annotation comments:
---------------------
No MF annotations were propagated in this tree.
There were experimental MF annotations for both human UTP3 and human NGDN to "poly(A) RNA binding" (GO:0044822) from two high throughput studies: PMID:22681889 and PMID:22658674. Between the fact that these were high throughput experiments, the fact that this protein is normally part of a large complex, and the fact that it is not clear that poly(A) RNA binding is biologically relevant, I have chosen not to propagate this MF annotation.
There was an experimental annotation to "RNA binding" for cerevisiae LCP5. However, I question whether the experiment done provides evidence for direct RNA binding of the U3 snoRNA by LCP5 as the eevidence shown was co-immunoprecipitation of U3 snoRNA by Lcp5, which may be due to precipitating the SSU processome, rather than by direct binding of LCP5 to the U3 snoRNA. I have chosen not to propagate ths MF annotation either.

# 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).