XB-FEAT-480637 - Revision history

imported>Xenbase: /* What’s up with chordin? */

2021-09-28T14:34:19Z

What’s up with chordin?

← Older revision		Revision as of 14:34, 28 September 2021
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	See models on JBrowse here:		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=		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~~

imported>Xenbase: /* What’s up with chordin? */

2018-11-15T18:36:59Z

What’s up with chordin?

← Older revision		Revision as of 18:36, 15 November 2018
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	=What’s up with chordin?=		=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 page is new~~.		Checking on Xenbase these days and you might be surprised to see 2 chordin gene pages: chrd.1 and chrd.2.

	In the latest laevis genome, both JGI and NCBI independently created tandem chordin genes in the 5L locus.		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).		Accordingly, based on Xenopus gene nomenclature guidelines, the models were designated as chordin, gene 1 (chrd.1) and chordin, gene 2 (chrd.2).

imported>Xenbase: /* chrd.1 */

2018-01-23T16:30:27Z

chrd.1

← Older revision		Revision as of 16:30, 23 January 2018
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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 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

imported>Xenbase gene generator at 12:00, 10 February 2010

2010-02-10T12:00:00Z

New page

=chrd=
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