XB-FEAT-6467132: Difference between revisions
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='' | =''ces2.6''= | ||
This is the community wiki page for the gene '' | This is the community wiki page for the gene ''ces2.6'' 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= | ||
28 December 2018 | |||
This gene symbol was changed from ''ces5a to ces3.5''. Evidence includes the Ensembl CES3 gene tree as well as partial synteny with human CES3 locus. | |||
28JULY23 | |||
human CES5A does not have any amphibian orthologs recognized by NCBI, so CES5A (Gene ID: 221223 ) and mouse Ces5a (geneId: 67935) have been removed from the ‘’ces3.5’’ gene page. Human and mouse/rat CES3 genes have been added as the more accurate orthologs. | |||
18SEPT | |||
The ''Xenopus ces'' genes appear to be tandem duplicates, that fall within a single clade which is most closely related to the Human CES2 genes, not the CES3 genes as previously thought. 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 genes on the ''X. laevis S '' subgenome. | |||
Therefore ''Xenopus tropicalis'' gene symbol and gene name changed from ''ces3.5, liver carboxylesterase 2-like'' to ''ces2.6, carboxylesterase 2 gene 6'' following phylogenetic and synteny analysis and by applying Xenopus nomenclature rules to this gene expansion on chromosome 4. | |||
Note that protein name for the ''X.tropicalis'' GeneID: 100493652 is ''carboxylesterase 5A''. We removed the synonym CES5A, as this is misleading, ie: these genes are not ortholgous as CES5A is mammal specific gene - no frog bird or or reptile genes should be called CES5A. See orthology and synteny analysis below. | |||
=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 with across species, with new '''ces2''' gene assignment in bold. Note that Human has 3 CES genes, 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 | |||
[[File:Screenshot 2023-09-18 at 3.06.15 PM.png|thumb]] | |||
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'' ''ces2''gene pages. | |||
Latest revision as of 07:22, 19 September 2023
ces2.6
This is the community wiki page for the gene ces2.6 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
nomenclature changes
28 December 2018
This gene symbol was changed from ces5a to ces3.5. Evidence includes the Ensembl CES3 gene tree as well as partial synteny with human CES3 locus.
28JULY23
human CES5A does not have any amphibian orthologs recognized by NCBI, so CES5A (Gene ID: 221223 ) and mouse Ces5a (geneId: 67935) have been removed from the ‘’ces3.5’’ gene page. Human and mouse/rat CES3 genes have been added as the more accurate orthologs.
18SEPT
The Xenopus ces genes appear to be tandem duplicates, that fall within a single clade which is most closely related to the Human CES2 genes, not the CES3 genes as previously thought. 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 genes on the X. laevis S subgenome.
Therefore Xenopus tropicalis gene symbol and gene name changed from ces3.5, liver carboxylesterase 2-like to ces2.6, carboxylesterase 2 gene 6 following phylogenetic and synteny analysis and by applying Xenopus nomenclature rules to this gene expansion on chromosome 4.
Note that protein name for the X.tropicalis GeneID: 100493652 is carboxylesterase 5A. We removed the synonym CES5A, as this is misleading, ie: these genes are not ortholgous as CES5A is mammal specific gene - no frog bird or or reptile genes should be called CES5A. See orthology and synteny analysis below.
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 with across species, with new ces2 gene assignment in bold. Note that Human has 3 CES genes, 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.