XB-FEAT-5812346: Difference between revisions
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The gene name and symbol was changed from ''spata18.2'' 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 ''spata18.2'' 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 ''Nanorana parkeri'' and caecillians ''Rhinatrema bivittatum'' and ''Microcaecaecilia unicolor''), the SPATA18 gene has resided ina conserved region | Going at least as far back as gnathostomes ( including ''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> | 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 that are unique to ''Xenopus''! | However in ''Xenopus'', the "spata18" gene is missing from this location, while two other ''spata18'' genes do occur at other locations that are unique to ''Xenopus''! | ||
These two 'other' regions are well conserved in tetrapods. The regions with these "Xenopus-specific" spata18 | 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'') | ||
b) FBXL13< ... ARMC10> ... NAPELD< "'''SPATA18'''"> ... PMPCB> ... DNAJC2< ... PSMC2> also on Chromosome 3 ( which we now call ''spata18a'') | 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.tropidalis and X.laevis LOST the canonical SPATA18 gene locus but also duplicated and translocated 2 "spata18" | So it appears that an ancestor to X.tropidalis 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. | 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. | 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. | ||
Revision as of 09:58, 2 January 2020
spata18b
This is the community wiki page for the gene spata18b 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 spata18.2 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 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 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.tropidalis 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.