XB-FEAT-22065629: Difference between revisions
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=uncharacterized protein XB22065629= | =uncharacterized protein XB22065629= | ||
This is the community wiki page for the gene ''XB22065629'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | |||
=protein identity and function= | =protein identity and function= | ||
04JAN2023 (cjz) | 04JAN2023 (cjz) | ||
The following protein accessions where run through DIOPT Eggnog to attempt to identify their gene and possible molecular function with | |||
The following protein accessions where both run through DIOPT Eggnog to attempt to identify their gene and possible molecular function with asmost identical results ( confirming both models are paralogs in ''Xenopus laevis'' sub-genomes despite ~100aa difference in length): | |||
1) ''uncharacterized protein XB22065629''.L [Xenopus laevis] | 1) ''uncharacterized protein XB22065629''.L [Xenopus laevis] | ||
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FVRHETVGVTSPKPNR | FVRHETVGVTSPKPNR | ||
results of EggNogg homology grouping: XB22065629 Xlaevis proteins hit the RBM43 homology group in 3 ( score 91) and 16 reptile/vertbrate species (score 76), but also has a Nmi/IFP 35 domain (NID), matching NMI and IFP35 genes/domains in 100+ species (32-47 score (ie low confidence)). | |||
=sequence conservation= | |||
alignment via Cobalt RID VDPN03A0212 (2 seqs) showed that the Xla.L and Xla.S proteins are moderately well conserved at 3' and 5" ends , with the Xal.S isoform has longer central aa string. | |||
alignment of the ''Xenopus'' seqs v human RBM3 aligns best to the 3' end of the Xla.L/S seqs (Cobalt RID VDR6U4B0212 (3 seqs)) as does the human NMI (Cobalt RID VDRBCG61212 (3 seqs)) | |||
sequences used: | |||
Human RBM43 (RNA binding motif protein 43) Gene ID: 375287 , 357aa NP_940959 | Human RBM43 (RNA binding motif protein 43) Gene ID: 375287 , 357aa NP_940959 | ||
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IVEDLINIHFQRAKNGGGEVDVVKCSLGQPHIAYFEE | IVEDLINIHFQRAKNGGGEVDVVKCSLGQPHIAYFEE | ||
=synteny = | |||
synteny is not conserved between human and Xenopus, using NMI as anchor, (note Xenopus has no annotated fab5p10 gene models). XB22065629 i on the end of Chr6L/S, surrounded by a 3' string of snoRNAs | |||
synteny | |||
synteny not conserved between human and Xenopus, using NMI as anchor, (note Xenopus has no annotated fab5p10 gene models) | |||
human chr 2: LOC107985826[ncRNA]> ... FABP5P10< ... '''RBM43'''< ... '''NMI'''< ... LOC107985827[ncRNA<]... | human chr 2: LOC107985826[ncRNA]> ... FABP5P10< ... '''RBM43'''< ... '''NMI'''< ... LOC107985827[ncRNA<]... | ||
Xenopus chr 9_10.L: rnd3.L[Rho family GTPase 3 ]< ... '''nmi'''< ... LOC108701325[protein mono-ADP-ribosyltransferase PARP15]> ... LOC108701839[protein mono-ADP-ribosyltransferase PARP15] | Xenopus chr 9_10.L: rnd3.L[Rho family GTPase 3 ]< ... '''nmi'''< ... LOC108701325[protein mono-ADP-ribosyltransferase PARP15]> ... LOC108701839[protein mono-ADP-ribosyltransferase PARP15] | ||
Xenopus chr6.L: znf577.L> .... 11x snoRNAs > .... ''XB22065629''> ... LOC108718457>[unconventional myosin-Id-like] ... LOC121393125> [unchar]> ... cdk5r1l.L | |||
=nomenclature changes= | =nomenclature changes= | ||
05JAN2023 | 05JAN2023 | ||
no changes can be made with great confidence at this time , but having 'uncharacterised' is not informative at all. | |||
we suggest ''Nmi/IFP 35 domain containing protein XB22065629'' and keeping XB22065629 as gene symbol as the best option at this time [cjz] | |||
Latest revision as of 07:39, 5 January 2023
uncharacterized protein XB22065629
This is the community wiki page for the gene XB22065629 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
protein identity and function
04JAN2023 (cjz)
The following protein accessions where both run through DIOPT Eggnog to attempt to identify their gene and possible molecular function with asmost identical results ( confirming both models are paralogs in Xenopus laevis sub-genomes despite ~100aa difference in length):
