# HISTORY
07 May 2016: Updated by: TOUCHUP-v1.18
17 Mar 2016: Updated by: TOUCHUP-v1.14
26 Mar 2016: Updated by: TOUCHUP-v1.15

# molecular_function
20160127: Chordata_PTN001469616 has function nuclear export signal receptor activity (GO:0005049) 
20160127: Viridiplantae_PTN001851625 has function guiding stereospecific synthesis activity (GO:0042349) 

# cellular_component
20160127: Chordata_PTN001469616 is found in nucleus (GO:0005634) 

# biological_process
20160127: Viridiplantae_PTN001851625 participates in phenylpropanoid biosynthetic process (GO:0009699) 

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

# NOTES
Comments on the tree:
-------------------
I think that this tree has combined some things that do not belong together, especially the joining of Viridiplantae_PTN001851625 and Unikonts_PTN001851595, but the Unikonts tree also looks dubious.
Viridiplantae_PTN001851625
- There is a duplication node within the Embryophyta (under Embryophyta_PTN001088176) with a large number of plant sequences. Four A.thaliana sequences are characterized within this duplication, ESB1, DIR6, DP1, and DIR5 and the cited papers suggest all four of these are dirigent proteins involved in specifying stereochemical specificity of chemical reactions. The alignment of all of these plant sequences does seem to contain a conserved core.
- Unikonts_PTN001851595: Most of this branch does not look like it belongs in the same alignment. The Dikarya_PTN001088168 node (with S.pombe amo1) looks somewhat close to the plant sequences, however many of the branch lengths under the Unikonts node are _very_ long.
-- Dikarya_PTN001088168: Based on the MSA, this node (which includes S.pombe amo1) looks like it might belong in the same family with the plant sequences in this family, having some of the residues conserved in the plant sequences. The description of S.pombe amo1 describes it as "nucleoporin-like" which would suggest it belongs with the animal sequences in this family. However, amo1 is annotated to "nuclear pore complex by one paper, in another paper (PMID:15797925), the authors say that "Amo1 is not required for the microtubule loading of several factors affecting microtubule dynamics, and does not seem to be required for nuclear pore function."
-- duplication node PTN001851597: This duplication node combines two things that do not really look like they align well to me. In addition, the scant available evidence for LENG9 does not suggest that it is related to nuclear pore function.
--- Deuterostomia_PTN001469604 - vertebrate LENG9  is not well characterized. There is a single large scale study suggesting involvement in autophagy.
---Deuterostomia_PTN000486695 - vertebrate NUPL2, which contains a protein characterized as being similar to a nucleoporin. Available evidence indicates that it is involved in protein export of NLS-containing proteins from the nucleus. There is no evidence that is part of the nuclear pore itself.

# 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).