XB-FEAT-986526 - Revision history

Christina: /* background to nomenclature changes */

2023-05-05T12:56:20Z

background to nomenclature changes

Christina: /* nomenclature changes */

2023-05-05T12:50:31Z

nomenclature changes

← Older revision		Revision as of 12:50, 5 May 2023
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	=nomenclature changes=		=nomenclature changes=
	''Xenopus'' gene symbol changed from ''loc100494546'' to ''XB986526 [provisional:hsd3b7]''		''Xenopus'' gene symbol changed from ''loc100494546'' to ''XB986526 [provisional:hsd3b7]''

	05May2023		05May2023

Christina: /* loc100494546 */

2023-05-05T12:50:21Z

loc100494546

← Older revision		Revision as of 12:50, 5 May 2023
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	=~~loc100494546~~=		=''hsd3b7l''=
	This is the community wiki page for the gene ''~~loc100494546~~'' 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 ''hsd3b7l'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase


			=nomenclature changes=
			''Xenopus'' gene symbol changed from ''loc100494546'' to ''XB986526 [provisional:hsd3b7]''

			05May2023

			''Xenopus'' gene name changed from ''provisional ortholog of hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7'' to ''hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7 like''

			''Xenopus'' gene symbol changed from ''XB986526 [provisional:hsd3b7]'' to ''hsd3b7l''

			=background to nomenclature changes=
			Jan/05/23

			'''HSD3B7 symbol applied to wrong chicken gene ( and thus the wrong ''Xenopus'' gene)'''

			reported by David Webb from NCBI RefSeq team. RSCOM-393

			Chicken GeneID: 417505 is named HSD3B7 (CGNC:1253) but isn't truly orthologous to human HSD3B7 (GeneID:80274).

			Xenopus has an unnamed gene (GeneID: 100494546, XB-GENE-986527) that is the ortholog of the misnamed chicken GeneID: 417505.
			chicken GeneID: 417505 resides at:

			IFT22< COL26A1> "HSD3B7"> MYL10< CUX1>

			while human is at:

			FBXL19> ORAI3> SETD1A> HSD3B7> STX1B< STX4> ZNF668<

			I think what's happening is that the true HSD3B7 gene is difficult to sequence and assemble in birds & crocodilians and so a similar gene, which mammals have lost, is being misnamed as "HSD3B7" in many non-mammals.

			In addition to mammals, this "HSD3B7" gene is also lost in squamates and caecilians though frogs, coelacanth & lungfish (Protopterus annectens) have both genes which suggests ancestral sarcopterygians had both HSD3B7 and "HSD3B7".

			The true HSD3B7 gene is older and goes back to vertebrata (and likely further) while "HSD3B7" arose in sarcopterygians.


			So my recommendations are:

			Gg GeneID: 417505 (CGNC:1253) needs to be renamed from HSD3B7 to something else ('''HSD3B7L'''? HSD3B8 and HSD3B9 are already used in mouse).

			Gg GeneID: 121108723 (CGNC:88598, HSD3B7L) should be named HSD3B7 (XP_040512766.1, lacks roughly aa 186-366 from the C-terminus).

			'''Xtr GeneID: 100145626 XB-GENE-1008841 is correctly named ''hsd3b7'''''

			'''Xtr GeneID: 100494546 XB-GENE-986527 needs to be named to match chicken GeneID: 417505/"HSD3B7"'''

			Dr GeneID: 327462 ZDB-GENE-030131-5673 is correctly named hsd3b7

imported>Xenbase: /* loc100494546 */Updated nomenclature, replaced: unnamed → loc100494546 (2)

2017-12-15T22:55:40Z

loc100494546: Updated nomenclature, replaced: unnamed → loc100494546 (2)

← Older revision		Revision as of 22:55, 15 December 2017
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	=~~unnamed~~=		=loc100494546=
	This is the community wiki page for the gene ''~~unnamed~~'' 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 ''loc100494546'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase

imported>Xenbase gene generator at 12:00, 10 February 2010

2010-02-10T12:00:00Z

New page

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

← Older revision		Revision as of 12:56, 5 May 2023
Line 21:		Line 21:
	Chicken GeneID: 417505 is named HSD3B7 (CGNC:1253) but isn't truly orthologous to human HSD3B7 (GeneID:80274).		Chicken GeneID: 417505 is named HSD3B7 (CGNC:1253) but isn't truly orthologous to human HSD3B7 (GeneID:80274).

