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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-bix4 were named, and with latest genome annotation, it was clear that the first 3 loci are tandem duplication 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 bix1.1

bix2 is now bix1.2

bix1 and bix4 are now bix 1.3