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

# molecular_function
20150427: root_PTN000421275 has function phosphatidylinositol binding (GO:0035091) 

# cellular_component
20150427: root_PTN000421275 is found in cilium (GO:0005929) 
20150326: Bilateria_PTN000421277 is found in intraciliary transport particle A (GO:0030991) 
20150427: Embryophyta_PTN001047131 is NOT found in cilium (GO:0005929) 

# biological_process
20150427: root_PTN000421275 participates in protein localization to cilium (GO:0061512) 
20150326: Bilateria_PTN000421277 participates in cilium assembly (GO:0042384) 
20150326: Bilateria_PTN000421277 participates in intraciliary retrograde transport (GO:0035721) 
20150427: node_PTN000421365 participates in receptor localization to nonmotile primary cilium (GO:0097500) 
20150427: node_PTN000421365 participates in protein localization to photoreceptor outer segment (GO:1903546) 
20150427: Embryophyta_PTN001047131 does NOT participate in protein localization to cilium (GO:0061512) 

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

# NOTES
Comment on tree:
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The MSA for this tree looks kind of odd. It looks really good for the sequences within the high level node Eukaryota_PTN000421319 (includes TUB, TULP1, TULP2, & TULP3). The alignment of the node Eukaryota_PTN000421276 (includes WDR35 and TULP4), which has fewer sequences, doesn't look that great compared to the other main node, particularly the TULP4 subclade). However, a recent review on "The tubby family proteins." by S Mukhopadhyay and Peter Jackson (PMID:21722349) includes the more distant and TULP4 sequence, indicating that it shares a more limited homology to the C-terminal tubby domain and that the IFT-A complex protein WDR35 is distantly related to TULP4. They also confirm the odd distribution of the plant sequences as an expansion that appears to have occurred only in plants separately from the other duplications that occurred in Bilateria.
The main conserved feature of this family is the conserved C-terminal tubby domain, which is similar to the phospholipid scramblase family (PLSCRs) and some members of the family have been shown to bind certain membrane phosphoinositides, predominantly phosphatidylinositol 4,5-bisphosphate (PIP2) (PMID:21722349).
Comments on annotations & propagations:
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While green algae are ciliated and some plant lineages form ciliated sperm, the vast majority of seed plants and some of the gymnosperms are non-ciliated, suggesting multiple losses of cilia during plant evolution (Hodges et al. 2012, PMID:22691130). Thus, I have blocked propagation of cilia related terms to the subclade of TULP and TLP proteins found in Arabadopsis and Oryza.
There are several At genes (Tlp1,  Tlp2,  Tlp5,  Tlp6,  Tlp7,  Tlp9,  Tlp10, & Tlp11)  in this family, all of which have a TAS annotation to "regulation of transcription, DNA-templated" from Riechmann et al. 2000 (PMID:11118137). They cite Boggon et al. 1999 (PMID:10591637) for the Tubby family of transcription factors, but in Boggon et al., they seems they have speculated wildly based on structural analysis. The one gene with any annotations that would corroborate this is TLP7 with an IPI annotation to "trancription regulatory region DNA binding" (Gaudinier et al. 2011, PMID:22037706). However, the Gaudinier et al paper describes a yeast-1 hybrid assay without much/any in the way of follow-up to demonstrate these interactions are real, so I do not have high confidence in this annotation and am not propagating annotations to transcription related terms.

# 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).