XB-FEAT-6257460: Difference between revisions

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= ''trim26'' =  
= ''trpm2l'' =  
This is the community wiki page for the gene ''trim26'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
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=
Line 12: Line 12:
1MAY2023
1MAY2023


Synteny (below) does not support the orthology between ''Xenopus'' 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 this gene 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:IS THIS GENE THE ORTHOLOG OF TRPM2?
Q:ARE THESE GENES THE ORTHOLOGS OF TRPM2?
A: No, Xtrop Gene ID: 100124999 is identified by BCI as the true ortholog of TRPM2, although synteny is not conserved.  
 
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:  
XB Actions:  


1) removed the vertebrate orthologs for TRIM26 from this gene page
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>


2) renamed these genes ''trpm2l, transient receptor potential cation channel, subfamily M, member 2 like''


-------------------------------------------------


TPP1 (cf Xenopus)


Synteny as of April 29th, 2023
Human Chr11: ILK> LOC> TAF10< '''TPP1'''< DCHS1< MRP17>


Human:  TRIM 10  TRIM15 PAIP1P1   '''TRIM26'''  TRIM26BP  HCG17
XTR.chr2:  ilk   '''tpp1'''  GeneID:100491139  zscan2


XTR.chr2:  ilk  tpp1   ''''trim26''''  zscan2
Xla.chr2L:  dynp1   rrp8.L  mgc822989  '''tpp1''' tif-if2  GeneID:108707608   zfp391


Xla.chr2L:  dynp1  rrp8.L mgc822989  tpp1  tif-if2  ''''trim26''''  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


Human chr21: ICOSLG<  DNMT3L AIRE PFKL> CFAP410. '''TRPM2'''  LRRC3 TSPEAR  UGE2G2< SUMO3 PTTG1IP<  ITGB2< SLX9>


Xtrop.Chr9:  col5a2> col3a1<. gulp1< cfap410< '''trmp2>''''''Bold text''' pth2r> pikfyve< c9h2orf80>
>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 08:13, 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

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