XB-FEAT-22062677: Difference between revisions
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XB curators reassessed this connexion gene, as no other vertebrate genes are called ''cx38'', just ''X. trop'' GeneID:100170463, and ''X. laevis'' GeneID:397866. | XB curators reassessed this connexion gene, as no other vertebrate genes are called ''cx38'', just ''X. trop'' GeneID:100170463, and ''X. laevis'' GeneID:397866. | ||
The synonym given | The synonym given was ''gja2'', and the Xlaevis protein was similar called ;gap junction alpha 2 protein', but NCBI currently only assigned to genes in a large number of fish species, but no other vertebrates ( not even frogs) . | ||
Synteny suggests this is NOT ''gja2'', but a duplicate of either ''gja4'' or ''gja3'' its flaking gene in ''Xenopus'', or a '''gjb''' gene. | Synteny suggests this is NOT ''gja2'', but a duplicate of either ''gja4'' or ''gja3'' its flaking gene in ''Xenopus'', or a '''gjb''' gene. True ''gja2'' oand its orthologs is on a different chromosome in Xenopus. | ||
A multispecies multisequence alignment of all of the adjacent genes in Human mouse chicken and the 3 Xenopus genes strongly support the renaming of this gene as a duplicate of ''gja4''. | |||
Revision as of 14:31, 9 October 2023
gja4
This is the community wiki page for the gene gja4 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
nomenclature changes
09 OCTOBER 2023
XB curators reassessed this connexion gene, as no other vertebrate genes are called cx38, just X. trop GeneID:100170463, and X. laevis GeneID:397866.
The synonym given was gja2, and the Xlaevis protein was similar called ;gap junction alpha 2 protein', but NCBI currently only assigned to genes in a large number of fish species, but no other vertebrates ( not even frogs) .
Synteny suggests this is NOT gja2, but a duplicate of either gja4 or gja3 its flaking gene in Xenopus, or a gjb gene. True gja2 oand its orthologs is on a different chromosome in Xenopus.
A multispecies multisequence alignment of all of the adjacent genes in Human mouse chicken and the 3 Xenopus genes strongly support the renaming of this gene as a duplicate of gja4.
Xenopus gene name therefore has changed from cx38, connexion 38 to gja4.2, gap junction alpha 4 gene 2.
synteny
09 OCTOBER 2023
X.tropicalis chr2: LOC105946490 LOC108645861 gjb4 LOC101734565 gjb3 cx38 gja4 smim12 zmpste24 tmem30b kdm1a
X.laevis chr2S: kcnq4.S smap2.S col9a2.S csmd2.S gjb5.S gjb3.S cx38.S gja4.S smim12.S zmpste24.S kdm1a.S
X.laevis chr2L: kdm1a.L tmem30b.L zmpste24.L smim12.L gja4.L gjb3.L gjb5.L gjb4.L luzp1.L mtfr1l.L rlf.L
M.musculus chr4: Gm52707 Smim12 Gm22221 Gm12948 Gja4 Gjb3 Gm40251 Gjb4 Gjb5 Gm12947 Gm40252
H.sapiens chr1: LOC105378641 MIR552 LOC105378642 GJB5 GJB4 GJB3 GJA4 SMIM12 DLGAP3 GPR199P TMEM35B
G.gallus Chr23: Tmem35b LOC100859615 Dlgap3 Smim12 Gja4 GJB3 GJB5 LOC121107457 LOC112530213 C1orf94 Csmd2
Dre: not found in Zebrafish.