	Xenopus has an unnamed gene (GeneID: 100494546, XB-GENE-986527) that is the ortholog of the misnamed chicken GeneID: 417505.		''Xenopus'' has an unnamed gene (GeneID: 100494546, XB-GENE-986527) that is the ortholog of the misnamed chicken GeneID: 417505.

	chicken GeneID: 417505 resides at:		chicken GeneID: 417505 resides at:

	IFT22< COL26A1> "HSD3B7"> MYL10< CUX1>		IFT22< COL26A1> "'HSD3B7'"> MYL10< CUX1>

	while human is at:		while human is at:

	FBXL19> ORAI3> SETD1A> HSD3B7> STX1B< STX4> ZNF668<		FBXL19> ORAI3> SETD1A> '''HSD3B7'''> STX1B< STX4> ZNF668<

	I think what's happening is that the true HSD3B7 gene is difficult to sequence and assemble in birds & crocodilians and so a similar gene, which mammals have lost, is being misnamed as "HSD3B7" in many non-mammals.		I think what's happening is that the true HSD3B7 gene is difficult to sequence and assemble in birds & crocodilians and so a similar gene, which mammals have lost, is being misnamed as "HSD3B7" in many non-mammals.

	In addition to mammals, this "HSD3B7" gene is also lost in squamates and caecilians though frogs, coelacanth & lungfish (Protopterus annectens) have both genes which suggests ancestral sarcopterygians had both HSD3B7 and "HSD3B7".		In addition to mammals, this "HSD3B7" gene is also lost in squamates and caecilians though frogs, coelacanth & lungfish (Protopterus annectens) have both genes which suggests ancestral sarcopterygians had both '''HSD3B7''' and '"HSD3B7-like'".

	The true HSD3B7 gene is older and goes back to vertebrata (and likely further) while "HSD3B7" arose in sarcopterygians.		The true '''HSD3B7''' gene is older and goes back to vertebrata (and likely further) while "HSD3B7 like" arose in sarcopterygians.


	So my recommendations are:		So my recommendations are:

	Gg GeneID: 417505 (CGNC:1253) needs to be renamed from HSD3B7 to something else ('''HSD3B7L'''? HSD3B8 and HSD3B9 are already used in mouse).		Gga GeneID: 417505 (CGNC:1253) needs to be renamed from HSD3B7 to something else ('''HSD3B7L'''? HSD3B8 and HSD3B9 are already used in mouse).

	Gg GeneID: 121108723 (CGNC:88598, HSD3B7L) should be named HSD3B7 (XP_040512766.1, lacks roughly aa 186-366 from the C-terminus).		Gga GeneID: 121108723 (CGNC:88598, HSD3B7L) should be named HSD3B7 (XP_040512766.1, lacks roughly aa 186-366 from the C-terminus).

	'''Xtr GeneID: 100145626 XB-GENE-1008841 is correctly named ''hsd3b7'''''		'''Xtr GeneID: 100145626 XB-GENE-1008841 is correctly named ''hsd3b7'''''

	'''Xtr GeneID: 100494546 XB-GENE-986527 needs to be named to match chicken GeneID: 417505/"~~HSD3B7~~"'''		'''Xtr GeneID: 100494546 XB-GENE-986527 needs to be named to match chicken GeneID: 417505/"HSD3B7like"'''

	Dr GeneID: 327462 ZDB-GENE-030131-5673 is correctly named hsd3b7		Dre GeneID: 327462 ZDB-GENE-030131-5673 is correctly named hsd3b7