XB-FEAT-984297 - Revision history

Christina: /* synteny and orthology */

2023-05-17T19:31:29Z

synteny and orthology

← Older revision		Revision as of 19:31, 17 May 2023
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	DIOPT/EggNog matches the proteins for the Xtrop genes ~~(seqs given below)~~ to 3 groups of CYP genes with high confidence:		DIOPT/EggNog matches the proteins for the Xtrop genes to 3 groups of CYP genes with high confidence:

	1) ~890 seqs from ~200 species, including Mouse, Pteropus vampyrus (bat), Otolemur garnettii (lemur) and Cavia porcellus (guinea pig) seqs for Cyp27b1, Cyp24a1 and Cyp27a1 (ie including '''cyp27a1''' as suggested by the provisional name for XB1001094 and XB984297)		1) ~890 seqs from ~200 species, including Mouse, Pteropus vampyrus (bat), Otolemur garnettii (lemur) and Cavia porcellus (guinea pig) seqs for Cyp27b1, Cyp24a1 and Cyp27a1 (ie including '''cyp27a1''' as suggested by the provisional name for XB1001094 and XB984297)

Christina: /* cyp27a1 */

2023-05-17T19:31:03Z

cyp27a1

← Older revision		Revision as of 19:31, 17 May 2023
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	= cyp27a1 =		= ''cyp27a1'' =
	This is the community wiki page for the gene ''cyp27a1'' 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 ''cyp27a1'' 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 =
	17MAY2023		17MAY2023

Christina: /* synteny and orthology */

2023-05-17T19:30:30Z

synteny and orthology

← Older revision		Revision as of 19:30, 17 May 2023
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	=synteny and orthology=		=synteny and orthology=

	There are 4 genes/loci tandemly duplicated that were provisionally annotated as ''cyp27a1'' in ''X. tropicalis'' v10 assembly:		'''There are 4 genes/loci tandemly duplicated that were provisionally annotated as ''cyp27a1'' in ''X. tropicalis'' v10 assembly:'''

	* LOC594905 (cyp27a1.3): Entrez Gene: 594905 XP_031749391.1 >> keeps symbol cyp27a1.3		* LOC594905 (cyp27a1.3): Entrez Gene: 594905 XP_031749391.1 >> keeps symbol cyp27a1.3
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	* XB984297 [provisional:cyp27a1]: Entrez Gene: 100145331 XB-GENEPAGE-984297, XB-GENE-984298 AAI60539.1 >> becomes cyp27a1.1		* XB984297 [provisional:cyp27a1]: Entrez Gene: 100145331 XB-GENEPAGE-984297, XB-GENE-984298 AAI60539.1 >> becomes cyp27a1.1

	in X. laevis there are 3x ''cyp27a1 .L'' genes:		'''In X. laevis there are 3x ''cyp27a1 .L'' genes:'''

	* XB984297.L [provisional:cyp27a1] Entrez Gene:446987 XB-GENEPAGE-984297 XP_041432757.1		* XB984297.L [provisional:cyp27a1] Entrez Gene:446987 XB-GENEPAGE-984297 XP_041432757.1 >> becomes cyp27a1.1.L

	~~>> becomes cyp27a1.1.L~~
	* LOC121398019 , Gene ID: 121398019 (no Xb gene page) XP_041432320.1 >>becomes cyp27a1.2.L		* LOC121398019 , Gene ID: 121398019 (no Xb gene page) XP_041432320.1 >>becomes cyp27a1.2.L

	* cyp27a1 Entrez Gene: 100381137 (no Xb gene page) XP_041433231.1 >> becomes cyp27a1.3.L		* cyp27a1 Entrez Gene: 100381137 (no Xb gene page) XP_041433231.1 >> becomes cyp27a1.3.L

	in Xlaevis.S there is only 1 cyp27a1 candidate		'''In Xlaevis.S there is only 1 cyp27a1 candidate'''

	* LOC108702937 Gene ID: 108702937 XP_041434454.1 >>becomes cyp27a1.3.S)		* LOC108702937 Gene ID: 108702937 XP_041434454.1 >>becomes cyp27a1.3.S)

Christina: /* nomenclature changes */

2023-05-17T19:29:28Z

nomenclature changes

← Older revision		Revision as of 19:29, 17 May 2023
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	''Xenopus'' gene name changes from ''provisional ortholog of cytochrome P450 family 27 subfamily A member 1'' to ''cytochrome P450 family 27 subfamily A member 1 gene 1''		''Xenopus'' gene name changes from ''provisional ortholog of cytochrome P450 family 27 subfamily A member 1'' to ''cytochrome P450 family 27 subfamily A member 1 gene 1''

			We are using synteny and protein sequence alignmnet to pre-computed homology groups to infer orthology and inform naming of these genes. See below for more details.

