XB-FEAT-29078738: Difference between revisions
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..." |
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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). | |||
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. | |||
Latest revision as of 15:42, 18 May 2026
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). 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).
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.