# molecular_function

# cellular_component
20140924: Ecdysozoa_PTN000456925 located in septate junction (GO:0005918)
20140924: Eumetazoa_PTN001067896 located in neuron projection (GO:0043005)
20140924: Eumetazoa_PTN001067896 located in neuronal cell body (GO:0043025)
20140924: Opisthokonta_PTN001067895 located in cell-cell junction (GO:0005911)
20140924: Opisthokonta_PTN001067895 located in plasma membrane (GO:0005886)
20140924: Opisthokonta_PTN001067895 located in cell surface (GO:0009986)
# biological_process
20140924: Ecdysozoa_PTN000456925 participates in septate junction assembly (GO:0019991)
20140924: Eumetazoa_PTN001067896 participates in regulation of neurogenesis (GO:0050767)
20140924: Opisthokonta_PTN001067895 participates in single organismal cell-cell adhesion (GO:0016337)
# Notes
Lack of evidences showing that OPCML family is an opioid receptor regarding its structure; disputed annotation: 
- PINC	protein	Q14982	GO:0004985	TAS	ECO:0000304	PMID:1333602		
Nature of dispute: This dispute concerns the GO term used
Details: The paper shows that this protein binds opioids, but not that it's a receptor. I suggest deleting this annotation. (Dispute ID: 1533)

- PINC	protein	Q14982	GO:0005887	TAS	ECO:0000304	PMID:1333602		
Nature of dispute: This dispute concerns the GO term used
This protein has no transmembrane domain; instead, it has lipid anchors. The better term would be "Anchored component of membrane [GO:0031225]". This is not shown in this paper though. (Dispute ID: 1534)


- RGD	protein	Q62718	GO:0070492	IDA	ECO:0000314	PMID:18729387		
Nature of dispute: This dispute concerns the GO term used
Details: I think Q62718 is annotated to GO:0070492 oligosaccharide binding because it is glycosylated. This is a sentence in the abstract which may have been misleading "Diverse oligosaccharides, including Lewis a/x-modified glycans, a brain-specific glycan known as BA-2, and Man-5, were found to be attached to the third Ig domain"; but this attachment is covalent; hence the annotation seems to be invalid.  (Dispute ID: 1693)


Annotated by VH, checked by PG. 
Created new dispute for Q62718, PG 2014-11-05	



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).