XB-FEAT-1221158

ift70

This is the community wiki page for the gene ift70 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase

nomenclature changes

27FEB2023

THE HGNC, after a request from some of our specialist advisors and a consultation with authors publishing on these genes , have updated the nomenclature of three flagellar transport genes in human as follows: from TTCP26 , tetratricopeptide repeat domain 26 to IFT56, intraflagellar transport 56. This is now more functionally informative and in line with their Chlamydomonas orthologs.

Xenopus gene names follow that of human, so the Xenopus gene name has also changed from ttcp26 , tetratricopeptide repeat domain 26 to ift56, intraflagellar transport 56.

Note the 3 Human genes in this group are now have the following synonyms, although IFT70B does not seem to have an ortholog in Xenopus:

GENE SYMBOL: IFT56
GENE NAME: intraflagellar transport 56
SYNONYMS: TTC26, FLJ12571, dyf-13, DYF13

GENE SYMBOL: IFT70A
GENE NAME: intraflagellar transport 70A
SYNONYMS: TTC30A, FLJ13946, FAP259, CFAP259

GENE SYMBOL: IFT70B
GENE NAME: intraflagellar transport 70B
SYNONYMS: TTC30B, FLJ30990, fleer

orthology & synteny

from David Web at NCBi ref-Seq:

• TTC30 genes of mammals appear to be a single-exon retrotransposed copy of the ancestral multi-exon TTC30 gene. Plus, the location of the mammalian retrotransposed gene differs from the ancestral gene. The retrotransposition, and loss of the ancestral gene, possibly happened in amniotes and then it got duplicated once in placental mammals to make TTC30a/b and duplicated again somewhere in rodents.

• confirmed, by synteny and BLASTp, that the ancestral gnathostome multi-exon TTC30 gene was (likely) retrotransposed in amniotes to a new location as a single-exon gene. See the attached word doc TTC30.docx for the synteny evolution with two tandem TTC30 genes in placental mammals and three tandem TTC30 genes in most rodents. A minimum evolution tree of aligned proteins confirms that non-placental gnathostomes have just one TTC30 encoding gene, placentals have two and most rodents three TTC30 genes (tree not shown).

• In mammals there's a notable absence of gene annotation in the region where the amphibian TTC30 gene resides between TMEM108< and NPHP3>but tBLASTn and other alignment attempts failed to find any relict of the TTC30 gene in amniotes (nor could I find a relict of TTC30 near GSG1L or C16orf89 in amniotes).

• So, I suggest the single gene in fish, amphibians, and reptiles/birds be called simply IFT70

• IFT70A and IFT70B should be used only for placental mammals.