XB-FEAT-22066195: Difference between revisions
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=nomenclature changes= | =nomenclature changes= | ||
April 2021 | |||
this gene page has been repeatedly flagged for update in the monthly Entrez gene report, so I looked into the reason why a bit further. | |||
this | There are 2 ''ndnfl'' genes in ''Xenopus laevis'' and ''X tropicalis.'' These were thought to be a tandem duplications, and thus assigned ''ndnfl1.1'' and ''ndnfl1.2''., However the below synteny analysis shows that this is likely incorrect, they are NOT tademly duplicated, sitting on different chromosomes in ''X. laevis and X. tropicalis'': ''n2nfl1.1'' is on Chr3 while ''ndnfl2'' is on Chr7 | ||
Also the genes are likely NOT both true orthologs of human NDNF. Xenopus ndnfl1 '''has''' a conserved synteny pattern with tnip1, but ndnfl1.2 '''does not''' show a significant conserved gene pattern with human.n | |||
human: Chr4: PRDM5< SETP12< '''NDNF<''' NDNF-AS1> '''TNIP3<''' | |||
Xtr chr3 (v10.0) ''synpo> myoz3> dctn4< smim3< '''ndnfl1.1<''' gpx3> '''tnip1<''' anxa6< slc7a2.2< zp4< LOC105946789[lincRNA]> sqstm1< tbc1d9b<'' | |||
Xla.L chr3 (v9.2) ''synpo.L> myoz3.L> dctn4.L< PROVsmim3.L< '''ndnfl1.1.L<''' gpx3.L> '''tnip1.L<''' anxa6.L< slc7a2.2.L< zp4.L< LOC105946789[lincRNA]> sqstm1< tbc1d9b<'' | |||
Xla.L chr3 (v9.2) ''synpo.L> myoz3.L> dctn4.L< PROVsmim3.L< '''ndnfl1.1.L<''' gpx3.L> tnip1.L< anxa6.L< slc7a2.2.L< zp4.L< LOC105946789[lincRNA]> sqstm1< tbc1d9b<'' | |||
Xtr Chr7: ''pcbd1> sgpl1< .LOC733728> tbata> mttp.2> LOC116412463> '''LOC100488368<''' ccser2>'' | Xtr Chr7: ''pcbd1> sgpl1< .LOC733728> tbata> mttp.2> LOC116412463> '''LOC100488368<''' ccser2>'' | ||
Xla Chr7.L: ''pcbd1.L> sgpl1.L< XB5893022.L> tbata.L> LOC108695783 [prov:mttp]> LOC108695784 [prov:star] '''ndnfl2.L<''' ccser2.L>'' | Xla Chr7.L: ''pcbd1.L> sgpl1.L< XB5893022.L> tbata.L> LOC108695783 [prov:mttp]> LOC108695784 [prov:star] '''ndnfl2.L<''' ccser2.L>'' | ||
considering this, Xenbase curators (CJZ) propose that ''ndnfl1.1'' is the true ortholog of human NDNF and should be called ''ndnf'', while ''ndnfl2.L'' should retain the symbol ndnfl2, and Xtr LOC100488368/Entrez Gene: 100488368 (XBXT10g012299) can be added to the ndnfl2 gene page as the v10 gene model | |||
Revision as of 15:21, 19 April 2021
ndnfl1.1
This is the community wiki page for the gene ndnfl1.1 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
nomenclature changes
April 2021 this gene page has been repeatedly flagged for update in the monthly Entrez gene report, so I looked into the reason why a bit further.
There are 2 ndnfl genes in Xenopus laevis and X tropicalis. These were thought to be a tandem duplications, and thus assigned ndnfl1.1 and ndnfl1.2., However the below synteny analysis shows that this is likely incorrect, they are NOT tademly duplicated, sitting on different chromosomes in X. laevis and X. tropicalis: n2nfl1.1 is on Chr3 while ndnfl2 is on Chr7
Also the genes are likely NOT both true orthologs of human NDNF. Xenopus ndnfl1 has a conserved synteny pattern with tnip1, but ndnfl1.2 does not show a significant conserved gene pattern with human.n
human: Chr4: PRDM5< SETP12< NDNF< NDNF-AS1> TNIP3<
Xtr chr3 (v10.0) synpo> myoz3> dctn4< smim3< ndnfl1.1< gpx3> tnip1< anxa6< slc7a2.2< zp4< LOC105946789[lincRNA]> sqstm1< tbc1d9b<
Xla.L chr3 (v9.2) synpo.L> myoz3.L> dctn4.L< PROVsmim3.L< ndnfl1.1.L< gpx3.L> tnip1.L< anxa6.L< slc7a2.2.L< zp4.L< LOC105946789[lincRNA]> sqstm1< tbc1d9b<
Xtr Chr7: pcbd1> sgpl1< .LOC733728> tbata> mttp.2> LOC116412463> LOC100488368< ccser2> Xla Chr7.L: pcbd1.L> sgpl1.L< XB5893022.L> tbata.L> LOC108695783 [prov:mttp]> LOC108695784 [prov:star] ndnfl2.L< ccser2.L>
considering this, Xenbase curators (CJZ) propose that ndnfl1.1 is the true ortholog of human NDNF and should be called ndnf, while ndnfl2.L should retain the symbol ndnfl2, and Xtr LOC100488368/Entrez Gene: 100488368 (XBXT10g012299) can be added to the ndnfl2 gene page as the v10 gene model