# HISTORY
06 Jun 2016: Saved by krc using Paint 2.0-beta19

# molecular_function
20160606: Eukaryota_PTN000411817 has function chromatin binding (GO:0003682) 

# cellular_component
20160606: Eukaryota_PTN000411817 is found in Rix1 complex (GO:0097344) 
20160606: Eukaryota_PTN000411817 is found in preribosome, large subunit precursor (GO:0030687) 
20160606: Eukaryota_PTN000411817 is found in MLL1 complex (GO:0071339) 

# biological_process
20160606: Eukaryota_PTN000411817 participates in regulation of DNA-dependent DNA replication initiation (GO:0030174) 
20160606: Eukaryota_PTN000411817 participates in maturation of LSU-rRNA (GO:0000470) 

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

# NOTES
I am skeptical that the nodes 9EUKA:PTN000411817 ( containing Sc IPI1 and vert TEX10) and 9EUKA:PTN000411873 (containing vertebrate RMDN1, and also vertebrate RMDN2 and RMDN3 as well as C elegans genes rmd-1, -2, -3, -5, -6 and sup-35) belong in the same tree together. 
- The overall MSA is terrible, and looking at the full length sequences, the IPI1/TEX10 sequences look good together, but terrible against the RMDN sequences. 
- While the RMDN sequences are not well annotated, RMDN3 has significant literature and it does not seem to possess functions/roles that are remotely related to IPI1/TEX10.
====================
Tree structure:
--------------------------
9ZZZZ:PTN001815870 - root
- 9ZZZZ:PTN001815871 - diamond node
-- 9ZZZZ:PTN001815872 - diamond node
.
--- 9EUKA:PTN000411817 (Sc IPI1, vert TEX10)
.
--- 9EUKA:PTN000411873
---- 9EUKA:PTN000411874
----- PTN001042635
------ 9ZZZZ:PTN001440970 (2 Monosiga brevicollis seqs)
------ 9METZ:PTN001815895
------- TRIAD:TRIADDRAFT_57227
------- 9ZZZZ:PTN000411816 (duplication node)
-------- PTN001042636 
--------- NEMVE:V1G247741
--------- 9BILA:PTN000411899 
---------- PTN000411900
------------ 9ZZZZ:PTN000411904
------------- 9EUTE:PTN000750609 (vert RMDN2)
------------- 9EUTE:PTN001815899 (vert RMDN3)
--------- PTN001042642 (insect & C elegans rmd-1, -2, -3, -5, -6; Cel sup-35)
--------- 9ZZZZ:PTN001042657 (2 Schistosoma seqs)
------- PTN001042666 
-------- NEMVE:v1g129440
-------- 9BILA:PTN000750610 (vert RMDN1)
----- 9ZZZZ:PTN001440971 (Dictystelium rmd1) [duplication node - 4 dicty seqs]
---- 9ZZZZ:PTN001042690 (2 Phytophthora seqs; duplication node)
---- 9TRYP:PTN001042693 (2 seqs: 1 Trypanosoma, 1 Leishmania)
.
-- GIAIC:GL50803_14322
- TRIVA:TVAG_499370
====================
IPI/TEX10 clade
-------------
Human TEX10 is experimentally characterized, though not well annotated. Skimming the abstracts suggests its role is consistent with what is annotated for ScIPI1 and Spombe_ipi1
- 1: Castle CD, et al. LAS1L interacts with the mammalian Rix1 
complex to regulate ribosome biogenesis. Mol Biol Cell. 2012 Feb;23(4):716-28. PMID:22190735; 
- 2: Fanis P, et al. Five friends of methylated
chromatin target of protein-arginine-methyltransferase[prmt]-1 (chtop), a complex
linking arginine methylation to desumoylation. Mol Cell Proteomics. 2012
Nov;11(11):1263-73. PMID:22872859
- 3: Finkbeiner E, et al. SUMO routes ribosome maturation.
Nucleus. 2011 Nov-Dec;2(6):527-32.  Review.  PMID:22064470
- 4: Ding J, et al. Tex10 Coordinates
Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming. 
Cell Stem Cell. 2015 Jun 4;16(6):653-68.  PMID: 25936917
- 5: Buganim Y. Tex10: A New Player in the Core Pluripotency Circuitry. Cell Stem
Cell. 2015 Jun 4;16(6):572-3.  PMID:26046753
====================
RMDN1/2/3 clade
-------------
- While human RMDN3 is experimentally characterized, there are not currently (20160606) sufficient experimental annotations made to annotate this 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).