XB-FEAT-876556

neff1

This is the community wiki page for the gene neff1 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

background to nomenclature changes

05May2023

NCBI refSeq and HGNC communicated the following....

...there seems to be some confusion in the Xenbase "nif" record XB-GENEPAGE-876556: there is an unrelated gene that has also been published as "XNIF" (PMID 15294863/AY280863) which from BLATing the sequence maps to chr 6 and appears to be ctdspl, and so rather confusingly the CTDSPL synonym is listed in the real "nif" gene record. And PMID 2307698 which talks about the unrelated "NIF-1" and "NIF-2" has crept into the "nif" record and I think it should be removed.

Overall, this confusion from the various uses of 'nif' - added to the fact that "NIF" is an alias for several mammalian genes - makes me think "nif" is not an ideal symbol. It seems only one group (BG Szaro) have published this Xenopus gene as NIF/XNIF/nif.

After some discussion , it was decided changes for the "nif" [XB-GENEPAGE-876556] genes at Xenbase and Zfin as follows:

SYMBOL: NEFF1 (found in Xenopus) NAME: neuronal intermediate filament family member 1 ALIAS: nif

and "NEFLL" genes: SYMBOL: NEFF2 (LOST IN FROGS) NAME: neuronal intermediate filament family member 2 ALIAS:

Xenbase actions: 1) removed 2 synonyms (Xnif and CTDSPL) from the "nif " gene page [XB-GENEPAGE-876556]

2) updated nomenclature to neff1, neuronal intermediate filament family member 1, with synonyms: nif

synteny in vertebrates

NEFL & NEFM - no loss

synteny conserved back to chondrichtyes as NEFL> NEFM<

tetrapods share DOCK5< NEFL> NEFM< ADAM#>...STC1>

NEFH- no loss synteny conserved back to chondricthyes, generally, as

AP1B1< NEFH> THOC5< NIPSNAP1<

NEFLL- lost in mammals and frogs(now called NEFF2)

Podarcis shows ancestral state: LBX2< PCGF1< TLX2> nefll> il12b-like< DQX1< insyn2b< bnip3L< AUP1< HTRA2>

Human shows mammalian state: LBX2< PCGF1< TLX2> DQX1< AUP1< HTRA2>

INA- no loss

synteny generally conserved back to chondrichthyes as NT5C2< INA> PCGF6< TAF5>

NIF - lost in birds, caecilians, and mammals. ( now neff1) '

synteny in tetrapods is generally MXD1> NIF> C2orf42<

synteny in lungfish, gar, D. rerio is MXD1> NIF>