XB-FEAT-22067945: Difference between revisions
Created page with "=''pgla.2''= This is the Xenbase wiki page for the Xenopus genes ''pgla.2''. Feel free to records here any information about these genes that is not captured elsewhere on Xenbase. =nomenclature changes= 28MARCH2024 In the v10 ''X.laevis'' NCBI annotation, this gene was incorrectly called ''pgla.S'', but it '''is placed on chromosome 6L'''. Synteny and the NCBI annotation name is as a prepro-PGLa, and as it falls adjacent to other prepro-PGLa genes, we have given it..." |
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=nomenclature changes= | =nomenclature changes= | ||
The ‘’Xenopus’’ ‘’pgla’’ genes on Chr6/6L/6S, a cluster of tadem uncharacterized proteins, were assessed by Xenbase curators. Based on synteny, protein alignment and phylogenetic analysis, the following provisional gene nomenclature was decided upon. | |||
Note that in the v10 NCBI assembly, geneID: 780753 was incorrectly given the ‘.S’ suffix even though the model was mapped to chr6L. | |||
In summary: | |||
• synteny patterns showed that ''X.laevis'' has 3 genes chr6L, and no genes on chr6S, while ''X.tropicalis'' has 2 genes on chr6. | |||
• Alignment showed that the protein Sequences are moderately-highly conserved. | |||
• ''Xla.pgla.2.L'' and ''Xla.pgla.3.L'' are almost identical, both 64aa | |||
• ''Xla.pgla.1.L'' was the longest protein (94aa) and closer to the 2 x Xtrop genes, which where 75 and 81 aa long, which in turn are each others closest ‘relative’ based on aa identity. | |||
• Naming is not straight forward however, as no other taxa have genes with similar names, and protein resources such as UniProt have not characterized these proteins. | |||
• Decision was to '''not''' call the Xtrop genes ‘pgla.1 and pgla.2’ or ‘pgla.2 and pgla.3’, because MSA and phlyogenetic tree shows Xtrop genes are a) duplicates of each other) and closer to Xla pgla.3 than others, but are still quite different, so INSTEAD we renamed them ''pgla.4'' and ''pgla.5'' so as not to imply they are ortholosg of the ‘’X. laevis’’ genes. They are likely independent tandem duplications, within X. tropicalis- ie in-paralogs. | |||
'''nomenclature changes''' | |||
. ‘’’’’X. laevis’’ genes’’’ | |||
1) pgla.L, prepro-PGLa L homeolog [ Gene ID: 397770] is on XB-GENEPAGE-6492177 , was renamed prepro-PGLa gene 1 L homeolog added the synonym pgla.1.L | |||
2) LOC780753 , previously carried gene symbol pgla.S was renamed pgla.2.L, prepro-PGLa gene 2 L homeolog, [gene ID 780753 ) with gene model XBXL10_1g27269) was put on XB-GENEPAGE-22067945. | |||
3) LOC121394631, PYLa/PGLa A-like (gene model: XBXL10_1g27268) put on a XB-GENEPAGE-29091430) was renamed pgla.3.L, prepro-PGLa gene 3 L homelog . | |||
‘’’’’X. tropicalis’’ genes’’’ | |||
4) LOC116411668 (PYLa/PGLa A-like) (gene model XBXT10g021597), was already on XB-GENEPAGE-29097510, renamed pgla.4, prepro-PGLa gene 4 | |||
5) LOC11641166790 (PYLa/PGLa A-like) [gene model:XBXT10g005644] was already on XB-GENEPAGE- 29097506, was renamed pgla.5, prepro-PGLa gene 5 | |||
=synteny= | |||
28MARCH2024 | 28MARCH2024 | ||
V10 gene symbols and (given names) '''before''' new nomenclature applied (see above for details) | |||
Xla.chr6L: ctnnb1.L> ulk4.L< trak1.L> LOC121394631.L(‘pgla-like’)< LOC780753.L(‘pgla.S’)< pgla.L< pgq.L< levi.L> levi.2.L> | |||
Xla.chr6S ctnnb1.S> LOC121395288(snRNA)< LOC121395094(ulk4-l)> trak1.S> LOC121395043(xenopsin peptides-like)< LOC121395045(preprocaerulein type I'-like< cck.S< eif1b.S< prlh.S> myrip.S> | |||
Xtrop v10 | |||
Xtr.Chr6: ctnnb1> ulk4< trak1> LOC116411668(PYLa/PGLa A-like)>. LOC11641166790(PYLa/PGLa A-like)< LOC116411669(trak1-like). LOC100488640(xenopsin)< pgq< | |||
=protein accessions used in COBALT= | |||
XP_041422017.1 (Xla LOC121394631) | |||
XP_041422018.1 (Xla LOC780753) | |||
NP_001081314.2 (Xla pgla. L) | |||
XP_031760293.1 (Xtr LOC116411668) | |||
XP_031760292.1 (Xtr LOC11641166790 ) | |||
Revision as of 11:49, 28 March 2024
pgla.2
This is the Xenbase wiki page for the Xenopus genes pgla.2. Feel free to records here any information about these genes that is not captured elsewhere on Xenbase.
