XB-FEAT-22066195: Difference between revisions
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1) the duplication of ndnfl1, 2) whether or not they are orthologs of the human NDNF gene and 3) if all the gene models for Xenopus are on the correct/appropriate gene pages on Xenbase | 1) the duplication of ndnfl1, 2) whether or not they are orthologs of the human NDNF gene and 3) if all the gene models for Xenopus are on the correct/appropriate gene pages on Xenbase | ||
1) In the Xtrop genome annotation version 9.1, ndnfl1.1 and ndnfl1.2 were thought to be a tandem duplications, and thus assigned '' | 1) In the Xtrop genome annotation version 9.1, ndnfl1.1 and ndnfl1.2 were thought to be a tandem duplications, and thus assigned ''.1'' and ''.2'' suffixes. However the below synteny analysis based on Xtrop genome v10.0 shows that this is likely incorrect, as here is no second .2 model. | ||
human: Chr4: PRDM5< SETP12< '''NDNF<''' NDNF-AS1> '''TNIP3<''' | human: Chr4: PRDM5< SETP12< '''NDNF<''' NDNF-AS1> '''TNIP3<''' | ||
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3) human does not have a named, 2nd, NDNF gene ( ie NDNF2) | 3) human does not have a named, 2nd, NDNF gene ( ie NDNF2) | ||
Looking at the genes adjacent to ndnfl2 in Xenopus, but in human, I can't find any conserved patterns/elements. | Looking at the genes adjacent to ndnfl2 in Xenopus, but in human, I can't find any conserved patterns/elements. | ||
Human: chr10 RGR> RPL12P29> '''CCSER2'''> | Human: chr10 RGR> RPL12P29> '''CCSER2'''> | ||
Human Chr4: TRMT10A< '''MTTP'''> C4ORF54< DAPP1> etc | Human Chr4: TRMT10A< '''MTTP'''> C4ORF54< DAPP1> etc | ||
therefore the Xenopus genes can keep both the 'like' and '2' suffixes- as they are like the ndnf gene yet are non-syntenic. | therefore the Xenopus genes can keep both the 'like' and '2' suffixes- as they are like the ndnf gene yet are non-syntenic. | ||
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>'' | ||
Xtr Chr7: ''pcbd1> sgpl1< .LOC733728> tbata> mttp.2> LOC116412463> '''LOC100488368<''' ccser2>'' | Xtr Chr7: ''pcbd1> sgpl1< .LOC733728> tbata> mttp.2> LOC116412463> '''LOC100488368<''' ccser2>'' | ||
Actions needed: | Actions needed: | ||
1)Xenbase curator propose that ''ndnfl1.1'' is the true ortholog of human NDNF and should be called ''ndnf'' | 1)Xenbase curator propose that ''ndnfl1.1'' is the true ortholog of human NDNF and should be called ''ndnf'' | ||
2) the gene page for ndnfl1.2 be taken down. | 2) the gene page for ndnfl1.2 be taken down. | ||
3) ''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 | 3) ''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 | ||
4) Xla LOC108695783 should be assigned to mttp gene page based on synteny. | 4) Xla LOC108695783 should be assigned to mttp gene page based on synteny. | ||
Revision as of 12:51, 22 November 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 3 ndnfl genes in Xenopus:
- neuron-derived neurotrophic factor like 1, gene 1 (XB-GENEPAGE-22066195) symbol:ndnfl1.1
- neuron-derived neurotrophic factor like 1, gene 2 (XB-GENEPAGE-22066202) symbol:ndnfl1.2
- neuron-derived neurotrophic factor like 2 (XB-GENEPAGE-22066209) symbol:ndnfl2
There are several points to consider to get these genes named correctly 1) the duplication of ndnfl1, 2) whether or not they are orthologs of the human NDNF gene and 3) if all the gene models for Xenopus are on the correct/appropriate gene pages on Xenbase
1) In the Xtrop genome annotation version 9.1, ndnfl1.1 and ndnfl1.2 were thought to be a tandem duplications, and thus assigned .1 and .2 suffixes. However the below synteny analysis based on Xtrop genome v10.0 shows that this is likely incorrect, as here is no second .2 model.
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[a lncRNA]> sqstm1< tbc1d9b<
2) the ndnfl1 genes are likely both TRUE orthologs of human NDNF as in Xenopus, ndnfl1 has a conserved [albeit loose] synteny pattern being adjacent to tnip1.
3) human does not have a named, 2nd, NDNF gene ( ie NDNF2)
Looking at the genes adjacent to ndnfl2 in Xenopus, but in human, I can't find any conserved patterns/elements.
Human: chr10 RGR> RPL12P29> CCSER2>
Human Chr4: TRMT10A< MTTP> C4ORF54< DAPP1> etc
therefore the Xenopus genes can keep both the 'like' and '2' suffixes- as they are like the ndnf gene yet are non-syntenic.
Xla Chr7.L: pcbd1.L> sgpl1.L< XB5893022.L> tbata.L> LOC108695783 [prov:mttp]> LOC108695784 [prov:star] ndnfl2.L< ccser2.L>
Xtr Chr7: pcbd1> sgpl1< .LOC733728> tbata> mttp.2> LOC116412463> LOC100488368< ccser2>
Actions needed:
1)Xenbase curator propose that ndnfl1.1 is the true ortholog of human NDNF and should be called ndnf
2) the gene page for ndnfl1.2 be taken down.
3) 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
4) Xla LOC108695783 should be assigned to mttp gene page based on synteny.