XB-FEAT-967821: Difference between revisions
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=gene annotation notes= | =gene annotation notes= | ||
27MARCH2024 | 27MARCH2024 (CJZ) | ||
''X. tropicalis aadacl4'' is on scaffold_5494 in v9.1, with no other genes represented on this scaffold (so no flanking genes) and there was no gene annotated as ''aadacl4'' in v10 | ''X. tropicalis aadacl4'' is on scaffold_5494 in v9.1, with no other genes represented on this scaffold (so no flanking genes) and there was no gene annotated as ''aadacl4'' in v10 | ||
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To determine is the Xenopsu genes should be called '''''aadacl3''''' or '''''aadacl4''''' I looked at the human and non mammal genes. | To determine is the Xenopsu genes should be called '''''aadacl3''''' or '''''aadacl4''''' I looked at the human and non mammal genes. | ||
As Xenopus names follows Human gene names, and NOTING THE Human 'AADACL4' IS CLOSEST TO DHRS3, AND ' AADACL3' is upstream of AADACL4, and as ''Xenopus'' only has 1 of these | As Xenopus names follows Human gene names, and NOTING THE Human 'AADACL4' IS CLOSEST TO DHRS3, AND ' AADACL3' is upstream of AADACL4, and as ''Xenopus'' only has 1 of these genes, synteny supports the ''Xenopus'' genes ( including the v10 Xtr model XBXT10g017274) being called '''''aadac4''''', not '''''aadacl3'''''. | ||
Note that the v9.1 EMSEMBL annotation had this gene correctly identified as ''Xtr.aadacl4'', adding support to my conclusion. | |||
I am putting v10 Xtr model XBXT10g017274 on the ''aadac4'' gene page, and thus renaming by doing so, and removing it from the XB-gene-22067946. As the v10 annotation doesn't support a ''aadacl3'' gene in ''Xenopus'', I am moving all the earlier trop model to this page as well. If it turns out there is a ''aadacl3'' in ''Xenopus'', we can easily restore this by moving them to a new gene page. | |||
=synteny= | =synteny= | ||
Latest revision as of 06:16, 28 March 2024
aadacl4
This is the community wiki page for the gene aadacl4 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
gene annotation notes
27MARCH2024 (CJZ)
X. tropicalis aadacl4 is on scaffold_5494 in v9.1, with no other genes represented on this scaffold (so no flanking genes) and there was no gene annotated as aadacl4 in v10
X. laevis aadacl4.S is on chr7S: using the flanking genes in X. laevis aadacl4.S, I looked for the Xtrop v10 aadaccl4 gene model. The Xtrop gene in this location is currently called aadacl3
To determine is the Xenopsu genes should be called aadacl3 or aadacl4 I looked at the human and non mammal genes.
As Xenopus names follows Human gene names, and NOTING THE Human 'AADACL4' IS CLOSEST TO DHRS3, AND ' AADACL3' is upstream of AADACL4, and as Xenopus only has 1 of these genes, synteny supports the Xenopus genes ( including the v10 Xtr model XBXT10g017274) being called aadac4, not aadacl3.
Note that the v9.1 EMSEMBL annotation had this gene correctly identified as Xtr.aadacl4, adding support to my conclusion.
I am putting v10 Xtr model XBXT10g017274 on the aadac4 gene page, and thus renaming by doing so, and removing it from the XB-gene-22067946. As the v10 annotation doesn't support a aadacl3 gene in Xenopus, I am moving all the earlier trop model to this page as well. If it turns out there is a aadacl3 in Xenopus, we can easily restore this by moving them to a new gene page.
synteny
X. laevis v10 chr7S: prdm2.S< lrrc38.S> aadacl4.S< dhrs3.S> fbxl4.S<
Xtrop v10 chr7: prdm2< pdpn< lrrc38> LOC101731600(crmn1)< cfap107< aadacl3< dhrs3> fbxl4<
Human Chr1: VPS12D> DHRS3< AADACL4> AADACL3> CFAP107> PRAMEF12> PRAMEF1>