XB-FEAT-22172613: Difference between revisions
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=nomenclature updates= | =nomenclature updates= | ||
01.13.20 | 01.13.20, [updated 7.29.2020 to make this wiki entry clearer and more succinct] | ||
The identity of this gene and similar | The identity of this gene and similar genes was assessed by David Webb from NCBI and Xenbase curators. | ||
Based on synteny and reciprocal BALSTp matches to Human, this gene is now recognized as the true ''Xenopus'' orthologue of human B3GALT2. | Based on synteny and reciprocal BALSTp matches to Human, this gene is now recognized as the true ''Xenopus'' orthologue of human B3GALT2, and is on ''Xenopus'' Chromosome 4. There is no clear ''X. laevis'' orthologs at this time. | ||
In all gnathostomes, and in caecilians too, | In all gnathostomes, and in caecilians too, the B3GALT2 gene sits inside an intron of CDC73''' on the opposite strand i.e., [ CDC73(...B3GALT2>)<...GLRX2>...RO60<...UCHL5> (for example, see Human GENEID:8707). | ||
Although the neighboring gene order is somewhat shuffled in the amphibians ''Nanorana'' and ''Xenopus'', the ''b3galt2'' gene still sits '''inside''' of ''cdc73''. | Although the neighboring gene order is somewhat shuffled in the amphibians ''Nanorana'' and ''Xenopus'', the ''b3galt2'' gene still sits '''inside''' of ''cdc73''. | ||
Consequently, Entrez GeneID:100380178 is now seen to be a '''like''' gene, one of up to nine different ''b3galt2-like'' genes downstream of ''ilf3'' on ''Xenopus'' chromosome 3. | Consequently, Entrez GeneID:100380178 is now seen to be a '''like''' gene, one of up to nine different ''b3galt2-like'' genes downstream of ''ilf3'' on ''Xenopus'' chromosome 3. The models in the Chr3 loci are complicated and will need a lot of work to determine which are in the b3galt2 gene family, and to determine orthology. | ||
David Webb notes that most reptiles, amphibians and basal mammals also have a few B3GALT2-like genes downstream of LIF3 gene ( e.g., see GeneID:115080934) but the genes seem to be frequently lost or unannotated. | David Webb notes that most reptiles, amphibians and basal mammals also have a few B3GALT2-like genes downstream of LIF3 gene ( e.g., see GeneID:115080934) but the genes seem to be frequently lost or unannotated. | ||
Revision as of 13:28, 28 July 2020
b3galt2
This is the community wiki page for the gene b3galt2 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
nomenclature updates
01.13.20, [updated 7.29.2020 to make this wiki entry clearer and more succinct]
The identity of this gene and similar genes was assessed by David Webb from NCBI and Xenbase curators.
Based on synteny and reciprocal BALSTp matches to Human, this gene is now recognized as the true Xenopus orthologue of human B3GALT2, and is on Xenopus Chromosome 4. There is no clear X. laevis orthologs at this time.
In all gnathostomes, and in caecilians too, the B3GALT2 gene sits inside an intron of CDC73 on the opposite strand i.e., [ CDC73(...B3GALT2>)<...GLRX2>...RO60<...UCHL5> (for example, see Human GENEID:8707).
Although the neighboring gene order is somewhat shuffled in the amphibians Nanorana and Xenopus, the b3galt2 gene still sits inside of cdc73.
Consequently, Entrez GeneID:100380178 is now seen to be a like gene, one of up to nine different b3galt2-like genes downstream of ilf3 on Xenopus chromosome 3. The models in the Chr3 loci are complicated and will need a lot of work to determine which are in the b3galt2 gene family, and to determine orthology.
David Webb notes that most reptiles, amphibians and basal mammals also have a few B3GALT2-like genes downstream of LIF3 gene ( e.g., see GeneID:115080934) but the genes seem to be frequently lost or unannotated.