XB-FEAT-22065629: Difference between revisions

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Created page with "=uncharacterized protein XB22065629= 05JAN2023 =protein identity and function= 04JAN2023 The following protein accessions where run through DIOPT Eggnog to attempt to identif..."
 
 
(7 intermediate revisions by the same user not shown)
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=uncharacterized protein XB22065629=
=uncharacterized protein XB22065629=
05JAN2023
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
04JAN2023 (cjz)
The following protein accessions where run through DIOPT Eggnog to attempt to identify their gene and possible molecular function:
 
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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PPDVGREAVNTREIHLPHPPNMGRSYTGANEKKTNHGDQDMTQVVRRKGSVTGSHQSGDSMRRETSTESSSVSSRTNSYAHGITHPKP
PPDVGREAVNTREIHLPHPPNMGRSYTGANEKKTNHGDQDMTQVVRRKGSVTGSHQSGDSMRRETSTESSSVSSRTNSYAHGITHPKP


this protein hits the RBM43 homology group in 3 ( score 91) and 16 species (score 76), but also has a Nmi/IFP 35 domain (NID), matching NMI and IFP35 gens in 100+ species.


2)  
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=
=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]

Retrieved from "https://wiki.xenbase.org/xenwiki/index.php?title=XB-FEAT-22065629&oldid=50119"