XB-FEAT-488120: Difference between revisions
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1) dtex3-like, deltex E3 ubiquitin ligase 3-like is on Chromsome 8 in Xenopus. | 1) dtex3-like, deltex E3 ubiquitin ligase 3-like is on Chromsome 8 in Xenopus. | ||
In ''X. laevis'' '''v9.2''' genome annotation, this region of the Chromosome 8 is poorly annotated, with most gene models uncharacterized and unnamed, so synteny is difficult to establish with certainty, and it differs considerably from the X. tropicalis v10.0 annoatation. | In ''X. laevis'' '''v9.2''' genome annotation, this region of the Chromosome 8 is poorly annotated, with most gene models uncharacterized and unnamed, so synteny is difficult to establish with certainty, and it differs considerably from the ''X. tropicalis'' v10.0 annoatation. | ||
In ''X. tropicalis'' '''v9.1''' genome this gene is found in this gene order: cd163> cd5l> cd163 dtx3-like< LOC#(vm2r26)< LOC#(gprc6a) < | In ''X. tropicalis'' '''v9.1''' genome this gene is found in this gene order: ''cd163> cd5l> cd163 '''dtx3-like'''< LOC#(vm2r26)< LOC#(gprc6a) <'' | ||
In ''X. tropicalis'' '''v10.0''' genome annotation , it is called LOC550107 and dtx3-like.1 in the lift over file. These were added as synonyms. | In ''X. tropicalis'' '''v10.0''' genome annotation , it is called ''LOC550107'' and ''dtx3-like.1'' in the lift over file. These were added as synonyms. | ||
2) The true ortholog of human DTX3L is Xenopus dtx3l Gene ID:100496352, based on conserved gene order/synteny, which is annotated on Scaffold_734 in X. tropicalis v9.1 (gene model gene26586) and in X. laevis v9.2 is on Chr9_10 (dtx3l.L gene ID:108701239; dtx3l.S gene ID:108702882). A new genepage is being built on Xenbase for these genes, and the vertebrate orthologs will be moved to this new gene pages. | 2) The true ortholog of human DTX3L is Xenopus dtx3l Gene ID:100496352, based on conserved gene order/synteny, which is annotated on Scaffold_734 in X. tropicalis v9.1 (gene model gene26586) and in ''X. laevis'' v9.2 is on Chr9_10 (dtx3l.L gene ID:108701239; dtx3l.S gene ID:108702882). A new genepage is being built on Xenbase for these genes, and the vertebrate orthologs will be moved to this new gene pages. | ||
Note also that the 'L' human in the gene DTX3L, doesn't appear stand for 'like' as it would in a Xenopus gene name. | Note also that the 'L' human in the gene DTX3L, doesn't appear stand for 'like' as it would in a ''Xenopus'' gene name. | ||
Latest revision as of 06:10, 20 August 2020
dtx3
This is the community wiki page for the gene dtx3 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
nomenclature changes
8.19.2020 name changed from deltex, E3 ubiquitan ligase 3, to deltex E3 ubiquitin ligase 3 ( removed comma)
Notes on Synteny
8.19.2020:
This is the true ortholgoue of Human DTX3, based on conserved gene order/synteny: KIF5A> PIP4K2C> "DTX3"> ARHGEF25>
In Xenopus, this gene is found on Chr2 in the same order: kif5a> pip4k2c> dtx3> arhgef25
Note that there are 2 other deltex 3 genes in human and Xenopus: 1) dtx3-like, and 2) dtx3L'.
1) dtex3-like, deltex E3 ubiquitin ligase 3-like is on Chromsome 8 in Xenopus.
In X. laevis v9.2 genome annotation, this region of the Chromosome 8 is poorly annotated, with most gene models uncharacterized and unnamed, so synteny is difficult to establish with certainty, and it differs considerably from the X. tropicalis v10.0 annoatation.
In X. tropicalis v9.1 genome this gene is found in this gene order: cd163> cd5l> cd163 dtx3-like< LOC#(vm2r26)< LOC#(gprc6a) <
In X. tropicalis v10.0 genome annotation , it is called LOC550107 and dtx3-like.1 in the lift over file. These were added as synonyms.
2) The true ortholog of human DTX3L is Xenopus dtx3l Gene ID:100496352, based on conserved gene order/synteny, which is annotated on Scaffold_734 in X. tropicalis v9.1 (gene model gene26586) and in X. laevis v9.2 is on Chr9_10 (dtx3l.L gene ID:108701239; dtx3l.S gene ID:108702882). A new genepage is being built on Xenbase for these genes, and the vertebrate orthologs will be moved to this new gene pages.
Note also that the 'L' human in the gene DTX3L, doesn't appear stand for 'like' as it would in a Xenopus gene name.