XB-FEAT-940519: Difference between revisions
imported>Xenbase →loc100489062: Updated nomenclature, replaced: unnamed → loc100489062 (2) |
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= | =''pak2''= | ||
This is the community wiki page for the gene '' | This is the community wiki page for the gene ''pak2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | ||
=Nomenclature changes= | |||
19AUG2022 | |||
Gene symbol changed from "XB940519 [provisional:pak2]" to "pak2 (provisional)". | |||
"XB940519" was added as a gene synonym. | |||
Gene name changed from "provisional ortholog of p21 (RAC1) activated kinase 2" to "p21 (RAC1) activated kinase 2 (provisional)". | |||
22MAy2023 | |||
Xenopus gene synbol and name changed from pak2 (provisional), p21 (RAC1) activated kinase 2 (provisional to pak2l, p21 (RAC1) activated kinase 2 like. | |||
=synteny and orthology= | |||
''pak2l'' in ''X. tropicalis'' and ''pak2l'' in ''X. laveis.L'' are on different chromsomes and '''do not'' share a syntenic, or common/conserved group of genes flanking them in the v10 genome assemblies. Here I compare synteny on the paralogous chromosome to see if we can better annotate these genes. | |||
Xtrop.Chr4: ''LOC101733630(ctsd)> '''pak2l>''' LOC100488209(muc5b)> tollip< brsk2> '' | |||
Xla.chr4L v10: '' LOC121402872(acp2) LOC121402941(unch)< LOC108713857(unch)< LOC108713832(lncRNA)< tollip.L< LOC108713833(brsk2)>'' | |||
Xla.chr4S: ''tnni2.S< LOC108715204(syt1)> MGC82347> ctsd.S> ifitm10.S> LOC108715206(mobka2)> LOC108715207(brsk2)> tollip.S> LOC121393064(muc5bl)< LOC108715209(muc5b)< fibin.S> bbox1.S>'' | |||
comparted with | |||
Xla.Chr7L: h6pd.L> spsb1.L> tnfrs14.L< '''pak2l.L>''' hes5.2.L< hes5.1.L> pank4.L> grk5l.1.L< | |||
Xla.Chr7S: h6pd.S> spsb1.S> X X hes5.2.S< hes5.1.S> pank4.S> grk5l.1.S< | |||
XTR.CHR7: h6pd.> spsb1> tnfrs14< X hes5.2< hes5.1> pank4> grk5l.1< | |||
Conclusions: | |||
* LOC121402941(unch)and LOC108713857(unch): DIOPT/Eggnog matches both these protein to ~100 bacterial proteins from 63 species (ie these are NOT a PAK2 genes) | |||
* | |||
* No candidate genes are annotated on Xla. Chromsomome 4L or Chromsomome 4S that would be an alternative 'best match' for ''pak2l'' gene page. | |||
* | |||
* Similarly, there is no X.tropicalis or Xlaevis.S candidate genes on Chr7/7S that would justify a new gene page. | |||
* | |||
* These genes can stay on this pak2-like gene page | |||
NOTE THAT TRUE PAK2 - p21 (RAC1) activated kinase 2 ORTHOLOGs IN XENOPUS are Xtrop Gene ID: 733718, | |||
X.laevis.L Gene: 108717139, and X.laevis.S Entrez Gene: 399090 ON CHROMOSOME 5/5L/5S. | |||
Note the conserved upstream flanking genes, NRROS and FBXO45. | |||
Xtrop.Chr5: gal3st3> aqp12a< '''pak2<''' nrros< fbox45< | |||
Human.CHR3: FBXO45< NRROS< CEP19< PIGX> '''PAK2>''' SENP5> NCBP2< NCBP2AS2> PIGZ< | |||
Latest revision as of 13:17, 22 May 2023
pak2
This is the community wiki page for the gene pak2 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
Nomenclature changes
19AUG2022
Gene symbol changed from "XB940519 [provisional:pak2]" to "pak2 (provisional)".
"XB940519" was added as a gene synonym.
Gene name changed from "provisional ortholog of p21 (RAC1) activated kinase 2" to "p21 (RAC1) activated kinase 2 (provisional)".
22MAy2023 Xenopus gene synbol and name changed from pak2 (provisional), p21 (RAC1) activated kinase 2 (provisional to pak2l, p21 (RAC1) activated kinase 2 like.
synteny and orthology
pak2l in X. tropicalis and pak2l in X. laveis.L are on different chromsomes and 'do not share a syntenic, or common/conserved group of genes flanking them in the v10 genome assemblies. Here I compare synteny on the paralogous chromosome to see if we can better annotate these genes.
Xtrop.Chr4: LOC101733630(ctsd)> pak2l> LOC100488209(muc5b)> tollip< brsk2>
Xla.chr4L v10: LOC121402872(acp2) LOC121402941(unch)< LOC108713857(unch)< LOC108713832(lncRNA)< tollip.L< LOC108713833(brsk2)>
Xla.chr4S: tnni2.S< LOC108715204(syt1)> MGC82347> ctsd.S> ifitm10.S> LOC108715206(mobka2)> LOC108715207(brsk2)> tollip.S> LOC121393064(muc5bl)< LOC108715209(muc5b)< fibin.S> bbox1.S>
comparted with
Xla.Chr7L: h6pd.L> spsb1.L> tnfrs14.L< pak2l.L> hes5.2.L< hes5.1.L> pank4.L> grk5l.1.L<
Xla.Chr7S: h6pd.S> spsb1.S> X X hes5.2.S< hes5.1.S> pank4.S> grk5l.1.S<
XTR.CHR7: h6pd.> spsb1> tnfrs14< X hes5.2< hes5.1> pank4> grk5l.1<
Conclusions:
- LOC121402941(unch)and LOC108713857(unch): DIOPT/Eggnog matches both these protein to ~100 bacterial proteins from 63 species (ie these are NOT a PAK2 genes)
- No candidate genes are annotated on Xla. Chromsomome 4L or Chromsomome 4S that would be an alternative 'best match' for pak2l gene page.
- Similarly, there is no X.tropicalis or Xlaevis.S candidate genes on Chr7/7S that would justify a new gene page.
- These genes can stay on this pak2-like gene page
NOTE THAT TRUE PAK2 - p21 (RAC1) activated kinase 2 ORTHOLOGs IN XENOPUS are Xtrop Gene ID: 733718,
X.laevis.L Gene: 108717139, and X.laevis.S Entrez Gene: 399090 ON CHROMOSOME 5/5L/5S.
Note the conserved upstream flanking genes, NRROS and FBXO45.
Xtrop.Chr5: gal3st3> aqp12a< pak2< nrros< fbox45<
Human.CHR3: FBXO45< NRROS< CEP19< PIGX> PAK2> SENP5> NCBP2< NCBP2AS2> PIGZ<