XB-FEAT-22062677: Difference between revisions
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=''gja4''= | =''gja4.2''= | ||
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. | This is the community wiki page for the gene ''gja4.2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. | ||
=nomenclature changes= | =nomenclature changes= | ||
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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''. | |||
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Dre: not found in Zebrafish. | Dre: not found in Zebrafish. | ||
=Proteins used in cladogram and multi species/multisequence alignment= | |||
09 October 2023 | |||
Species genesymbol(>change) NCBIgeneID proteinaccession chromosome# | |||
Xtropicalis gjb4 100486331 XP_017947077.1 2 | |||
Xtropicalis LOC101734565>gjb5 101734565 XP_004911667.1 2 | |||
Xtropicalis gjb3 100038103 NP_001106371.1 2 | |||
Xtropicalis cx38>gja4.2 100170463 NP_001123717.1 2 | |||
Xtropicalis gja4 780366 NP_001072904.1 2 | |||
Xlaevis gjb5.S 108709592 XP_018105071.1 2S | |||
Xlaevis gjb3.S 378649 NP_001079327.1 2S | |||
Xlaevis cx38.S>gja4.2.S 397866 NP_001081487.1 2S | |||
Xlaevis gja4.S 444216 NP_001085789.1 2S | |||
Xlaevis gja4.L 100335149 NP_001165443.1 2L | |||
Xlaevis gjb3.L 443903 XP_018100518.1 2L | |||
Xlaevis gjb5.L 108708260 XP_018102256.1 2L | |||
Xlaevis gjb4.L, LOC108708261 108708261 XP_018102257.1 2L | |||
Human GJB5 2709 NP_005259.1 1 | |||
Human GJB4 127534 NP_694944.1 1 | |||
Human GJB3 2707 NP_001005752.1 1 | |||
Human GJA4 2701 NP_002051.2 1 | |||
Mouse Gja4 14612 NP_032146.1 4 | |||
Mouse Gjb3 14620 NP_001153484.1 4 | |||
Mouse Gjb4 14621 NP_001407797.1 4 | |||
Mouse Gjb5 14622 NP_034421.1 4 | |||
Chicken Gja4 404529 NP_996867.3 23 | |||
Chicken Gjb3 101748282 XP_040507710.1 23 | |||
Chicken Gjb5 428225 XP_015153310.1 23 | |||
=cladogram= | |||
[[File:Undefined-3.pdf|thumb|vertebrate gap junctions (Gja4, Gjb3, Gjb4 and Gjb5) Protein accession in ML cladogram confirms ''Xenopus cx38''s are duplicates of ''gja4'' ]] | |||
[[File:Undefined-4.pdf|thumb|''Xenopus'' Gap junction genes on Chromosome 4/4L/4S. ]] | |||
Latest revision as of 13:48, 9 October 2023
gja4.2
This is the community wiki page for the gene gja4.2 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.
Proteins used in cladogram and multi species/multisequence alignment
09 October 2023
Species genesymbol(>change) NCBIgeneID proteinaccession chromosome#
Xtropicalis gjb4 100486331 XP_017947077.1 2
Xtropicalis LOC101734565>gjb5 101734565 XP_004911667.1 2
Xtropicalis gjb3 100038103 NP_001106371.1 2
Xtropicalis cx38>gja4.2 100170463 NP_001123717.1 2
Xtropicalis gja4 780366 NP_001072904.1 2
Xlaevis gjb5.S 108709592 XP_018105071.1 2S
Xlaevis gjb3.S 378649 NP_001079327.1 2S
Xlaevis cx38.S>gja4.2.S 397866 NP_001081487.1 2S
Xlaevis gja4.S 444216 NP_001085789.1 2S
Xlaevis gja4.L 100335149 NP_001165443.1 2L
Xlaevis gjb3.L 443903 XP_018100518.1 2L
Xlaevis gjb5.L 108708260 XP_018102256.1 2L
Xlaevis gjb4.L, LOC108708261 108708261 XP_018102257.1 2L
Human GJB5 2709 NP_005259.1 1
Human GJB4 127534 NP_694944.1 1
Human GJB3 2707 NP_001005752.1 1
Human GJA4 2701 NP_002051.2 1
Mouse Gja4 14612 NP_032146.1 4
Mouse Gjb3 14620 NP_001153484.1 4
Mouse Gjb4 14621 NP_001407797.1 4
Mouse Gjb5 14622 NP_034421.1 4
Chicken Gja4 404529 NP_996867.3 23
Chicken Gjb3 101748282 XP_040507710.1 23
Chicken Gjb5 428225 XP_015153310.1 23