XB-FEAT-967616
cetn2
This is the community wiki page for the gene cetn2 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
nomenclature changes
24JAN2023
Nomenclature changed following analayis by David Webb as NCBI RefSeq.
Basic issue: CETN1 is only in placental mammals and CETN4 is a pseudogene in humans.
XB-GENEPAGE-967616 (Xtr GeneID: 549903) was renamed, changes from "CETN1" to "CETN2" - see details below.
Details of the CETN1, CETN2, and CETN4 analysis and orthology below:
The CETN1 gene of human (GeneID: 1068, HGNC: 1866) and all placental mammals likely arose as a retrotransposition event because only placentals have this single-coding-exon gene between COLEC12 and CLUL1. The gene is absent in other animals despite the gene synteny being very stable.
Thus, chicken and Xenopus should not have genes named "CETN1". The "CETN1" genes of chicken (GeneID: 422303, CGNC:51692) and X. tropicalis (GeneID: 549903, XB-GENE-967617) are actually the orthologs of human CETN2 (GeneID:1069, HGNC: 1867) based on highly conserved synteny of CETN2 always being adjacent to ZNF185 and NSDHL throughout gnathostomes.
Furthermore, chicken and other archosaurs have tandemly duplicated "CETN1" (ie CETN2) and thus chicken "CETN1L" (GeneID:422304, CGNC: 66428) should actually be named CETN2L. I've confirmed with a NJ tree of nt alignments that "CETN1L" (GeneID:422304) is a duplication of the chicken CETN2 gene.
In addition, chicken GeneID: 422668 is misnamed "CETN2" (CGNC:66439) but is actually the ortholog of CETN4 (eg, mouse GeneID:207175) based on highly conserved synteny of this gene between BBS12 and ADAD1 throughout gnathostomes. In human and higher-(non-prosimian) primates CETN4 is a pseudogene (human CETN4P GeneID: 729338, HGNC:35450).
A NJ tree of RefSeq nt accessions (not shown) supports these conclusions.
Gg
ZNF185< NSDHL< "CETN1"> CETN1L> GATD3AL2< LOC>
emu
ZNF185< NSDHL< cetn2> cetnL> gatd3al2< LOC> acod1> GLOD5<
gharial
ZNF185< NSDHL< cetn2> cetnL> gatd3al2< LOC>
Chelonia mydas
ZNF185< NSDHL< cetn2> aire< LOC< SCLY> KLHL30>
Chrysemys picta, Trachemys scripta
ZNF185< NSDHL< cetn2> AIRE< LOC< SCLY> ESPNL> KLHL30>
lizards
ZNF185< NSDHL< cetn2> DACH2< CHM> POF1B>
Hs
ZNF185< NSDHL< CETN2> MAGEA6> CSAG3< MAGEA2> MAGEA12< CSAG1>
Bufo
ZNF185< NSDHL< CETN2> OR> OR> P2RY10< LPAR4<
Xtr
ZNF185< NSDHL< "CETN1"> P2RY10< LPAR4<
Coelacanth
ZNF185< NSDHL< CETN2>//
Protopterus lungfish
OGT<…LOC< NSDHL< CETN2> PRPS1> HDAC8>
Osteichthyes
ZNF185< NSDHL< CETN2> GCNA< OGT<
Thorny skate
slain-like< NSDHL< cetn2> ENOX2< LOC>
Gg
SPATA5< NUDT6> FGF2< BBS12< "CETN2"> IL21> IL2> adad1< KIAA1109<
emu, Calypte anna
SPATA5< NUDT6> FGF2< BBS12< cetn4> IL21> ADAD1< kiaa1109<
Crocidilians, turtles, lizards
SPATA5< NUDT6> FGF2< BBS12< cetn4> ADAD1< KIAA1109<
Human, apes, NWmonkeys, OWmonkeys
SPATA5< NUDT6> FGF2< BBS12< CETN4p> IL21> IL2> ADAD1< KIAA1109<
Non-anthropoid-primate placental mammals, tree shrew, lemurs,
SPATA5< NUDT6> FGF2< BBS12< CETN4> IL21> IL2> ADAD1< KIAA1109<
Ampibia
SPATA5< NUDT6> FGF2< BBS12< CETN4> IL21> IL2> ADAD1< KIAA1109<
Coelacanth
BBS12< CETN4>
Protopterus lungfish
SPATA5< NUDT6> FGF2< BBS12< CETN4> FAT4> LOC<
Osteichthyes, chondrichthyes
SPATA5< NUDT6> FGF2< BBS12< CETN4> ADAD1< KIAA1109<
Placental mammals
USP14> THOC1< COLEC12< CETN1> CLUL1> TYMS> ENOSF1< YES1<
Non-placental sarcopterygians
USP14> THOC1< COLEC12< /// CLUL1> TYMS> ENOSF1< YES1<
Non-sarcopterygian gnathostomes
COLEC12< /// CLUL1> TYMS> ENOSF1< YES1<