XB-FEAT-6257460: Difference between revisions
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= '' | = ''trpm2l'' = | ||
This is the community wiki page for the gene '' | This is the community wiki page for the gene ''trpm2l'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | ||
=nomenclature changes= | =nomenclature changes= | ||
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Synteny (below) does not support the orthology between ''Xenopus'' GeneID:100491139 and GeneID:108707608 and human trim26/TRIM26, and NCBI orthology analysis also does not identify Xtrop Gene ID:100491139 as an ortholog of TRIM26. Thus we conclude that these genes has been misannotated and incorrectly named ''trim26''. | Synteny (below) does not support the orthology between ''Xenopus'' GeneID:100491139 and GeneID:108707608 and human trim26/TRIM26, and NCBI orthology analysis also does not identify Xtrop Gene ID:100491139 as an ortholog of TRIM26. Thus we conclude that these genes has been misannotated and incorrectly named ''trim26''. | ||
Q: | Q:ARE THESE GENES THE ORTHOLOGS OF TRPM2? | ||
A: No, Xtrop Gene ID: 100124999 is identified by NBCI as the true ortholog of TRPM2, although synteny is not | |||
A: No, Xtrop Gene ID: 100124999 is identified by NBCI as the true ortholog of TRPM2, although synteny is WEAKLY conserved, it is flanked by CFAP410 in human and frog. | |||
Q:ARE THESE GENES THE ORTHOLOGS OF TRPM4 (a previous gene symbol used for these genes)? | |||
A: No, synteny also rejects this ortholgy. | |||
Q:ARE THESE GENES a TRPM2, Transient receptor potential cation channel, subfamily M, member 2, gene? | |||
A: YES! DIOPT/EggNog confirms this is in fact a Transient receptor potential cation channel, subfamily M, member 2 gene, matching the protein with very high confidence to | |||
362 TRPM2 proteins for > 160 species. | |||
Xenbase already has a ''Xenopus trpm2'' gene page, XB-GENEPAGE-996774. with Xtrop gene ID:100124999 and Xla.L GeneID: 108701480, both on chr9/9_10L. NCBI recognizes the Xtrop gene as a true ortholog of Human. | |||
Q. does human genome has a gene in this conserved orthologous pattern that would also be a trpm2-like gene? | |||
A> Apparently not. looking at gene pattern next to TPP1, there are no candidates a TRPM2L in humans, although there might be in other mammals. Further investigation nd BLAST may help answer this. | |||
