XB-FEAT-5889258: Difference between revisions
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18SEPT2023 | 18SEPT2023 | ||
Although these gene models (Xtrop GENEID:733992 and Xlaevis GENEID:779169) are not in the current v10 assembly, alignment of the proteins for X. laevis accession from v10 and v6.0 ( done using NCBIs COBALT tool ) and the phylogenetic tree/cladogram from these Xla proteins, show that these are very unlikely to be coding for the same gene ( ie they are not mhc2-daa) . | Although these gene models (Xtrop GENEID:733992 and Xlaevis GENEID:779169) are not in the current v10 assembly, alignment of the proteins for ''X. laevis'' accession from v10 and v6.0 ( done using NCBIs COBALT tool ) and the phylogenetic tree/cladogram from these Xla proteins, show that these are very unlikely to be coding for the same gene ( ie they are not ''mhc2-daa'') . | ||
[[File:Mhc2.daa2 msa.png|thumb]] | [[File:Mhc2.daa2 msa.png|thumb]] | ||
Therefore, I have provisionally added a ' | Therefore, I have provisionally added a 'like ' suffix to this gene page to distinguish it from ''mhc2-daal'' genes on XB-GENEPAGE-5999631. | ||
=Protein Accessions & Sequences in FASTA format= | =Protein Accessions & Sequences in FASTA format= | ||
Latest revision as of 08:25, 2 October 2023
mhc2-daal
This is the community wiki page for the gene mhc2-daal please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
nomenclature changes
18AUGUST2022
Xenopus MHC genes are currenly under nomenclature review by HGNC/VGNC. Current names are considered provisional.
gene symbol changed from hla-dqa2 to mhc2-daa
gene name changed from 'major histocompatibility complex, class II, DQ alpha 2' to 'major histocompatibility complex, class II, DA alpha'
18SEPT2023
Although these gene models (Xtrop GENEID:733992 and Xlaevis GENEID:779169) are not in the current v10 assembly, alignment of the proteins for X. laevis accession from v10 and v6.0 ( done using NCBIs COBALT tool ) and the phylogenetic tree/cladogram from these Xla proteins, show that these are very unlikely to be coding for the same gene ( ie they are not mhc2-daa) .
Therefore, I have provisionally added a 'like ' suffix to this gene page to distinguish it from mhc2-daal genes on XB-GENEPAGE-5999631.
Protein Accessions & Sequences in FASTA format
Xlaevis seqs
>XBmRNA66883_Xlav10 MRSGEMISVCALLVLGLKASDAVTVDYIDYGAMFYQTYGPSGEYLMDYNGNELFHVDLESKSVVWTLPGLEKYTSFDPQGGLQQINVAKYNVDGYKKSRNSTPATSIPPLISLYAAKPVVLGEPNILICCVNNIFPPVMSTTWFKNGQKISDGFSETSYLPAQDHSFSRLHYLAFLPNEHDIYTCEVEHWGLEKPTRRIWEHEAPTPISEAYQNVICALGLAVGIIGIIAGVMLIIKGMKQSAAQGRSQR*
>lXelaev16058833m-Xlav7.2 MISVCALLVLGLKASDAVTVDYIDYGAMFYQTYGPSGEYLMDYNGNELFHVDLESKSVVWTLPGLEKYTSFDPQGGLQQINVAKYNVDGYKKSRNSTPATSIPPLISLYAAKPVVLGEPNILICCVNNIFPPVMSTTWFKNGQKISDGFSETSYLPAQDHSFSRLHYLAFLPNEHDIYTCEVEHWGLEKPTRRIWEHEAPTPISEAYQNVICALGLAVGIIGIIAGVMLIIKGMKQSAAQGRSQR*
>rna51160_Xla_v9.2 MRSGEMISVCALLVLGLKASDAVTVDYIDYGAMFYQTYGPSGEYLMDYNGNELFHVDLESKSVVWTLPGLEKYTSFDPQGGLQQINVAKYNVDGYKKSRNSTPATSIPPLISLYAAKPVVLGEPNILICCVNNIFPPVMSTTWFKNGQKISDGFSETSYLPAQDHSFSRLHYLAFLPNEHDIYTCEVEHWGLEKPTRRIWEHEAPTPISEAYQNVICALGLAVGIIGIIAGVMLIIKGMKQSAAQGRSQR*
>AAH84644|NCBI Protein_Xla_mhc2-daa_Scaffold279844_v6.0 MVPVCALLVLLLKASEAVTVDYFDYGADYYQTYGPSGQYLFDYNGNEMFHVDLESKSVVWTLPGLEKYASFDPQGGLQDINIAKYNLDIRIKRSNRTVAPNIPPLVSVYISNPVVLGEPNILICCTKNIFPPVMNTTWIKNGEIIREGFKETSYLPAQDGTFRKLHYLAFIPNDHDIYTCEVEHWGLEKPTKRIWKHEGSTPISEAYQNVICALGLAVGIIGIIAGVMLIIKGMKQSTAQGRNQR
>NP_001090263|RefSeq_Xla_Scaffold279844_v6.0 MVPVCALLVLLLKASEAVTVDYFDYGADYYQTYGPSGQYLFDYNGNEMFHVDLESKSVVWTLPGLEKYASFDPQGGLQDINIAKYNLDIRIKRSNRTVAPNIPPLVSVYISNPVVLGEPNILICCTKNIFPPVMNTTWIKNGEIIREGFKETSYLPAQDGTFRKLHYLAFIPNDHDIYTCEVEHWGLEKPTKRIWKHEGSTPISEAYQNVICALGLAVGIIGIIAGVMLIIKGMKQSTAQGRNQR
>XeXenL6RMv10024389m_Xla_mhc2-daa_Scaffold279844_v6.0x PPLVSVYISNAVVLGEPNILICCTKNIFPPVMNTTWIKNGEIIRGFKETSYLPAQDGTFRKLHYLAFIPNDHDIYTCEVEHWGLERPTKRIWSKYCTLLLQI*
>XeXenL6RMv10043591m_Xlav6.0 MSTTWFKNGQKISDGFSETSYLPAQDHSFSRLHYLAFLPNEHDIYTCEVEHWGLEKPTRRIWGKYVN*
X . tropicalis Seqs
>Novel protein similar to MHC class II antigen alpha chain [Xenopus tropicalis_GENEID:733992_v7.1] MLLLCALLALALKPSEAATVDCFDYGAEFYQTRRPTGEYLFDYNGNEMFHVDLESKSVVWTLPGLEKTASFDPQAALQDISVMKFSLDVFK
>Xetro.F00205.1[JGI_Xtrop_mhc.daa.2 model] MLLLCALLALALKPSEAATVDCFDYGAEFYQTRRPTGEYLFDYNGNEMFHVDLESKSVVWTLPGLEKTASFDPQAALQDISVMKFSLDVCMKISNTTAATNS*
>CAJ83087|NCBI Protein_Xtrop.mhc2-daa.2
MLLLCALLALALKPSEAATVDCFDYGAEFYQTRRPTGEYLFDYNGNEMFHVDLESKSVVWTLPGLEKTASFDPQAALQDISVMKFSLDVFK