XB-FEAT-29079882: Difference between revisions
Created page with "= ''pgc.3'’= This is the community wiki page for the gene '' pgc.3 '' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. =Nomenclature changes= 30SEPT2024 ‘’Xenopus’’ gene symbol changed from ‘’ LOC100489782 ‘’ to ‘’ pgc.3 ‘’ ’Xenopus ‘’ gene name changed from ''gastricsin'' to ''progastricsin gene 3''" |
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= ''pgc.3' | = ''pgc.3''= | ||
This is the community wiki page for the gene '' pgc.3 '' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. | This is the community wiki page for the gene ''pgc.3'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. | ||
=Nomenclature changes= | =Nomenclature changes= | ||
30SEPT2024 | 30SEPT2024 | ||
‘’Xenopus’’ gene symbol changed from | ‘’Xenopus’’ gene symbol changed from ''LOC100489782'' to ''pgc.3'' | ||
’'Xenopus‘’ gene name changed from ''gastricsin'' to ''progastricsin gene 3'' | |||
=Synteny= | |||
Xtrop. Chr2: ''frs3> pgc.4> pgc.3> pgc.2> pgc.1> MGC108380> tfeb>'' | |||
Xla. 2L: ''frs3.L> pgc.4.L> pgc.3.L> pgc.2.L> pgc.1.L> LOC108708147(sorting nexin 18 like)< LOC121399969(PSEUDO)< LOC108708144(MAPK13)<'' | |||
Xla.2S: frs3.S> pgc.4.S> pgc.3.S> pgc.2.S> pgc.1.S> tfeb.S>. LOC108709461.S(MYOD inhibitor)< foxp4.S< | |||
=annotation notes= | |||
30.09.2024 | |||
Add ''X. laevis'' v10 gene model to this gene page based on synteny, but at this point the ''X. laevis'' gene is officially 'uncharacterised'. | |||
Note that there are 4 duplicates of ''pgc'' genes on chromosome2 in v10 ''X. tropicalis'' genome annotation, which we have numbered, from right to left, flanked by ''frs3'' and ''tfeb''. The synteny matches that of ''X.laevis S'', as each model was already characterized by NCBI as a provisional orthology of ''pgc/progasticsin''. The 4 x genes in ''X. laevis'' were however 'uncharacterised' and have been provisionally added to the Xenbase ''pgc.1-.4'' gene pages solely based on synteny ( this is to ideal - BLAST and MSA needs to be done as well) . The Xlaevis.: genes all seem very truncated in comparison to .S and Xtrop models, although they are also all protein coding, so this may be a case where the S sub genome gene are functional and L genes less so. | |||
Latest revision as of 11:06, 30 September 2024
pgc.3
This is the community wiki page for the gene pgc.3 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
Nomenclature changes
30SEPT2024
‘’Xenopus’’ gene symbol changed from LOC100489782 to pgc.3
’'Xenopus‘’ gene name changed from gastricsin to progastricsin gene 3
Synteny
Xtrop. Chr2: frs3> pgc.4> pgc.3> pgc.2> pgc.1> MGC108380> tfeb>
Xla. 2L: frs3.L> pgc.4.L> pgc.3.L> pgc.2.L> pgc.1.L> LOC108708147(sorting nexin 18 like)< LOC121399969(PSEUDO)< LOC108708144(MAPK13)<
Xla.2S: frs3.S> pgc.4.S> pgc.3.S> pgc.2.S> pgc.1.S> tfeb.S>. LOC108709461.S(MYOD inhibitor)< foxp4.S<
annotation notes
30.09.2024
Add X. laevis v10 gene model to this gene page based on synteny, but at this point the X. laevis gene is officially 'uncharacterised'.
Note that there are 4 duplicates of pgc genes on chromosome2 in v10 X. tropicalis genome annotation, which we have numbered, from right to left, flanked by frs3 and tfeb. The synteny matches that of X.laevis S, as each model was already characterized by NCBI as a provisional orthology of pgc/progasticsin. The 4 x genes in X. laevis were however 'uncharacterised' and have been provisionally added to the Xenbase pgc.1-.4 gene pages solely based on synteny ( this is to ideal - BLAST and MSA needs to be done as well) . The Xlaevis.: genes all seem very truncated in comparison to .S and Xtrop models, although they are also all protein coding, so this may be a case where the S sub genome gene are functional and L genes less so.