XB-FEAT-18034129

What’s up with chordin?

01/22/2018

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 page is new.

In the latest laevis genome, 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=)

See MUSCLE alignment here: https://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=muscle-I20180122-181713-0191-14786194-pg