nomenclature changes
The ‘’Xenopus’’ ‘’pgla’’ genes on Chr6/6L/6S, a cluster of tadem uncharacterized proteins, were assessed by Xenbase curators. Based on synteny, protein alignment and phylogenetic analysis, the following provisional gene nomenclature was decided upon.
Note that in the v10 NCBI assembly, geneID: 780753 was incorrectly given the ‘.S’ suffix even though the model was mapped to chr6L.
In summary: • synteny patterns showed that X.laevis has 3 genes chr6L, and no genes on chr6S, while X.tropicalis has 2 genes on chr6. • Alignment showed that the protein Sequences are moderately-highly conserved. • Xla.pgla.2.L and Xla.pgla.3.L are almost identical, both 64aa • Xla.pgla.1.L was the longest protein (94aa) and closer to the 2 x Xtrop genes, which where 75 and 81 aa long, which in turn are each others closest ‘relative’ based on aa identity. • Naming is not straight forward however, as no other taxa have genes with similar names, and protein resources such as UniProt have not characterized these proteins. • Decision was to not call the Xtrop genes ‘pgla.1 and pgla.2’ or ‘pgla.2 and pgla.3’, because MSA and phlyogenetic tree shows Xtrop genes are a) duplicates of each other) and closer to Xla pgla.3 than others, but are still quite different, so INSTEAD we renamed them pgla.4 and pgla.5 so as not to imply they are ortholosg of the ‘’X. laevis’’ genes. They are likely independent tandem duplications, within X. tropicalis- ie in-paralogs.
nomenclature changes . ‘’’’’X. laevis’’ genes’’’ 1) pgla.L, prepro-PGLa L homeolog [ Gene ID: 397770] is on XB-GENEPAGE-6492177 , was renamed prepro-PGLa gene 1 L homeolog added the synonym pgla.1.L
2) LOC780753 , previously carried gene symbol pgla.S was renamed pgla.2.L, prepro-PGLa gene 2 L homeolog, [gene ID 780753 ) with gene model XBXL10_1g27269) was put on XB-GENEPAGE-22067945.
3) LOC121394631, PYLa/PGLa A-like (gene model: XBXL10_1g27268) put on a XB-GENEPAGE-29091430) was renamed pgla.3.L, prepro-PGLa gene 3 L homelog .
‘’’’’X. tropicalis’’ genes’’’
4) LOC116411668 (PYLa/PGLa A-like) (gene model XBXT10g021597), was already on XB-GENEPAGE-29097510, renamed pgla.4, prepro-PGLa gene 4
5) LOC11641166790 (PYLa/PGLa A-like) [gene model:XBXT10g005644] was already on XB-GENEPAGE- 29097506, was renamed pgla.5, prepro-PGLa gene 5
synteny
28MARCH2024
V10 gene symbols and (given names) before new nomenclature applied (see above for details)
Xla.chr6L: ctnnb1.L> ulk4.L< trak1.L> LOC121394631.L(‘pgla-like’)< LOC780753.L(‘pgla.S’)< pgla.L< pgq.L< levi.L> levi.2.L>
Xla.chr6S ctnnb1.S> LOC121395288(snRNA)< LOC121395094(ulk4-l)> trak1.S> LOC121395043(xenopsin peptides-like)< LOC121395045(preprocaerulein type I'-like< cck.S< eif1b.S< prlh.S> myrip.S>
Xtrop v10 Xtr.Chr6: ctnnb1> ulk4< trak1> LOC116411668(PYLa/PGLa A-like)>. LOC11641166790(PYLa/PGLa A-like)< LOC116411669(trak1-like). LOC100488640(xenopsin)< pgq<
protein accessions used in COBALT
XP_041422017.1 (Xla LOC121394631) XP_041422018.1 (Xla LOC780753) NP_001081314.2 (Xla pgla. L) XP_031760293.1 (Xtr LOC116411668) XP_031760292.1 (Xtr LOC11641166790 )