XB-FEAT-5853032: Difference between revisions
imported>Xenbase →mgc69520: Updated nomenclature, replaced: unnamed → mgc69520 (2) |
|||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
= | =''gpr4.2''= | ||
This is the community wiki page for the gene '' | This is the community wiki page for the gene ''gpr4.2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | ||
=nomenclature changes= | |||
18OCT23 | |||
''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= | |||
18OCT23 | |||
Note that true orthologs of GPR4 are flanked by ''elm1/2'' and ''opa3'' , while these 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. | |||
[[File:Screenshot 2023-10-18 at 4.10.09 PM.png|thumb]] | |||
Latest revision as of 13:21, 18 October 2023
gpr4.2
This is the community wiki page for the gene gpr4.2 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
nomenclature changes
18OCT23
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
18OCT23
Note that true orthologs of GPR4 are flanked by elm1/2 and opa3 , while these 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.