			=synteny and orthology=

			There are 4 genes/loci tandemly duplicated that were provisionally annotated as ''cyp27a1'' in ''X. tropicalis'' v10 assembly:

			* LOC594905 (cyp27a1.3): Entrez Gene: 594905 XP_031749391.1 >> keeps symbol cyp27a1.3

			* XB1001094 [provisional:cyp27a1]: Entrez Gene 100496109, XB-GENEPAGE-1001094; XP_002933985.3 >> becomes [cyp27a1.4]

			* LOC116407844(cyp27a1): Entrez Gene: 116407844 XP_031749759.1 >> becomes cyp27a1.2

			* XB984297 [provisional:cyp27a1]: Entrez Gene: 100145331 XB-GENEPAGE-984297, XB-GENE-984298 AAI60539.1 >> becomes cyp27a1.1

			in X. laevis there are 3x ''cyp27a1 .L'' genes:

			* XB984297.L [provisional:cyp27a1] Entrez Gene:446987 XB-GENEPAGE-984297 XP_041432757.1

			>> becomes cyp27a1.1.L
			* LOC121398019 , Gene ID: 121398019 (no Xb gene page) XP_041432320.1 >>becomes cyp27a1.2.L
			* cyp27a1 Entrez Gene: 100381137 (no Xb gene page) XP_041433231.1 >> becomes cyp27a1.3.L

			in Xlaevis.S there is only 1 cyp27a1 candidate
			* LOC108702937 Gene ID: 108702937 XP_041434454.1 >>becomes cyp27a1.3.S)

			These analyses support naming these genes in ''Xenopus'' as ''cyp27a1, genes 1-4'' as indicated above.

			The suffixed serial number is designed to keep genes aligned compared to Human and mouse, so the primary ortholog ''cyp27a1 gene 1'' lies immediately adjacent to ''wnt6'', while the ''cyp27a1.3'' gene is between ''grsf1'' and ''plcd4''.

			Note: LOC121398283(unch)Gene ID: 121398283 XP_041433230.1 (matches 42 Ensembl seqs from Xenopus tropicalis but none have actual names- just ID numbers- so pretty sure this is NOT a CYP gene)


			Synteny pattern:

			Xtr.chr9 : slc22a3< prkag3< ttll4< cnppd1< abcb6< (NB: no sign of the CYP genes near ttll4) [Chr9:83051487..83122986] ////

			Xtr.chr9: plcd4> znf142< bcs1l> '''LOC594905(cyp27a1.3)>'''< grsf1> '''XB1001094[cyp27a1.4]<''' LOC116407845[Grsf1-like]> '''LOC116407844(cyp27a1.2)>''' '''XB984297[cyp27a1.1]<''' wnt6> wnt10a>

			Mouse CHR1: Stk36> Ttll4> '''Cyp27a1'''> Prkag3> > Wnt6> Wnt10a>

			Human: TTLL4> '''CYP27A1'''> PRKAG3> RPL23AP31> WNT6> WNT10A>


			In ''X. laevis'' the gene read in reverse are in this pattern:

			Xla.Chr9_10L: wnt10a.L< wnt6.L< XB984297.L[cyp27a1.1.L]> LOC121398019[cyp27a1.2.L]> grsf1.L> cyp27a1.3.L> LOC121398283(unch)> bcs1l.L< znf142.L<

			Xla.Chr9_10S: wnt10a.S< wnt6.S< grsf1.S< LOC108702937(cyp27a1.3.S)> plcd4.S< LOC108702939(ccr4not)


			DIOPT/EggNog matches the proteins for the Xtrop genes (seqs given below) to 3 groups of CYP genes with high confidence:

			1) ~890 seqs from ~200 species, including Mouse, Pteropus vampyrus (bat), Otolemur garnettii (lemur) and Cavia porcellus (guinea pig) seqs for Cyp27b1, Cyp24a1 and Cyp27a1 (ie including '''cyp27a1''' as suggested by the provisional name for XB1001094 and XB984297)

			2) Mouse genes called Cyp27b1, Cyp11b2, Cyp11b1, Cyp24a1, Cyp11a1, '''Cyp27a1'''

			and

			3) >1700 sequences in >800 species, and the majority of genes/proteins (where named) are called CYP11A1, '''not cyp27a1'''

Christina: /* loc100145331 */

2023-05-17T19:27:24Z

loc100145331

← Older revision		Revision as of 19:27, 17 May 2023
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	=~~loc100145331~~=		= cyp27a1 =
	This is the community wiki page for the gene ''~~loc100145331~~'' 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 ''cyp27a1'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
			= nomenclature changes =
			17MAY2023

			''Xenopus'' gene symbol changed from ''XB984297 [provisional:cyp27a1]'' to ''cyp27a1''

			''Xenopus'' gene name changes from ''provisional ortholog of cytochrome P450 family 27 subfamily A member 1'' to ''cytochrome P450 family 27 subfamily A member 1 gene 1''

imported>Xenbase: /* loc100145331 */Updated nomenclature, replaced: unnamed → loc100145331 (2)

2017-12-15T22:57:54Z

loc100145331: Updated nomenclature, replaced: unnamed → loc100145331 (2)

← Older revision		Revision as of 22:57, 15 December 2017
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	=~~unnamed~~=		=loc100145331=
	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 ''loc100145331'' 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