XB-FEAT-876507: Difference between revisions
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The gene is in both the v10 assembly for ''X.tropicalis'' and ''X. laevis'', however the v10 gene models for Xlaeivs are not yet placed on the ''vn2r1'' gene page. A request for this update has been made. | The gene is in both the v10 assembly for ''X.tropicalis'' and ''X. laevis'', however the v10 gene models for Xlaeivs are not yet placed on the ''vn2r1'' gene page. A request for this update has been made. | ||
=protein sequences alignmnet= | |||
A MSA of the following protein accessions for the v10 Xenopus ''vn2r1'' genes in NCBI's Cobalt tool (RID ES20S5UB212) and synteny confirm these genes as the paralogs/homeologs. The protein are highly conserved | |||
ref|XP_012818896.1| X. tropicalis vn2r1 Gene ID: 100496607 | |||
ref|XP_018119256.2| X.laevis vn2r1.L LOC108717043 Gene ID: 108717043 | |||
ref|XP_018120288.1| X. laevis vn2r1.S LOC108717582 Gene ID: 108717582 | |||
=synteny= | =synteny= | ||
Revision as of 11:09, 4 August 2022
vn2r1
This is the community wiki page for the gene vn2r1 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
nomenclature changes
17JULY2022
the mis-match between Xenopus and human gene symbols/names will consistently trigger a gene name change alert in the monthly Entrez Gene report- (ie Human symbol has changed for genepage ID: 876507 From vn2r1 to VN2R1P). This is because the human gene is a pseudogene, and thus has a 'P" added to the gene symbol.
DO NOT change the Xenopus gene symbol as this is a protein coding gene in the v10 genome assemblies.
The gene is in both the v10 assembly for X.tropicalis and X. laevis, however the v10 gene models for Xlaeivs are not yet placed on the vn2r1 gene page. A request for this update has been made.
protein sequences alignmnet
A MSA of the following protein accessions for the v10 Xenopus vn2r1 genes in NCBI's Cobalt tool (RID ES20S5UB212) and synteny confirm these genes as the paralogs/homeologs. The protein are highly conserved
ref|XP_012818896.1| X. tropicalis vn2r1 Gene ID: 100496607
ref|XP_018119256.2| X.laevis vn2r1.L LOC108717043 Gene ID: 108717043
ref|XP_018120288.1| X. laevis vn2r1.S LOC108717582 Gene ID: 108717582
synteny
Xtrop chr5: tlparp ... ssr3 ... kcnab1 ... vn2r1 .. LOC100496788 .. gmps ... slc33a1 ... c53orf33 ... plch1 Xla chr5L: tlparp.L ..ssr3.L ... LOC121393808 ... LOC108717042[kcnab1.L] .. LOC108717043[vn2r1.L] .. .. gmps.L ... slc33a1.L ... c53orf33.L ... LOC108717044
Xla chr5S: tlparp.S ... ssr3.S ... kcnab1.S ... LOC10871782[vn2r1.S] ... gmps.S