XB-FEAT-1221158: Difference between revisions
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=ift70a= | =''ift70a''= | ||
This is the community wiki page for the gene ''ift70a'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | This is the community wiki page for the gene ''ift70a'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. | ||
=nomenclature changes= | =nomenclature changes= | ||
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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. | 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 '' | ''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 genes in this group are now have the following synonyms: | 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 SYMBOL: IFT56 | ||
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GENE NAME: intraflagellar transport 70B | GENE NAME: intraflagellar transport 70B | ||
SYNONYMS: TTC30B, FLJ30990, fleer | SYNONYMS: TTC30B, FLJ30990, fleer | ||
05JUNE 2023 | |||
‘’Xenopus’’ symbol has changed for XB-GENEPAGE-1221158. From ttc30a to ift70a | |||
Human symbol has changed for Entrez Gene: 92104. From TTC30A to IFT70A | |||
Human name has changed for Entrez Gene: 92104. From tetratricopeptide repeat domain 30A to intraflagellar transport 70A | |||
=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> |
Latest revision as of 09:20, 7 June 2023
ift70a
This is the community wiki page for the gene ift70a 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
05JUNE 2023
‘’Xenopus’’ symbol has changed for XB-GENEPAGE-1221158. From ttc30a to ift70a
Human symbol has changed for Entrez Gene: 92104. From TTC30A to IFT70A
Human name has changed for Entrez Gene: 92104. From tetratricopeptide repeat domain 30A to intraflagellar transport 70A
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>