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1) removed the vertebrate orthologs for TRIM26 from this gene page XB-GENEPAGE-6257460. | 1) removed the vertebrate orthologs for TRIM26 from this gene page XB-GENEPAGE-6257460. | ||
2) renamed these genes ''trpm2l, transient receptor potential cation channel, subfamily M, member 2 like'' | 2) renamed these genes ''trpm2l, transient receptor potential cation channel, subfamily M, member 2 '''like''''' as it is in this homology group, but is a 2nd gene in ''Xenopus'', on Chr2/2L, while true ''trpm2'' is on chr9/9_10. | ||
3) removed the synonyms ''trim26'', ''trpm4'' and ''trpm4b'' for this XB-GENEPAGE-6257460 | |||
=Synteny= | |||
April 29th, 2023 | |||
TRIM26 ( confirming these are not ''Xenopus trim26'' genes) | |||
Human: TRIM10 TRIM15 PAIP1P1 '''TRIM26''' TRIM26BP HCG17 | |||
XTR.chr2: ilk tpp1 ''''GeneID:100491139'''' zscan2 | |||
Xla.chr2L: dynp1 rrp8.L mgc822989 tpp1 tif-if2 '''' GeneID:108707608 '''' zfp391 | |||
----------------------------------------------- | |||
TRPM2 | |||
Human chr21: ICOSLG< DNMT3L AIRE PFKL> CFAP410> '''TRPM2''' LRRC3> TSPEAR UGE2G2< SUMO3 PTTG1IP< ITGB2< SLX9> | |||
Xtrop.Chr9: col5a2> col3a1<. gulp1< cfap410< ''trmp2>'' pth2r> pikfyve< c9h2orf80> | |||
------------------------------------------------- | |||
TRPM4 (cf Xenopus) | |||
Human chr19: SNRNP70> C19ORF73> PPFIA3> '''TRPM4'''> LOC107985340> SLC6A21P< SUMO1P4> SLC6A16< CD37> TEAD2< DKKL1> | |||
------------------------------------------------- | |||
TPP1 (cf Xenopus) | |||
Human Chr11: ILK> LOC> TAF10< '''TPP1'''< DCHS1< MRP17> | |||
XTR.chr2: ilk '''tpp1''' GeneID:100491139 zscan2 | |||
Xla.chr2L: dynp1 rrp8.L mgc822989 '''tpp1''' tif-if2 GeneID:108707608 zfp391 | |||
=proteins used in DIOPT/EggNog homology group analysis= | |||
>XP_031753324.1 transient receptor potential cation channel subfamily M member 2 isoform X1 [Xenopus tropicalis] | |||
MGNTKSKSPVPDRIDGVQLHSTVGSPYRPGTADPKKKKKTAPKFIDGEKVDVLNSWVTRNIRKKECVAFI | |||
PPAPEAPGDRDTCGCGHTRRTHFAAQVSAPLEPGTVWDPHKHVREFPSDAHGDLTFTGTTRTWAKYVRAS | |||
NDTPPRSLFDLMTQQWDLRVPNLLISVTGGAKNFNISPRLKTEFSRGLVTAAQSTGAWIITGGSHAGVMK | |||
HVGEAVRDFSGGQHETEIVLIGIATWGIVHNRESLISEAGGAPAVYPMDEGSQGALCCLDNNHTHFILVD | |||
NGTYGKYGVEIPLRTKLEKFISEQTMENAGTAIKIPIVCVVLEGGPGTLDTIYNSMCNNTPCVIVEGSGR | |||
VADIIAQVANLSISQITISVVKEKLQNLFQDTFESFTEAQIIMWTKKIQDIVRMGSLLTILREDKTEEQG | |||
MDVAILQALLKASRSTDYSGQENWDHQLKLAVAWNRADIAESQIFTEDWMWKPSDLYPSLMVSLIDDKPS | |||
FLRLFLERGVSLSEFITWDMLTELYNNTEPSSLIHSKLERQAMLDESTEMNGGLKIQLHHVSHVLQELLG | |||
GLTESLYLDRRSHRTRTLPYINIKISGKVSSMRSECDSTVKLEHPVRDLLIWCIVQNRAELAEIIWCQSQ | |||
