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<