XB-FEAT-482520: Difference between revisions
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=bix1 | =''bix1''= | ||
This is the community wiki page for the gene ''bix1 | This is the community wiki page for the gene ''bix1'' 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= | ||
November 1st, 2018. | November 1st, 2018. | ||
The orthology and homology of the bix gene family (brachyury-inducible homeobox genes) has been reassessed | The orthology and homology of the bix gene family (brachyury-inducible homeobox genes) has been reassessed. | ||
Following nomenclature guidelines, the following changes have been made to the naming system for the ''Xenopus'' '''bix''' genes. | |||
Previously, only ''bix1'' to ''bix4'' were named, however, with the latest genome annotation, it was clear that the first 3 loci are tandem duplications of the same orthologue, and as such should be named bix1, genes 1, 2 and 3. | |||
In addition, ''X. tropicalis'' has 3 additional bix genes, before ''acbd3''. These bix genes are named in order, from left to right, bix1 genes 4, 5 and 6. | |||
The earlier names are now recorded as synonyms on the Xenbase gene pages. | |||
X. tropicalis | The order of the genes ( and flanking genes) on chromosome 5 for ''X. tropicalis, X. laevis.L and X. laevis.S'' are shown below. (# indicates newly annotated bix gene; < and > symbols indicate directionality). | ||
'''Previous annotation:''' | |||
X. | ''X. tropicalis : lin9>; mixer>; mix1>; <bix#: bix#>; bix#>; bix#>; bix#>; bix#>; acbd3>'' | ||
''X. laevis.L: lin9>; mixer>; mix1>; <'''bix3'''; bix#>; '''bix1'''>;acbd3>'' | |||
''X. laevis.S: lin9>; mixer>; mix1>; <bix#; '''bix2'''>; '''bix4'''>; acbd3>'' | |||
'''new nomenclature''' | |||
X. | ''X. tropicalis'' : ''lin9>; mixer>; mix1>; <bix1.1: bix1.2> ; bix1.3>; bix1.4>; bix1.5>; bix1.6>; acbd3>'' | ||
X. laevis . | ''X. laevis.L'': ''lin9>; mixer>; mix1>; <bix1.1; bix1.2>; bix1.3>; acbd3>'' | ||
''X. laevis.S'': ''lin9>; mixer>; mix1>; <bix1.1; bix1.2>; bix1.3>; acbd3>'' | |||
synonyms: | synonyms: | ||
'''bix3''' is now bix1.1 | '''bix3''' is now ''bix1 aka bix1.1'' | ||
'''bix2''' is now ''bix1.2'' | |||
'''bix1''' and '''bix4''' are now ''bix 1.3'' | |||
New gene pages for ''X. tropicalis'' genes ''bix1.4, bix1.5'' and ''bix1.6'' were constructed. | |||
20SEPT2024 | |||
''' | Note: to simplify orthology mappings, gene symbol ''bix1.1'' symbol was updated/reverted to ''bix1'', with ''bix1.1'' recorded as a synonym | ||
Latest revision as of 11:00, 23 September 2024
bix1
This is the community wiki page for the gene bix1 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
nomenclature changes
November 1st, 2018.
The orthology and homology of the bix gene family (brachyury-inducible homeobox genes) has been reassessed.
Following nomenclature guidelines, the following changes have been made to the naming system for the Xenopus bix genes.
Previously, only bix1 to bix4 were named, however, with the latest genome annotation, it was clear that the first 3 loci are tandem duplications of the same orthologue, and as such should be named bix1, genes 1, 2 and 3. In addition, X. tropicalis has 3 additional bix genes, before acbd3. These bix genes are named in order, from left to right, bix1 genes 4, 5 and 6.
The earlier names are now recorded as synonyms on the Xenbase gene pages.
The order of the genes ( and flanking genes) on chromosome 5 for X. tropicalis, X. laevis.L and X. laevis.S are shown below. (# indicates newly annotated bix gene; < and > symbols indicate directionality).
Previous annotation:
X. tropicalis : lin9>; mixer>; mix1>; <bix#: bix#>; bix#>; bix#>; bix#>; bix#>; acbd3>
X. laevis.L: lin9>; mixer>; mix1>; <bix3; bix#>; bix1>;acbd3>
X. laevis.S: lin9>; mixer>; mix1>; <bix#; bix2>; bix4>; acbd3>
new nomenclature
X. tropicalis : lin9>; mixer>; mix1>; <bix1.1: bix1.2> ; bix1.3>; bix1.4>; bix1.5>; bix1.6>; acbd3>
X. laevis.L: lin9>; mixer>; mix1>; <bix1.1; bix1.2>; bix1.3>; acbd3>
X. laevis.S: lin9>; mixer>; mix1>; <bix1.1; bix1.2>; bix1.3>; acbd3>
synonyms:
bix3 is now bix1 aka bix1.1
bix2 is now bix1.2
bix1 and bix4 are now bix 1.3
New gene pages for X. tropicalis genes bix1.4, bix1.5 and bix1.6 were constructed.
20SEPT2024
Note: to simplify orthology mappings, gene symbol bix1.1 symbol was updated/reverted to bix1, with bix1.1 recorded as a synonym