DCMVSALACSKMLKALSKEEDDTESMESMKVLANVYEERAAGVFSECYASDESRAEQLLIRVSSKWGKTT | |||
SLDLAQESQGQLFMSQSGVQMFLTKTWFGRLSVDNGLLAILLCMLLFPLIYTDLIMYRKESVAPRSSRGQ | |||
DKRSAARSSRARNCLWKFFDFFSAPIVKFYYNVVSYIGFLWLFAYVLMMDFQTYPSWTEYLLYVWVFSIL | |||
CEELRQLLYDPDRLGFVVKSMQYISEFWNQVDTLALSLFAVGLICRLASLNTVYLGRVFLSVDYMIFCIR | |||
LMNIFTVSKVLGPKIIMLRRMIMDLFFFLFLLAIWIVSFGVAKQAILTSNETRLDWIFRNVIYGPYLILF | |||
GQIPSEVDGLNFDPTKCSQSGTDPTLPKCVYNDGSGKTLFPEWLTILLLCIYLLMANILLLNLLIAMFSN | |||
TFGDVESHTDQIWKFYRFGLIKEYNERPVAPPPFILLSHLYFLLKYGLSKRSTLSHQAMRSVMDEAGESS | |||
LLSWELYMRDNYLHNQQLVDSQSQENVVKNTAQSVSAVLNLLNMRKDGEGQQLETRLILLEEEVLKSSEQ | |||
LQWIISALGEKGFTGRAQRLVHSSSQDSGDSATHGLDPSTERKSIYHVNSRTLQYPDSPVSRYPVPDEMV | |||
PWEVPFPGYEPPFYTAERGDRGAYDPHSEMSQTNRKYNAVDGALDLRSSCGTYAVQDGFPLNPMGRTGLR | |||
GVGSLRWFGPNHSLHLVITRWNTRANGSADKKLPRKMLEVLVVKEKKNELWALPGGTLSPGEEIPSKLQS | |||
ILSQTYGERFSELLRGGREVFRGYLDDPRNTDNSWIETLAVNIHLDTEETLSQFLQNLNQSSPEVSLRWQ | |||
ILDHKIPIYANEKEILQRTAEVHGTHY | |||
>XP_041438825.1 transient receptor potential cation channel subfamily M member 2 [Xenopus laevis] | |||
MGNTKSKSSVPDGIDGVQLHSNVNSPHRPGTADPKKKKKTAPKFIDGEKVDVLNSWVSQNIRKKECVAFI | |||
PRVSEAPSDRDSCSCGHTRHTHFGDHKSSSVEPGTVWDPHKHVREFPSDAHGDLTFTGTTRTWAKYVRAS | |||
NDTPPRLLFDLMTQQWDLSVPNLLISVTGGAKNFNISPRLKTEFSRGLVTAAQSTGAWIITGGSHAGVMK | |||
HVGEAVRDFSGGQHESDIVLIGIATWGIVHNRELLISEAGGAPAVYQMDEGSQGSLCCLDNNHTHFILVD | |||
NGTFGRYGVEIPLRAKLEKYISAQTMEKAGTAIKIPIVCVVLEGGPGTLDTIYNSMCNNTPCVIVEGSGR | |||
VADIIAQVANLNISRITISLVKEKLQNLFQDTYESFTEAQIIMWTKKIQDIVRMGSLLTILREDKTEEQG | |||
MDVAILQALLKASRSTDLSGQENWDHQLKLAVAWNRPDIAESQIFTEDWMWKPSDLYPSLMVSLIDDKPS | |||
FLRLFLERGVSLSEFLTWDVLTELYNNTEPSSLIRSKLERQAMLDESTEINGPTIQLHHVSRVLQELLGG | |||
RTEPLYPDVRSHRTRNLPHIKIKISGKVSSMRLASDCTLQLEHPVRDLLIWCIVQNRAELAEIIWCQSQD | |||
CIVGALACSKILKALSKEEDDTESMENMKVLADVYEERAAGVFSECYESDESRAEQLLIRVSSIWGKTTS | |||
LDLAQESQGQAFMSQGGVQMFLNKTWCGKLSVDNGLLAILLCMLLFPLIYTGLVMYRNKPLAPRSSRRPD | |||
INGQMKSPVRSSQTRNCLKKFLHFFTAPIVKFYYNVVSYIGFLWLFAYVLMMDFQTSPSWREYLLYIWVF | |||
SIFCEELRQLLYDPDRLGFVVKSAQYISEFWNQIDSTALVLFAVGLICRLASVDTVYLGRVFLSIDFMIF | |||
CVRLLHIFTVSKVLGPKIIMLRRMVMDLFFFLFLLAIWIVSYGVAKQAILTSNEIRLNWIFRNIVYEPYL | |||
TLFGQMPSDIDGLNFDPTKCSQDGTNPLLPKCVYNDGSGNPLFPEWLTIILTCIYLLMANILLLNLLIAM | |||
FSNTFGDVESHTDQIWKFYRFGLIKEYNERPAAPPPFILLSHFYFLLKYGLSKRSTMSHKAMRSVIDEAG | |||
ESSLLSWELYMRDNYVHNRQLLDAQSQENVVKNTAESVSAVLKMLSMEKGSDGQNMERRMFLLEDEVSKS | |||
SQKLQWIISALREKGFTGKAQMFVHSNSQDLEEKASLGSDSLGDKKSIYHVNSRTLQYPNSNTTRYPVPD | |||
