XB-FEAT-22062677 - Revision history

Xenbase: /* synteny */

2023-10-09T20:48:03Z

synteny

← Older revision		Revision as of 20:48, 9 October 2023
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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. ]]

Xenbase: /* gja4 */

2023-10-09T20:38:43Z

gja4

← Older revision		Revision as of 20:38, 9 October 2023
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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=

Xenbase: /* nomenclature changes */

2023-10-09T20:31:45Z

nomenclature changes

← Older revision		Revision as of 20:31, 9 October 2023
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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 is ''gja2'', ~~which in~~ NCBI is currently only assigned to genes in a large number of fish species, but no other vertebrates.		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.

	~~Amultispecies multi sequence~~ alignment of all of the adjacent genes ~~inHuman~~ mouse chicken and the 2 Xenopus ~~gens~~ strongly support the renaming of this gene as a duplicate of ~~the~~ ''gja4'' ~~genes~~.		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''.

Xenbase: /* nomenclature */

2023-10-09T20:29:27Z

nomenclature

← Older revision		Revision as of 20:29, 9 October 2023
Line 2:		Line 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'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

	=nomenclature=		=nomenclature changes=
	09 OCTOBER 2023		09 OCTOBER 2023

	XB curators ~~currently reassessing~~ 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 is ''gja2'', which in NCBI is currently only assigned to genes in a large number of fish species, but no other vertebrates.		The synonym given is ''gja2'', which in NCBI is currently only assigned to genes in a large number of fish species, but no other vertebrates.

	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.

	~~Use caution when using~~ this gene ~~symbol~~, ~~and look for updated nomenclature~~ .		Amultispecies multi sequence alignment of all of the adjacent genes inHuman mouse chicken and the 2 Xenopus gens strongly support the renaming of this gene as a duplicate of the ''gja4'' genes.


			''Xenopus'' gene name therefore has changed from ''cx38, connexion 38'' to ''gja4.2, gap junction alpha 4 gene 2''.

	=synteny=		=synteny=

Xenbase: /* cx38 */

2023-10-09T20:24:18Z

cx38

← Older revision		Revision as of 20:24, 9 October 2023
Line 1:		Line 1:
	=''~~cx38~~''=		=''gja4''=
	This is the community wiki page for the gene ''~~cx38~~'' 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'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

	=nomenclature=		=nomenclature=

Xenbase: /* synteny */

2023-10-09T19:07:11Z

synteny

← Older revision		Revision as of 19:07, 9 October 2023
Line 32:		Line 32:

	G.gallus Chr23: Tmem35b LOC100859615 Dlgap3 Smim12 '''Gja4 GJB3 GJB5 LOC121107457 LOC112530213''' C1orf94 Csmd2		G.gallus Chr23: Tmem35b LOC100859615 Dlgap3 Smim12 '''Gja4 GJB3 GJB5 LOC121107457 LOC112530213''' C1orf94 Csmd2


			Dre: not found in Zebrafish.

Xenbase: /* nomenclature */

2023-10-09T19:04:36Z

nomenclature

← Older revision		Revision as of 19:04, 9 October 2023
Line 4:		Line 4:
	=nomenclature=		=nomenclature=
	09 OCTOBER 2023		09 OCTOBER 2023
	~~Note: no other vertebrate genes are called ''cx38'', just ''X. trop'' GeneID:100170463, and ''X. laevis'' GeneID:397866.~~

	The ~~Synonym~~ given is ''gja2'', which in NCBI is currently only assigned to genes in a large number of fish species, but no other vertebrates.		XB curators currently reassessing this connexion gene, as no other vertebrate genes are called ''cx38'', just ''X. trop'' GeneID:100170463, and ''X. laevis'' GeneID:397866.

			The synonym given is ''gja2'', which in NCBI is currently only assigned to genes in a large number of fish species, but no other vertebrates.

	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.

	Use caution when using this gene symbol, and look for updated nomenclature ~~. XB curators currently reassessing~~.		Use caution when using this gene symbol, and look for updated nomenclature .

	=synteny=		=synteny=

Xenbase: /* nomenclature */

2023-10-09T19:03:37Z

nomenclature

← Older revision		Revision as of 19:03, 9 October 2023
Line 8:		Line 8:
	The Synonym given is ''gja2'', which in NCBI is currently only assigned to genes in a large number of fish species, but no other vertebrates.		The Synonym given is ''gja2'', which in NCBI is currently only assigned to genes in a large number of fish species, but no other vertebrates.

	Synteny suggests this is not ''gja2'', but a duplicate of either ''gja4'' or ''gja3'' its flaking gene in Xenopus, or .		Synteny suggests this is not ''gja2'', but a duplicate of either ''gja4'' or ''gja3'' its flaking gene in Xenopus, or a '''gjb''' gene.

	Use caution when using this gene symbol.		Use caution when using this gene symbol, and look for updated nomenclature . XB curators currently reassessing.

	=synteny=		=synteny=

Xenbase: Created page with "=''cx38''= This is the community wiki page for the gene ''cx38'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. =nomenclature= 09 OCTOBER 2023 Note: no other vertebrate genes are called ''cx38'', just ''X. trop'' GeneID:100170463, and ''X. laevis'' GeneID:397866. The Synonym given is ''gja2'', which in NCBI is currently only assigned to genes in a large number of fish species, but no other vert..."

2023-10-09T19:02:02Z

Created page with "=''cx38''= This is the community wiki page for the gene ''cx38'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. =nomenclature= 09 OCTOBER 2023 Note: no other vertebrate genes are called ''cx38'', just ''X. trop'' GeneID:100170463, and ''X. laevis'' GeneID:397866. The Synonym given is ''gja2'', which in NCBI is currently only assigned to genes in a large number of fish species, but no other vert..."

New page

=''cx38''=
This is the community wiki page for the gene ''cx38'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

=nomenclature=
09 OCTOBER 2023
Note: no other vertebrate genes are called ''cx38'', just ''X. trop'' GeneID:100170463, and ''X. laevis'' GeneID:397866.

The Synonym given is ''gja2'', which in NCBI is currently only assigned to genes in a large number of fish species, but no other vertebrates.

Synteny suggests this is not ''gja2'', but a duplicate of either ''gja4'' or ''gja3'' its flaking gene in Xenopus, or .

Use caution when using this gene symbol.

=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