1) uncharacterized protein XB22065629.L [Xenopus laevis] NCBI Reference Sequence: XP_018122493.1 538 aa linear VRT 14-MAY-2021
MSCYKRGLRVCGVPGHLFEEELLRDKLLIHFLRPKNQGGEIQNLHYPTKDEGVAILTFEEEEVAERILKTQHLLDVNGQLFPLEVMRLQF SMPVITSLDLSRLKNKKLLVDLFEKHKVMILNKRDEMFIISAEFEDLRQLRSEIMATVLTCDTSPLGQRSQKQISESGPESPVKDNLGVK PSSQQPSGNDNNVEKPQSRRTSSRSNSQEKHPSRARRREANMAPTFSNAHILGHRPTTDSVAQGSNPTSEGGMSFKTTRDPIVRMNNDSA SQMLSDLNLGSSTNRGQPSIEATRTTRNPSAITKDFPSQASLVKSFSVDNDVLYYIRIFETERVDEVLKRCAVNIQVAEGEDISNVTLKS QSPSLKLLFSDCCDEILQIFSEWQSNLRTEDLDLTQFPTLERRKMTEKIQHLGRAHGVAIIASEDGLHLIGGPSQIHWLIDWWKTISQPR PPDVGREAVNTREIHLPHPPNMGRSYTGANEKKTNHGDQDMTQVVRRKGSVTGSHQSGDSMRRETSTESSSVSSRTNSYAHGITHPKP
2) uncharacterized protein XB22065629.S isoform X1 [Xenopus laevis]
NCBI Reference Sequence: XP_018124435.1 646 aa linear VRT 14-MAY-2021
MTWYKRGVQVCGVPGHLFEEELLRDKLIIHFLRPKNQGGEIQELRYPTKDSGVAILTFEDEEVAERILKTTHLLDVNGQSFVLEVMRLQF SMLVITSLDLSRFKNLNLLVDLLEKHRVTILGRRDETLNISAEFEDLRKFRSEIMAKALTCDTSPLGQRSRKQISVSGLESPVKDNLGVR PTSRQPSGNANNMEKPQSRRTPNMSSSHEKLPSRSSSHEKLPSRSNSHEKPPSRSNSHDKPPSRSNSHEKPPSRSNSHEKPPSRSNSYEI LPSRSNSHEKPPSRSNSHEKPPSRSNSHEKPPSRSNSHEKPPSRSNSYEILPSRTMRREADMAPTFRNADTLRVRPMASTIDSVVQGSNT TSEGGMSFKATMNPRVRMNNDSVSQKLTDLNLVSSTIVRSRPSGEAIRTTRKPSAVTKDFPSEKALVKSFPVDKDVLHYIGVFKKQYIDE VLRRGFTDIEVAEGEDISYVTLKSQSPFLQVLFTDCCDKISELFSKGQNSLRTEDLDLTQVPPLARRDITKEIENLGRANSVAVVDYKDL LHLIGGSSHIHLLKERWKTISQSRPPYAGQEALSSGQISLPHPPDMGRSYAGANEKKTNHGDQDVAQAVRHKAGVTSSPQTVRTGNQSKG FVRHETVGVTSPKPNR
results of EggNogg homology grouping: XB22065629 Xlaevis proteins hit the RBM43 homology group in 3 ( score 91) and 16 reptile/vertbrate species (score 76), but also has a Nmi/IFP 35 domain (NID), matching NMI and IFP35 genes/domains in 100+ species (32-47 score (ie low confidence)).
sequence conservation
alignment via Cobalt RID VDPN03A0212 (2 seqs) showed that the Xla.L and Xla.S proteins are moderately well conserved at 3' and 5" ends , with the Xal.S isoform has longer central aa string.
alignment of the Xenopus seqs v human RBM3 aligns best to the 3' end of the Xla.L/S seqs (Cobalt RID VDR6U4B0212 (3 seqs)) as does the human NMI (Cobalt RID VDRBCG61212 (3 seqs))
sequences used:
Human RBM43 (RNA binding motif protein 43) Gene ID: 375287 , 357aa NP_940959 MASVLNVKESKAPERTVVVAGLPVDLFSDQLLAVLVKSHFQDIKNEGGDVEDVIYPTRTKGVAYVIFKEKKVAENVIRQKKHWLARKTRH AELTVSLRVSHFGDKIFSSVNAILDLSVFGKEVTLETLVKDLKKKIPSLSFSPLKPNGRISVEGSFLAVKRLRESLLARACSLLEKDRNF TSEERKWNRQNPQRNLQRSNNSLASVRTLVPETARSGEMLVLDTDVFLYLKHKCGSYESTLKKFHILSQEKVDGEITTICLKSIQVGSQP NNAKHVKELIEEWSHALYLKLRKETFILEGKENREKRMIKRACEQLSSRYLEVLINLYRTHIDIIGSSSDTYLFKKGVMKLIGQKVS
human NMI [N-myc and STAT interactor] Gene ID: 9111 307aa NP_004679.2 MEADKDDTQQILKEHSPDEFIKDEQNKGLIDEITKKNIQLKKEIQKLETELQEATKEFQIKEDIPETKMKFLSVETPENDSQLSNISCSF QVSSKVPYEIQKGQALITFEKEEVAQNVVSMSKHHVQIKDVNLEVTAKPVPLNSGVRFQVYVEVSKMKINVTEIPDTLREDQMRDKLELS FSKSRNGGGEVDRVDYDRQSGSAVITFVEIGVADKILKKKEYPLYINQTCHRVTVSPYTEIHLKKYQIFSGTSKRTVLLTGMEGIQMDEE IVEDLINIHFQRAKNGGGEVDVVKCSLGQPHIAYFEE
synteny
synteny is not conserved between human and Xenopus, using NMI as anchor, (note Xenopus has no annotated fab5p10 gene models). XB22065629 i on the end of Chr6L/S, surrounded by a 3' string of snoRNAs
human chr 2: LOC107985826[ncRNA]> ... FABP5P10< ... RBM43< ... NMI< ... LOC107985827[ncRNA<]...
Xenopus chr 9_10.L: rnd3.L[Rho family GTPase 3 ]< ... nmi< ... LOC108701325[protein mono-ADP-ribosyltransferase PARP15]> ... LOC108701839[protein mono-ADP-ribosyltransferase PARP15]
Xenopus chr6.L: znf577.L> .... 11x snoRNAs > .... XB22065629> ... LOC108718457>[unconventional myosin-Id-like] ... LOC121393125> [unchar]> ... cdk5r1l.L
nomenclature changes
05JAN2023 no changes can be made with great confidence at this time , but having 'uncharacterised' is not informative at all.
we suggest Nmi/IFP 35 domain containing protein XB22065629 and keeping XB22065629 as gene symbol as the best option at this time [cjz]