EMVPWEVTFPGYDPPFLIADRDDRGAYDPHSEMSQTNRKYNGVDGALDFRSSCGTYLVHEGVPLNPMGRT | |||
GLRGVGSLRWFGPNHSLHPVITRWNTLPNGSLDRKISRKKLEVLVVKQIDNELWALPGGTLSPGEDIPPK | |||
LKSILNEKYVKKFSDLLRGGTEVFRGYLDDPRNTDNSWIETRAVNIHMDSDEKLSRFLQNVNDSSPGVSL | |||
RWQILDHKIPIYADEKEILQRTAEVHGTHY | |||
Latest revision as of 09:13, 16 May 2023
trpm2l
This is the community wiki page for the gene trpm2l please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
nomenclature changes
06.30.2020
Human symbol has changed for genepage ID: 6257460 From trpm2l to trim26
Human symbol has changed for genepage ID: 6257460 From transient receptor potential cation channel, subfamily M, member 2 like to tripartite motif containing 26
1MAY2023
Synteny (below) does not support the orthology between Xenopus GeneID:100491139 and GeneID:108707608 and human trim26/TRIM26, and NCBI orthology analysis also does not identify Xtrop Gene ID:100491139 as an ortholog of TRIM26. Thus we conclude that these genes has been misannotated and incorrectly named trim26.
Q:ARE THESE GENES THE ORTHOLOGS OF TRPM2?
A: No, Xtrop Gene ID: 100124999 is identified by NBCI as the true ortholog of TRPM2, although synteny is WEAKLY conserved, it is flanked by CFAP410 in human and frog.
Q:ARE THESE GENES THE ORTHOLOGS OF TRPM4 (a previous gene symbol used for these genes)?
A: No, synteny also rejects this ortholgy.
Q:ARE THESE GENES a TRPM2, Transient receptor potential cation channel, subfamily M, member 2, gene?
A: YES! DIOPT/EggNog confirms this is in fact a Transient receptor potential cation channel, subfamily M, member 2 gene, matching the protein with very high confidence to 362 TRPM2 proteins for > 160 species.
Xenbase already has a Xenopus trpm2 gene page, XB-GENEPAGE-996774. with Xtrop gene ID:100124999 and Xla.L GeneID: 108701480, both on chr9/9_10L. NCBI recognizes the Xtrop gene as a true ortholog of Human.
Q. does human genome has a gene in this conserved orthologous pattern that would also be a trpm2-like gene?
A> Apparently not. looking at gene pattern next to TPP1, there are no candidates a TRPM2L in humans, although there might be in other mammals. Further investigation nd BLAST may help answer this.
XB Actions:
1) removed the vertebrate orthologs for TRIM26 from this gene page XB-GENEPAGE-6257460.
2) renamed these genes trpm2l, transient receptor potential cation channel, subfamily M, member 2 like as it is in this homology group, but is a 2nd gene in Xenopus, on Chr2/2L, while true trpm2 is on chr9/9_10.
