XB-FEAT-480637: Difference between revisions
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=chrd= | =chrd.1= | ||
This is the community wiki page for the gene ''chrd'' 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 ''chrd.1'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | ||
=What’s up with chordin?= | |||
Checking on Xenbase these days and you might be surprised to see 2 chordin gene pages: chrd.1 and chrd.2. | |||
chrd.1 is the gene we all know and love, and the chrd.2 is the new gene. | |||
In the latest X. laevis genome annoatation, both JGI and NCBI independently created tandem chordin genes in the 5L locus. | |||
Accordingly, based on Xenopus gene nomenclature guidelines, the models were designated as chordin, gene 1 (chrd.1) and chordin, gene 2 (chrd.2). | |||
We ran a MUSCLE alignment on the translated CDS of the 4 genes: X. tropicalis chrd, and X. laevis chrd.1.L, chrd.2.L, and chrd.S. | |||
This shows almost full sequence for both of the L locus genes. Running a pairwise comparison of just these L locus genes reveals small, but distinct differences, including a likely missing exon. | |||
These results indicate that there was a tandem duplication in X. laevis. | |||
More analysis is needed to determine functionality of the duplicated gene. | |||
Xenbase is running another round of genome integration, which will include putting the latest model and sequences on the chrd.2 genepage | |||
See models on JBrowse here: | |||
http://jbrowse-test.xenbase.org/JBrowse/?data=data%2Fxl9_2&loc=chr5L%3A97155957..97474956&tracks=DNA%2CXL9_2_Xenbase%2CXL9_2_GCF%2CXL9_2_GCA&highlight= | |||
Latest revision as of 07:34, 28 September 2021
chrd.1
This is the community wiki page for the gene chrd.1 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
What’s up with chordin?
Checking on Xenbase these days and you might be surprised to see 2 chordin gene pages: chrd.1 and chrd.2.
chrd.1 is the gene we all know and love, and the chrd.2 is the new gene.
In the latest X. laevis genome annoatation, both JGI and NCBI independently created tandem chordin genes in the 5L locus.
Accordingly, based on Xenopus gene nomenclature guidelines, the models were designated as chordin, gene 1 (chrd.1) and chordin, gene 2 (chrd.2). We ran a MUSCLE alignment on the translated CDS of the 4 genes: X. tropicalis chrd, and X. laevis chrd.1.L, chrd.2.L, and chrd.S.
This shows almost full sequence for both of the L locus genes. Running a pairwise comparison of just these L locus genes reveals small, but distinct differences, including a likely missing exon. These results indicate that there was a tandem duplication in X. laevis.
More analysis is needed to determine functionality of the duplicated gene.
Xenbase is running another round of genome integration, which will include putting the latest model and sequences on the chrd.2 genepage See models on JBrowse here: http://jbrowse-test.xenbase.org/JBrowse/?data=data%2Fxl9_2&loc=chr5L%3A97155957..97474956&tracks=DNA%2CXL9_2_Xenbase%2CXL9_2_GCF%2CXL9_2_GCA&highlight=