XB-FEAT-22172606: Difference between revisions
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=spata18a= | =''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 | 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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'''12.31.2019''' | '''12.31.2019''' | ||
The gene name and symbol was changed from ''spata18.1'' to '' | The gene name and symbol was changed from ''spata18.1'' to ''spata18a'' 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: | 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: | ||
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DCUN1D4> ... LRRC66< ... SGCB< ... ''''''SPATA18''''''> ... (PSUEDO)GENE< ... USP46< ... DANCR ... RASL11B> | 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 | However in ''Xenopus'', the "spata18" gene is missing from this location, while two other ''spata18'' genes do occur at other locations in the genome that are unique to ''Xenopus''! | ||
These two 'other' regions are well conserved in tetrapods. The regions with these "Xenopus-specific" spata18 genes insertions are: | 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'') | a) AEBP1> ... POLD2< ... "'''SPATA18'''"> ... MYL7< ... GCK< ... YKT6> on Chromosome 3 (which we now call ''spata18b'') | ||
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'''01.13.2020''' | '''01.13.2020''' | ||
note: in NCBI, the X laevis L and S genes are called by | 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. | ||
2020/06/04 | 2020/06/04 | ||
Human symbol has changed for genepage ID: 5812346 From spata18b to SPATA18- DO NOT change on Xenbase gene page as we have the a and b duplications, and both are orthologous to human SPATA18. | Human symbol has changed for genepage ID: 5812346 From spata18b to SPATA18- DO NOT change on Xenbase gene page as we have the a and b duplications, and both are orthologous to human SPATA18. | ||
Human symbol has changed for genepage ID: 22172606 From spata18a to SPATA18-DO NOT change on Xenbase gene page as we have the a and b duplications, and both are orthologous to human SPATA18. | |||
Latest revision as of 14:55, 28 July 2023
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 spata18a 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 the genome 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.
2020/06/04
Human symbol has changed for genepage ID: 5812346 From spata18b to SPATA18- DO NOT change on Xenbase gene page as we have the a and b duplications, and both are orthologous to human SPATA18.
Human symbol has changed for genepage ID: 22172606 From spata18a to SPATA18-DO NOT change on Xenbase gene page as we have the a and b duplications, and both are orthologous to human SPATA18.