3) removed the synonyms trim26, trpm4 and trpm4b for this XB-GENEPAGE-6257460
Synteny
April 29th, 2023
TRIM26 ( confirming these are not Xenopus trim26 genes)
Human: TRIM10 TRIM15 PAIP1P1 TRIM26 TRIM26BP HCG17
XTR.chr2: ilk tpp1 'GeneID:100491139' zscan2
Xla.chr2L: dynp1 rrp8.L mgc822989 tpp1 tif-if2 ' GeneID:108707608 ' zfp391
TRPM2
Human chr21: ICOSLG< DNMT3L AIRE PFKL> CFAP410> TRPM2 LRRC3> TSPEAR UGE2G2< SUMO3 PTTG1IP< ITGB2< SLX9>
Xtrop.Chr9: col5a2> col3a1<. gulp1< cfap410< trmp2> pth2r> pikfyve< c9h2orf80>
TRPM4 (cf Xenopus)
Human chr19: SNRNP70> C19ORF73> PPFIA3> TRPM4> LOC107985340> SLC6A21P< SUMO1P4> SLC6A16< CD37> TEAD2< DKKL1>
TPP1 (cf Xenopus)
Human Chr11: ILK> LOC> TAF10< TPP1< DCHS1< MRP17>
XTR.chr2: ilk tpp1 GeneID:100491139 zscan2
Xla.chr2L: dynp1 rrp8.L mgc822989 tpp1 tif-if2 GeneID:108707608 zfp391
proteins used in DIOPT/EggNog homology group analysis
>XP_031753324.1 transient receptor potential cation channel subfamily M member 2 isoform X1 [Xenopus tropicalis] MGNTKSKSPVPDRIDGVQLHSTVGSPYRPGTADPKKKKKTAPKFIDGEKVDVLNSWVTRNIRKKECVAFI PPAPEAPGDRDTCGCGHTRRTHFAAQVSAPLEPGTVWDPHKHVREFPSDAHGDLTFTGTTRTWAKYVRAS NDTPPRSLFDLMTQQWDLRVPNLLISVTGGAKNFNISPRLKTEFSRGLVTAAQSTGAWIITGGSHAGVMK HVGEAVRDFSGGQHETEIVLIGIATWGIVHNRESLISEAGGAPAVYPMDEGSQGALCCLDNNHTHFILVD NGTYGKYGVEIPLRTKLEKFISEQTMENAGTAIKIPIVCVVLEGGPGTLDTIYNSMCNNTPCVIVEGSGR VADIIAQVANLSISQITISVVKEKLQNLFQDTFESFTEAQIIMWTKKIQDIVRMGSLLTILREDKTEEQG MDVAILQALLKASRSTDYSGQENWDHQLKLAVAWNRADIAESQIFTEDWMWKPSDLYPSLMVSLIDDKPS FLRLFLERGVSLSEFITWDMLTELYNNTEPSSLIHSKLERQAMLDESTEMNGGLKIQLHHVSHVLQELLG GLTESLYLDRRSHRTRTLPYINIKISGKVSSMRSECDSTVKLEHPVRDLLIWCIVQNRAELAEIIWCQSQ DCMVSALACSKMLKALSKEEDDTESMESMKVLANVYEERAAGVFSECYASDESRAEQLLIRVSSKWGKTT SLDLAQESQGQLFMSQSGVQMFLTKTWFGRLSVDNGLLAILLCMLLFPLIYTDLIMYRKESVAPRSSRGQ DKRSAARSSRARNCLWKFFDFFSAPIVKFYYNVVSYIGFLWLFAYVLMMDFQTYPSWTEYLLYVWVFSIL CEELRQLLYDPDRLGFVVKSMQYISEFWNQVDTLALSLFAVGLICRLASLNTVYLGRVFLSVDYMIFCIR LMNIFTVSKVLGPKIIMLRRMIMDLFFFLFLLAIWIVSFGVAKQAILTSNETRLDWIFRNVIYGPYLILF GQIPSEVDGLNFDPTKCSQSGTDPTLPKCVYNDGSGKTLFPEWLTILLLCIYLLMANILLLNLLIAMFSN