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

# molecular_function
20131111: Eumetazoa_PTN000931062 has function thiol-dependent ubiquitin-specific protease activity (GO:0004843) 
20140311: Euteleostomi_PTN000216327 has function Lys63-specific deubiquitinase activity (GO:0061578) 

# cellular_component
20131111: cellular organisms_PTN000216320 is found in cytosol (GO:0005829) 

# biological_process
20131111: Eumetazoa_PTN000931062 participates in protein K63-linked deubiquitination (GO:0070536) 
20131112: Euteleostomi_PTN000216327 participates in necroptotic process (GO:0070266) 
20131112: Euteleostomi_PTN000216327 participates in negative regulation of NF-kappaB transcription factor activity (GO:0032088) 
20131112: Euteleostomi_PTN000216327 participates in positive regulation of extrinsic apoptotic signaling pathway (GO:2001238) 
20131112: Euteleostomi_PTN000216327 participates in regulation of mitotic cell cycle (GO:0007346) 
20140311: Euteleostomi_PTN000216327 participates in regulation of intrinsic apoptotic signaling pathway (GO:2001242) 
# PRUNED

07 May 2016: Euteleostomi_PTN000931065 has been pruned from tree

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

# NOTES
07 May 2016: Euteleostomi_PTN000931065 has been pruned from tree
25 Mar 2016: Euteleostomi_PTN000931065 has been pruned from tree
14 Mar 2016: Euteleostomi_PTN000931065 has been pruned from tree
- this family seems to be a merge of two separate families, cyld and some ribosomal proteins (rps3a, and rps1). notified the panther group to have a look at the tree.
- Sequences descending from node PTN000931065 also seem quite divergent. Pruned.
- Rat sequences in the CYLD clade seem to have assembly issues.
*CYLD clade
- Has Lys63 deubiquitinase acivity.
- Some other BPs are going though NFKB and RIPK. RIPK family is also problematic, but does seem to be present only in animals, so the BPs were only propagated to Euteleostomi_PTN000216327.
- Regulation of mitotic cycle is via action on PLK1; found in Deuterostomia; so propagated to Euteleostomi_PTN000216327.
- Necroptotic process is via CASP8  (First evolved in the Osteichthytes according to PTHR10454).

# 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).