XB-FEAT-876507: Difference between revisions
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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. | 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. | '''DO NOT change the ''Xenopus'' gene symbol''' as this is a protein coding gene in the v10 genome assemblies. | ||
=protein sequences alignment= | |||
A MSA of the following protein accessions for the v10 genes in Cobalt (RID ES20S5UB212) and synteny confirm these genes as the paralogs/homeologs. | 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 proteins are highly conserved, 98-99% identical. | ||
ref|XP_012818896.1| X. tropicalis vn2r1 Gene ID: 100496607 | ref|XP_012818896.1| X. tropicalis vn2r1 Gene ID: 100496607 | ||
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=synteny= | =synteny= | ||
Xtrop chr5: ''tlparp ... ssr3 ... kcnab1 ... '''vn2r1''' .. LOC100496788 .. gmps ... slc33a1 ... c53orf33 ... plch1 | 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 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'' | Xla chr5S: ''tlparp.S ... ssr3.S ... kcnab1.S ... '''LOC10871782[vn2r1.S]''' ... gmps.S'' | ||
Latest revision as of 04:57, 5 April 2023
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.
protein sequences alignment
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 proteins are highly conserved, 98-99% identical.
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