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

# molecular_function

# cellular_component
20131114: Eukaryota_PTN000303342 is found in small-subunit processome (GO:0032040) 
20131114: Eukaryota_PTN000303342 is found in nucleolus (GO:0005730) 

# biological_process
20131114: Eukaryota_PTN000303342 participates in rRNA processing (GO:0006364) 
20131114: Eukaryota_PTN000303342 participates in ribosomal small subunit biogenesis (GO:0042274) 

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

# NOTES
This family comprises the UTP11 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. It is thus specifically involved in the biogenesis of the small ribosomal subunit. The UTP11 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 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 November 2013, it has only just 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).
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 (Srivastava et al. 2014, PMID:24631428).
Utp11 is one of the 51 confirmed proteins that is highly conserved across the 77 eukaryotic species, as listed in Table 1 of Feng et al. 2013 (PMID:24214024). It is also found in the parasitic protist Entamoeba histolytica (Srivastava et al. 2014, PMID:24631428).
Annotation comments
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Cellular Component and general Biological Process annotations related to the function of the SSU processome have been propagated to the root node of the tree. No Molecular Function annotations have been propagated as the individual role of Utp11 within the SSU processome, or independently, is not known.
Various other Biological Process annotations from other species (human, C. elegans, D. melanogaster, and A. thaliana) have not been propagated. Most of these are based on IMP evidence from large scale phenotype screens and appear to be relatively general processes expected or unsurprising from disrupting ribosomal biogenesis. Annotations relating to apoptosis made by IDA for human have also not been propagated as it is well characterized that disruption of ribosomal biogenesis or the nucleolus leads to an increase in nuclear p53 and then cell cycle arrest or apoptosis (Boisvert et al. 2007, PMID:17519961; Skarie et al. 2008, PMID:18469340; Lempiainen H & Shore D. 2009, PMID: 19796927; Dutt et al. 2011, PMID:21068437). It is not clear if human UTP11L is specifically involved in regulation of apoptosis or if this is just due to the general effect of disrupting ribosome biogenesis, and additionally, there is no confirmation of a specific role in apoptosis in any 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).