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/IFT70 genes of mammals appear to be a single-exon retrotransposed copy of the ancestral multi-exon TTC30/IFT70 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 [IFT70A/B] and duplicated again somewhere in rodents.

• confirmed, by synteny and BLASTp, that the ancestral gnathostome multi-exon TTC30/IFT70 gene was (likely) retrotransposed in amniotes to a new location as a single-exon gene.

• See the below 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/IFT70 encoding gene, placentals have two and most rodents three TTC30/IFT70 genes (tree not shown).

• In mammals there's a notable absence of gene annotation in the region where the amphibian TTC30/IFT70 gene resides between TMEM108< and NPHP3>but tBLASTn and other alignment attempts failed to find any relict of the TTC30/IFT70 gene in amniotes (nor could I find a relict of TTC30/IFT70 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.

Synteny patterns:

In ancestral gnathostomes the multi-exon TTC30! resided between GSG1L and C16orf89

skate Gene ID: 116985866 TTC30/FLR

KATNIP< gsg1L< TTC30!< C16orf89< ALG1> EEF2KMT<

great white shark muc>> LOC< qrich2<< TTC30!< C16orf89< ALG1> EEF2KMT<

D.rerio Gene ID: 797829 NP_001098119.2

SEPT12> FBXL16< GSG1L< LOC< TTC30!< C16orf89< ALG1> EEF2KMT<

reedfish GeneID: 114661144 XP_028670140.1

sept12> fbxl16< GSG1L< LOC< TTC30!< C16orf89< alg1> tfap4> gde1< ccp110>

gar GeneID: 102687908 XP_015215915.1

SEPT12> FBXL16< gsg1L< TTC30!< C16orf89< ALG1> EEF2KMT< PIGQ>

lungfish GeneID:122816772 XP_043945724.1

cyp2#<<<<<< gsg1L< TTC30!< c16orf89< eef2kmt> ALG1< PERCC1<

Coelacanth Gene ID: 102356032 XP_006000164.1

[assembly gap] TTC30!< ALG1> EEF2KMT< enpp7<

But then in amphibians the multi-exon TTC30! got moved between TMEM108 and NPHP3 and lost at GSG1L< C16orf89<

Amphibians Xtr NM_001102833.1:NP_001096303.1 XB-GENE-1221159

CDV3< BFSP2< TMEM108< TTC30!< NPHP3> UBA5< ACAD11>

katnip> GSG1L< C16orf89< ALG1> EEF2KMT< enpp7<

and then in amniotes it got retrotransposed as a single-exon gene elsewhere (see TTC30 below)

Saurians (most)

CDV3< BFSP2< TMEM108< NPHP3> UBA5< ACAD11>

katnip> GSG1L< IL20RB<

SEC14L5> NAGPA< C16orf89< ALG1> EEF2KMT<

mammals (marsupials & monotemes go crazy near C16orf89)

CDV3< BFSP2< TMEM108< NPHP3> UBA5< ACAD11> katnip> GSG1L< XPO6< SBK1> SEC14L5> NAGPA< C16orf89< ALG1> EEF2KMT<

non-tetrapods:

D.rerio

VPS41> CDV3< TMEM108< TOPBP1< UBA5> NPHP3< gpr17< etl4<

Reedfish

cdv3< bfsp2< tmem108< gpr17> serpinb1a< serpinb1a<

KDSR< VPS4B< NPHP3> UBA5> ACAD11> acad11>

Gar

CDV3< BFSP2< TMEM108< cyb5a< C18orf63> FAM69C<

RPP40> CDYL< gpr17> NPHP3> UBA5< acad11> ACAD11>

Lungfish

CDV3< BFSP2< TMEM108< LOC><><

CCNA2< BBS7< TRPC3< NPHP3> UBA5< ACAD11>

Coelacanth TMEM108< [many assembly gaps] NPHP3> UBA5< ACAD11>

The single exon TTC30 retrotransposon was inserted between AGPS and PDE11A in amniotes

saurians (*cyct is often not annotated but may actually be there)

HNRNPA3> NFE2L2< AGPS> TTC30B< PDE11A< cyct*< RBM45>

monotremes & marsupials

HNRNPA3> NFE2L2< AGPS> TTC30B< PDE11A< RBM45>

non-rodent placental mammals

HNRNPA3> NFE2L2< AGPS> TTC30B< TTC30A< PDE11A< RBM45>

Mm, rat, rodents

HNRNPA3> NFE2L2< AGPS> TTC30B< TTC30A2< TTC30A1< PDE11A< RBM45>

most amphibians

HNRNPA3> NFE2L2< AGPS> PDE11A< cyct< RBM45>

Xenopus

HNRNPA3> NFE2L2< AGPS> PDE11A< cyct< ITLN2>

coelacanth

HNRNPA3> NFE2L2< AGPS> PDE11A<//

lungfish

AGPS> PDE11A<//

gar, reedfish, bichir

HNRNPA3> NFE2L2< AGPS> PDE11A< cyct< RBM45>

skate

HNRNPA3> NFE2L2< AGPS> PDE11A< cyct< RBM45>