Difference between revisions of "XB-FEAT-22172606"

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Revision as of 17:04, 13 January 2020

nomenclature changes

12.31.2019

The gene name and symbol was changed from spata18.1 to spata18b to reflect information gained from a review of these genes by David Webb at NCBI. [details follow]

Going at least as far back as gnathostomes (including the frog Nanorana parkeri and caecillians Rhinatrema bivittatum and Microcaecaecilia unicolor), the SPATA18 gene has resided ina conserved region with this gene order:

DCUN1D4> ... LRRC66< ... SGCB< ... 'SPATA18'> ... (PSUEDO)GENE< ... USP46< ... DANCR ... RASL11B>

However in Xenopus, the "spata18" gene is missing from this location, while two other spata18 genes do occur at other locations in th egenome that are unique to Xenopus!

These two 'other' regions are well conserved in tetrapods. The regions with these "Xenopus-specific" spata18 genes insertions are:

a) AEBP1> ... POLD2< ... "SPATA18"> ... MYL7< ... GCK< ... YKT6> on Chromosome 3 (which we now call spata18b)

b) FBXL13< ... ARMC10> ... NAPELD< "SPATA18"> ... PMPCB> ... DNAJC2< ... PSMC2> also on Chromosome 3 (which we now call spata18a)

So it appears that an ancestor to X.tropicalis and X.laevis LOST the canonical SPATA18 gene locus but also duplicated and translocated 2 "spata18" genes.

Given that the exon and protein structure of the canonical tetrapod SPATA18 is maintained by these 2 "spata18" genes, we propose that they should be treated as orthologous to human SPATA18, rather than considered "spata18-like" genes.

Accordingly, we have given them "a" and "b" designations to reflect this duplication of the orthologue, rather than gene 1 and "gene 2 which is used for tandem duplications.