XB-FEAT-29078738 - Revision history

Xenbase: /* nomenclature updates */

2026-05-18T15:42:00Z

nomenclature updates

← Older revision		Revision as of 15:42, 18 May 2026
Line 15:		Line 15:

	Although not perfect, as these ''cd2'' paralogs aren't always each others closest match based on alignment and sequence similarity, we have numbered the duplicates sequentially from ''cd2'' to ''cd2.4'', and determined that for ''X.laevis'' chr2S, the '2nd' gene is best called ''cd2.2''(XB-GENEPAGE-29094598).		Although not perfect, as these ''cd2'' paralogs aren't always each others closest match based on alignment and sequence similarity, we have numbered the duplicates sequentially from ''cd2'' to ''cd2.4'', and determined that for ''X.laevis'' chr2S, the '2nd' gene is best called ''cd2.2''(XB-GENEPAGE-29094598).

			these are the protein seas used to look at seq similarity, with human CD2 as outgrip.

			ref\|XP_017945849.2\|
			ref\|XP_018104516.1\|
			ref\|XP_041437300.1\|
			ref\|XP_031752265.1\|
			ref\|XP_041437303.1\|
			ref\|XP_031753193.1\|
			ref\|XP_041437305.1\|
			ref\|XP_031752262.1\|
			ref\|XP_041437296.1\|
			ref\|XP_041439230.1\|
			ref\|NP_001315538.1\|

			Note that COBALT kicks out ''Xtr.cd2.4'' and ''Xla.cd2.3.L'' from tree- prob due to xtra long transcript which poorly align.

Xenbase: /* nomenclature updates */

2026-05-18T15:37:22Z

nomenclature updates

← Older revision		Revision as of 15:37, 18 May 2026
Line 8:		Line 8:

	LOC100487379 is best match for CD2 ortholog, with 3 ''X. tropicalis'' duplicates in the v10 assembly: ''LOC116408729 (cd.2), LOC116408910 (Xtr. cd.3)'', and ''LOC101734364 (Xtr.cd.4)''.		LOC100487379 is best match for CD2 ortholog, with 3 ''X. tropicalis'' duplicates in the v10 assembly: ''LOC116408729 (cd.2), LOC116408910 (Xtr. cd.3)'', and ''LOC101734364 (Xtr.cd.4)''.
			X.laevis chr2L also has 4 genes and chr2S only 2.

			''X.laevis'' genes geneID:121399783 (L) and geneID:108709305 (S) have also been added to this page.

			''Xla.cd2.L'' and ''Xla.cd2.S'' form a nice pair/clade based on protein seq. similarity in COBALT multi-alignment NJ tree.

			Although not perfect, as these ''cd2'' paralogs aren't always each others closest match based on alignment and sequence similarity, we have numbered the duplicates sequentially from ''cd2'' to ''cd2.4'', and determined that for ''X.laevis'' chr2S, the '2nd' gene is best called ''cd2.2''(XB-GENEPAGE-29094598).

Xenbase: Created page with "=''cd2''= This is the community wiki page for the gene ''cd2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. =nomenclature updates= 14MAY2026 ''Xenopus'' gene nomenclature was updated to follow the names of human orthologs as assessed by Xenbase and NCBI, from ''LOC100487379, T-cell surface antigen CD2'' to ''cd2, CD2 molecule’’. LOC100487379 is best match for CD2 ortholog, with 3 ''X. t..."

2026-05-14T19:24:22Z

Created page with "=''cd2''= This is the community wiki page for the gene ''cd2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. =nomenclature updates= 14MAY2026 ''Xenopus'' gene nomenclature was updated to follow the names of human orthologs as assessed by Xenbase and NCBI, from ''LOC100487379, T-cell surface antigen CD2'' to ''cd2, CD2 molecule’’. LOC100487379 is best match for CD2 ortholog, with 3 ''X. t..."

New page

=''cd2''=
This is the community wiki page for the gene ''cd2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

=nomenclature updates=
14MAY2026

''Xenopus'' gene nomenclature was updated to follow the names of human orthologs as assessed by Xenbase and NCBI, from ''LOC100487379, T-cell surface antigen CD2'' to ''cd2, CD2 molecule’’.

LOC100487379 is best match for CD2 ortholog, with 3 ''X. tropicalis'' duplicates in the v10 assembly: ''LOC116408729 (cd.2), LOC116408910 (Xtr. cd.3)'', and ''LOC101734364 (Xtr.cd.4)''.

← Older revision		Revision as of 15:42, 18 May 2026
Line 15:		Line 15:

	Although not perfect, as these ''cd2'' paralogs aren't always each others closest match based on alignment and sequence similarity, we have numbered the duplicates sequentially from ''cd2'' to ''cd2.4'', and determined that for ''X.laevis'' chr2S, the '2nd' gene is best called ''cd2.2''(XB-GENEPAGE-29094598).		Although not perfect, as these ''cd2'' paralogs aren't always each others closest match based on alignment and sequence similarity, we have numbered the duplicates sequentially from ''cd2'' to ''cd2.4'', and determined that for ''X.laevis'' chr2S, the '2nd' gene is best called ''cd2.2''(XB-GENEPAGE-29094598).

			these are the protein seas used to look at seq similarity, with human CD2 as outgrip.

			ref\|XP_017945849.2\|
			ref\|XP_018104516.1\|
			ref\|XP_041437300.1\|
			ref\|XP_031752265.1\|
			ref\|XP_041437303.1\|
			ref\|XP_031753193.1\|
			ref\|XP_041437305.1\|
			ref\|XP_031752262.1\|
			ref\|XP_041437296.1\|
			ref\|XP_041439230.1\|
			ref\|NP_001315538.1\|

			Note that COBALT kicks out ''Xtr.cd2.4'' and ''Xla.cd2.3.L'' from tree- prob due to xtra long transcript which poorly align.