XB-FEAT-6467124: Difference between revisions
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= | =''ces2.8''= | ||
This is the community wiki page for the gene '' | This is the community wiki page for the gene ''ces2.8'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. | ||
=nomenclature changes= | |||
18SEPT2023 | |||
''Xenopus'' gene symbol and gene name changed from ''ces3.7, carboxylesterase 3, gene 7'' to ''ces2.8, carboxylesterase 2, gene 8'' following phylogenetic analysis, synteny analysis and by applying ''Xenopus'' nomenclature rules to this gene expansion on chromosome 4. | |||
=synteny and orthology= | |||
18SEPT2023= | |||
There are 5 ''ces'' genes in ''X. laevis'' and 8 ''ces#'' genes in ''X. tropicalis'' on chromosome 4/4L, 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 anayslis= | |||
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. | |||
=nomenclature changes= | =nomenclature changes= | ||
On December 28, 2018 this gene was changed from ces1 to ces3.7. Evidence includes belonging to the ces3 gene tree in Ensembl as well as partial synteny to human ces3 gene. | On December 28, 2018 this gene was changed from ces1 to ces3.7. Evidence includes belonging to the ces3 gene tree in Ensembl as well as partial synteny to human ces3 gene. | ||
Revision as of 14:01, 18 September 2023
ces2.8
This is the community wiki page for the gene ces2.8 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
nomenclature changes
18SEPT2023
Xenopus gene symbol and gene name changed from ces3.7, carboxylesterase 3, gene 7 to ces2.8, carboxylesterase 2, gene 8 following phylogenetic analysis, synteny analysis and by applying Xenopus nomenclature rules to this gene expansion on chromosome 4.
synteny and orthology
18SEPT2023=
There are 5 ces genes in X. laevis and 8 ces# genes in X. tropicalis on chromosome 4/4L, 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 anayslis
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.
nomenclature changes
On December 28, 2018 this gene was changed from ces1 to ces3.7. Evidence includes belonging to the ces3 gene tree in Ensembl as well as partial synteny to human ces3 gene.