XB-FEAT-22066209

ndnfl2

This is the community wiki page for the gene ndnfl2 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

nomenclature changes

note from XB curators 02.10.2021

This is a little known gene, but may be flagged repeatedly in Entrez gene reports. Looking at close neighbourhood synteny does not show anything when compared to human. Literally nothing- no genes in X laevis v9.2 are in common pattern on Chr7.L cf human ( see ccer2)

More clarification may come in the v10 of X laevis genome.

We will need to push this to NCBIs ref seq group to compare with other vertebrates.

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. ( in jan2023, we removed the 'like' from the name, and I edited the below passges, removing the 'l' from symbols and 'like' from names to [hopefully] reduce confusion)

There are supposedly 3 ndnf genes in Xenopus according to v9 genomes:

- neuron-derived neurotrophic factor 1, gene 1 (XB-GENEPAGE-22066195) symbol:ndnf1.1 on chromosome 3 (formerly called ndnfl1.1)

- neuron-derived neurotrophic factor 1, gene 2 (XB-GENEPAGE-22066202) symbol:ndnf1.2on chromosome 3 (formerly called ndnfl1.2)

- neuron-derived neurotrophic factor like (XB-GENEPAGE-22066209) symbol:ndnflon chromosome 7 (formerly called ndnf2)

There are several points to consider to get these genes named correctly 1) the duplication of 'ndnf1'

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

Addressing points below: 1) In the Xtrop genome annotation version 9.1, ndnf1.1 and ndnf1.2 were thought to be a tandem duplications, and thus were 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< ndnf1.1< gpx3> tnip1< anxa6< slc7a2.2< zp4< LOC105946789[lincRNA]> sqstm1< tbc1d9b<

Xla.L chr3 (v9.2) synpo.L> myoz3.L> dctn4.L< PROVsmim3.L< ndnf1.1.L< gpx3.L> tnip1.L< anxa6.L< slc7a2.2.L< zp4.L< LOC105946789[a lncRNA]> sqstm1< tbc1d9b<

2) the ndnf1 genes are likely TRUE orthologs of human NDNF as in Xenopus, ndnf1 has a conserved [albeit loose] synteny pattern being adjacent to tnip1.( see above synteny patterns)

3) human does not have a named, 2nd, NDNF gene (ie no human NDNF2)

Looking at the genes adjacent to ndnf2 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

Conclusions:

• the Xenopus ndnf2 gene shoudl be called a like gene, not '2' suffixes- as RefSEq wouldn't accpect a 2nd new gene named just in Xenopus, ie they won't set a precedent of naming this gene with a anew serial number. As the gene is very much like the ndnf gene yet are non-syntenic, we propose calling it ndnfl.

Xla Chr7.L: pcbd1.L> sgpl1.L< XB5893022.L> tbata.L> LOC108695783 [prov:mttp]> LOC108695784 [prov:star] ndnfl.L< ccser2.L>

Xtr Chr7: pcbd1> sgpl1< .LOC733728> tbata> mttp.2> LOC116412463> LOC100488368[nfndl]< ccser2>

Actions needed:

1)Xenbase curator propose that ndnf1.1 is the true ortholog of human NDNF and should be called ndnf [updated 31JAN2023 to ndnf]

2) the gene page for ndnfl1.2 could taken down, or ammended.[2FEB2023 put not in current assembly on XB-GENEPAGE-22066202]

3) ndnf2.L should change to the symbol ndnfl, [done]

4) Xtr LOC100488368/Entrez Gene: 100488368 (XBXT10g012299) can be added to the ndnfl gene page as the v10 gene model.[done]

31JAN2023

Xenopus gene symbol changed from ndnf2 to ndnfl