XB-FEAT-964428: Difference between revisions
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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. | 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. | ||
=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< | |||
Latest revision as of 10:05, 30 September 2024
pgc.4
This is the community wiki page for the gene pgc.4 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 XB964428 to pgc.4
Xenopus gene name changed from provisional ortholog of progastricsin to progastricsin gene 4
annotation notes
30.09.2024
Add X. laevis v10 gene model XBXL10_1g7085 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.
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<