Revision as of 14:37, 18 October 2023

synteny

18OCT23

Note that true orthologs of GPR4 are flanked by elm1/2 and opa3 , while these grp4-like genes are flanked by shkbp1 and sptbn4.

Human: chr19: VASP> OPA3< GPR4< EML2< EML2-AS1>

ZFISH: CHR15: nova2> polr1g< gpr4< eml2< gipr>

Xtrop.chr8: fbxo46< gipr< eml1> gpr4> opa3>

Xtrop v10.chr8: shkbp1< XB5959819> MGC69520> sptbn4<

Annotation notes: XB5959819 and MGC69520 may end u/require merging as they seem to be partial/fragmented sequence accessions of the same gene. In this case, I still think the merged model should be grp4-like based on EggNog 5.0 analysis which matches both to the GRP4 protein tree.

@@ Line 1: / Line 1: @@
-=nomenclature changes=
-OCT23
-''Xenopus'' gene changed from ''MGC69520 , Novel 7 transmembrane receptor (rhodopsin family) protein'' to ''gpr4l.2, G protein-coupled receptor 4 like gene 2''.
-This change was motivated to replace the MGC# symbol with something more meaningful, and was based on lack of synteny to true grp4 (see below) and  a DIOPT/EggNog analysis, which aligned the protein to GPR4 in ~100 other species with very high confidence and similarity.
-Although on the same chromosome as true ''gpr4'' gene, these 2 genes are not adjacent to true ''gpr4'', and therefore are not considered as gpr4 duplicates ( in which case they could be named ''gpr4.2'' and ''grp4.3''), but will be provisionally called 'like' genes.
-XB5959819 symbol changed to ''grp4l.1/gpr4l''
-MGC69520 symbol changed to ''grp4l.2''
 =synteny=
 OCT23

XB-FEAT-940811: Difference between revisions

Revision as of 14:37, 18 October 2023

synteny

Navigation menu