TFGDVESHTDQIWKFYRFGLIKEYNERPVAPPPFILLSHLYFLLKYGLSKRSTLSHQAMRSVMDEAGESS LLSWELYMRDNYLHNQQLVDSQSQENVVKNTAQSVSAVLNLLNMRKDGEGQQLETRLILLEEEVLKSSEQ LQWIISALGEKGFTGRAQRLVHSSSQDSGDSATHGLDPSTERKSIYHVNSRTLQYPDSPVSRYPVPDEMV PWEVPFPGYEPPFYTAERGDRGAYDPHSEMSQTNRKYNAVDGALDLRSSCGTYAVQDGFPLNPMGRTGLR GVGSLRWFGPNHSLHLVITRWNTRANGSADKKLPRKMLEVLVVKEKKNELWALPGGTLSPGEEIPSKLQS ILSQTYGERFSELLRGGREVFRGYLDDPRNTDNSWIETLAVNIHLDTEETLSQFLQNLNQSSPEVSLRWQ ILDHKIPIYANEKEILQRTAEVHGTHY
>XP_041438825.1 transient receptor potential cation channel subfamily M member 2 [Xenopus laevis]
MGNTKSKSSVPDGIDGVQLHSNVNSPHRPGTADPKKKKKTAPKFIDGEKVDVLNSWVSQNIRKKECVAFI
PRVSEAPSDRDSCSCGHTRHTHFGDHKSSSVEPGTVWDPHKHVREFPSDAHGDLTFTGTTRTWAKYVRAS
NDTPPRLLFDLMTQQWDLSVPNLLISVTGGAKNFNISPRLKTEFSRGLVTAAQSTGAWIITGGSHAGVMK
HVGEAVRDFSGGQHESDIVLIGIATWGIVHNRELLISEAGGAPAVYQMDEGSQGSLCCLDNNHTHFILVD
NGTFGRYGVEIPLRAKLEKYISAQTMEKAGTAIKIPIVCVVLEGGPGTLDTIYNSMCNNTPCVIVEGSGR
VADIIAQVANLNISRITISLVKEKLQNLFQDTYESFTEAQIIMWTKKIQDIVRMGSLLTILREDKTEEQG
MDVAILQALLKASRSTDLSGQENWDHQLKLAVAWNRPDIAESQIFTEDWMWKPSDLYPSLMVSLIDDKPS
FLRLFLERGVSLSEFLTWDVLTELYNNTEPSSLIRSKLERQAMLDESTEINGPTIQLHHVSRVLQELLGG
RTEPLYPDVRSHRTRNLPHIKIKISGKVSSMRLASDCTLQLEHPVRDLLIWCIVQNRAELAEIIWCQSQD
CIVGALACSKILKALSKEEDDTESMENMKVLADVYEERAAGVFSECYESDESRAEQLLIRVSSIWGKTTS
LDLAQESQGQAFMSQGGVQMFLNKTWCGKLSVDNGLLAILLCMLLFPLIYTGLVMYRNKPLAPRSSRRPD
INGQMKSPVRSSQTRNCLKKFLHFFTAPIVKFYYNVVSYIGFLWLFAYVLMMDFQTSPSWREYLLYIWVF
SIFCEELRQLLYDPDRLGFVVKSAQYISEFWNQIDSTALVLFAVGLICRLASVDTVYLGRVFLSIDFMIF
CVRLLHIFTVSKVLGPKIIMLRRMVMDLFFFLFLLAIWIVSYGVAKQAILTSNEIRLNWIFRNIVYEPYL
TLFGQMPSDIDGLNFDPTKCSQDGTNPLLPKCVYNDGSGNPLFPEWLTIILTCIYLLMANILLLNLLIAM
FSNTFGDVESHTDQIWKFYRFGLIKEYNERPAAPPPFILLSHFYFLLKYGLSKRSTMSHKAMRSVIDEAG
ESSLLSWELYMRDNYVHNRQLLDAQSQENVVKNTAESVSAVLKMLSMEKGSDGQNMERRMFLLEDEVSKS
SQKLQWIISALREKGFTGKAQMFVHSNSQDLEEKASLGSDSLGDKKSIYHVNSRTLQYPNSNTTRYPVPD
EMVPWEVTFPGYDPPFLIADRDDRGAYDPHSEMSQTNRKYNGVDGALDFRSSCGTYLVHEGVPLNPMGRT
GLRGVGSLRWFGPNHSLHPVITRWNTLPNGSLDRKISRKKLEVLVVKQIDNELWALPGGTLSPGEDIPPK
LKSILNEKYVKKFSDLLRGGTEVFRGYLDDPRNTDNSWIETRAVNIHMDSDEKLSRFLQNVNDSSPGVSL
RWQILDHKIPIYADEKEILQRTAEVHGTHY