XB-FEAT-964428 - Revision history

Xenbase: /* annotation notes */

2024-09-30T17:05:49Z

annotation notes

← Older revision		Revision as of 17:05, 30 September 2024
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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<

Xenbase: /* annotation notes */

2024-09-30T17:05:27Z

annotation notes

← Older revision		Revision as of 17:05, 30 September 2024
Line 13:		Line 13:

	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'.		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.

Xenbase: /* Nomenclature changes */

2024-09-30T17:04:28Z

Nomenclature changes

← Older revision		Revision as of 17:04, 30 September 2024
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	30SEPT2024		30SEPT2024

	~~‘’Xenopus’’~~ gene symbol changed from ‘’ XB964428 ‘’ to ‘’ pgc.4 ‘’		''Xenopus'' gene symbol changed from ''XB964428'' to ''pgc.4''

	~~‘’Xenopus ‘’~~ gene name changed from provisional ortholog of progastricsin'' to ''progastricsin gene 4''		''Xenopus'' gene name changed from provisional ortholog of progastricsin'' to ''progastricsin gene 4''

	=annotation notes=		=annotation notes=

Xenbase: /* Nomenclature changes */

2024-09-30T16:43:04Z

Nomenclature changes

← Older revision		Revision as of 16:43, 30 September 2024
Line 8:		Line 8:

	‘’Xenopus ‘’ gene name changed from provisional ortholog of progastricsin'' to ''progastricsin gene 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'.

Xenbase: /* loc496913 */

2024-09-30T16:06:15Z

loc496913

← Older revision		Revision as of 16:06, 30 September 2024
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	=~~loc496913~~=		=''pgc.4''=
	This is the community wiki page for the gene ''~~loc496913~~'' 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.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''

imported>Xenbase: /* loc496913 */Updated nomenclature, replaced: unnamed → loc496913 (2)

2017-12-15T19:59:42Z

loc496913: Updated nomenclature, replaced: unnamed → loc496913 (2)

← Older revision		Revision as of 19:59, 15 December 2017
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	=~~unnamed~~=		=loc496913=
	This is the community wiki page for the gene ''~~unnamed~~'' 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 ''loc496913'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase

imported>Xenbase gene generator at 12:00, 10 February 2010

2010-02-10T12:00:00Z

New page

=unnamed=
This is the community wiki page for the gene ''unnamed'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase