Difference between revisions of "XB-FEAT-22172606"

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(Created page with "=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...")
 
(nomenclature changes)
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=spata18a=
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This is the community wiki page for the gene ''spata18a'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
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=nomenclature changes=
 
=nomenclature changes=
12.31.2019
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'''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]
 
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]
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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.
 
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.
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'''01.13.2020'''
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note: in NCBI, the X laevis  L and S genes are called by  LOC numbers and "mitochondria-eating protein-like" genes. The new name of "spermatogenesis associated 18" homologs should cascade up through the databases with a few months.

Revision as of 17:14, 13 January 2020

spata18a

This is the community wiki page for the gene spata18a please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase

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.

01.13.2020

note: in NCBI, the X laevis L and S genes are called by LOC numbers and "mitochondria-eating protein-like" genes. The new name of "spermatogenesis associated 18" homologs should cascade up through the databases with a few months.