XB-FEAT-22066195

ndnf

This is the community wiki page for the gene ndnf 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. ( 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 2 (XB-GENEPAGE-22066209) symbol:ndnf2on chromosome 7 (formerly called ndnfl2)

There are several points to consider to get these genes named correctly 1) the duplication of ndnf1, ( thus gene 1 (.1) and gene 2 (.2))

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, 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.

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

Looking at the genes adjacent to ndnf2 in Xenopus, but present in human, I can't find any conserved patterns/elements.

Human: chr10 RGR> RPL12P29> CCSER2>

Human Chr4: TRMT10A< MTTP> C4ORF54< DAPP1> etc

Conclusion:

• the Xenopus ndnf2 gene should 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 new serial number, and it woont cascade anywhere.

• As the gene is very much like the ndnf gene yet are non-syntenic, we proposed 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, and Xtr LOC100488368/Entrez Gene: 100488368 (XBXT10g012299) can be added to the ndnfl gene page as the v10 gene model.

4) Xla LOC108695783 should be assigned to mttp gene page based on synteny.

31JAN2023

Human symbol has changed for genepage ID: 22066195 From ndnfl1 to NDNF

Xenopus gene name Change name from ndnfl1 to ndnf