XB-FEAT-5765837

ces2.4

This is the community wiki page for the gene ces2.4 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

nomenclature changes

December 28, 2018 this gene name/symbol was changed from ces2 to ces3.4. Evidence includes the Ensembl ces3 gene tree as well as partial synteny with human CES3 locus.

18SEPT2023

Xenopus gene name and gene symbol changes from ces3.4, carboxylesterase 3, gene 4 to ces2.4, carboxylesterase 2, gene 4 following gene family review.

The Xenopus ces genes appear to be tandem duplicates, that fall within a single clade which is most closely relates to the Human CES2 genes, not the CES3 genes as previously thought. The X.laevis L gene/protein was previously called ces5a-like and cocaine esterase-like.

Applying Xenopus nomenclature, we have renamed all CES2 orthologs , with X. tropicalis ces2.1-ces2.8, from left to right, and X. laevis' genes ces2.1.L-ces2.5.L from left to right. There are no ces genes on the X. laevis S subgenome.

synteny and orthology

18SEPT2023=

There are 5 x ces genes in X. laevis on Chr4L and 8 x ces# genes in X. tropicalis on chromosome 4, flanked by wtip and uba2 downstream, and ankar-like, rrad, and cdh16 upstream. There are no ces2 paralogs in the v10 annotation X. laevis S sub genome

Here the order of genes are compared within and across species, with new ces2 gene assignment in bold. Note that Human has 3x CES genes, on Chr6, all likely a result of a duplication event, and the goal was to determine which of these genes is the closest ortholog to the frog genes expansion.

Xtrop chr4: wtip< uba2< (GeneID: 100144981)ces3.1>ces2.1 LOC100493994(ces2-like)>ces2.2 (GeneID:394897)ces5A> ces2.3 (GeneID:779633)ces3.4>ces2.4 LOC116410405>ces2.5 (GeneID:100493652)ces3.5>ces2.6 LOC100493819>ces2.7 (GeneID:100494149)ces3.7>ces2.8 LOC105945786(ankar-like)< rrad> cdh16>

Xlaevis chr4L: wtip.L< uba2.L< LOC108714107(ces5a)>ces2.1.L (GeneID:100381172)ces3.4.L>ces2.2 LOC108713509>ces2.3 LOC108714105(ces5a-like)>ces2.4 LOC108713647(cesE2)>ces2.5 LOC121403150(ankar-like) rrad.L

X.laevis chr4S: wtip.S< uba2.S> rrad.S> pdp2.S ca7.S cyba.S

H.sapiens Chr6: B3GNT9 PHAF1 CBFB RN7SL543P CES4A CES3 LOC107984881(ncRNA) CES2 CIAO2B RRAD CDH16

H.sapiens Chr6: LOC107984815(ncRNA) LOC105375100)ncRNA) LOC124903694(ncRNA) LOC107986539(ncRNA) NPM1P36 GeneID:221223; CES5A CES1 CES1P1 BMP5 CES1P2 LOC105371280

protein alignment and phylogenetic analysis

18SEPT2023

An alignment and cladogram of all isoforms of the Xenopus ces# proteins was run against all isoforms of the 3 Human CES genes (CES2 CES3 and CES4A, which are all adjacent to each other on CHR6). The results strongly support the hypothesis that the Xenopus clade most closely related to the human CES2 gene, not CES3 (or CES4A) as previously thought.

All Xenopus genes cluster with each other, and not any of the human genes.

proteins accession used in this analysis: NP_001120019.1 XP_004913616.1 NP_001265277.1 NP_001072187.1 XP_031756663.1 XP_031756661.1 XP_002935836.3 XP_002943465.3 XP_018113499.1 XP_018113497.1 XP_018112562.1 XP_041446147.1 XP_041446153.1 NP_001352334.1 NP_001172105.1 NP_001177130.1 XP_031756662.1 XP_004913614.2 XP_041446148.1 NP_001352335.1 NP_001172106.1 NP_001177131.1 XP_031756660.1 XP_041446149.1 NP_001352336.1 NP_079198.2 NP_001305435.1

Furthermore, note that human CES5A does not have any amphibian orthologs recognized by NCBI, and it does not share a conserved syntenic position(s) with Xenopus. Furthermore EBI's EggNogg gene/protein family/homology tree for CES5A indictates that CES5A is a mammal specific gene, thus frog genes should NOT be called ces5A , although several were annotated as ces5a in the v10 genome annotations.

Human CES5A (Gene ID: 221223 ) and mouse Ces5a (geneId: 67935) have been removed from all of these Xenopus ces2gene pages.