XB-FEAT-940377 - Revision history

Christina: /* orthology and homology groups */

2023-05-22T19:02:54Z

orthology and homology groups

← Older revision		Revision as of 19:02, 22 May 2023
Line 39:		Line 39:
	note that:		note that:
	Ccna2, is cylin A2		Ccna2, is cylin A2

	Ccnf, is cyclin F		Ccnf, is cyclin F

	Ccna1,is cylin A1		Ccna1,is cylin A1
	Ccng1, ~~i s~~ cyclin G1
			Ccng1, is cyclin G1

	Ccno is cyclin O		Ccno is cyclin O

	SO we can confidently say this is another cyclin gene. The cyclins consist of 8 classes of cell cycle regulators, designated A-G, also Q & S ~~in invertebates~~, that regulate cyclin dependent kinases (CDKs)~~, so further~~ phylogenetic assessment is required to classify this protein.
			based on these results, we can confidently say this is another 'cyclin gene'. The cyclins consist of 8 classes of cell cycle regulators, designated A-G, also O, Q & S, that regulate cyclin dependent kinases (CDKs). Further phylogenetic assessment is required to fully classify this protein.

	=protein accession=		=protein accession=

Christina: /* ccnob.4 */

2023-05-22T19:01:16Z

ccnob.4

← Older revision		Revision as of 19:01, 22 May 2023
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	=ccnob.4=		=''ccnob.4''=
	This is the community wiki page for the gene ''ccnob.4'' 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 ''ccnob.4'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

Christina: /* nomencatrue changes */

2023-05-22T19:01:05Z

nomencatrue changes

← Older revision		Revision as of 19:01, 22 May 2023
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	=~~nomencatrue~~ changes=		=nomenclature changes=

	This gene is definately a cyclin, ~~and most likely~~ one of many ''cyclin o, b'' or ''cyclin o, b like'' genes.		This gene is definately a true '''cyclin''' gene, an is one of many ''cyclin o, b'' or ''cyclin o, b like'' genes annotated in 'Xenopus'.

	Thus we are provisonally updating its name from unnamed/ XB940377 to ''cyclin-o- b gene 4, ccnob.4'' as it is the 4th when counting left to right) in this string of 12 duplicated genes.		Thus we are provisonally updating its name from unnamed/ XB940377 to ''cyclin-o- b gene 4, ccnob.4'' as it is the 4th (when counting left to right) in this string of 12 duplicated genes. See synteny pattern below.

	=orthology and homology groups=		=orthology and homology groups=

Christina: /* unnamed */

2023-05-22T18:56:59Z

unnamed

← Older revision		Revision as of 18:56, 22 May 2023
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	=~~unnamed~~=		=ccnob.4=
	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 ''ccnob.4'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

	=synteny=		=synteny=

Christina: /* unnamed */

2023-05-22T18:56:40Z

unnamed

@@ Line 1: / Line 1: @@
 =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
+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.
 =orthology and homology groups=

Christina: /* unnamed */

2023-05-22T18:38:21Z

unnamed

← Older revision		Revision as of 18:38, 22 May 2023
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	=unnamed=		=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		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


			=orthology and homology groups=
			22MAY2023

			Using DIOPT/EGGNOG tool to assess the likely identity of this gene, it matches >2400 proteins from >400 species.


			The NCBI refSeq Protein accession for this''X. tropicalis'' gene matches 17 sequences for ''X.tropicalis'' in ENSMBL dtabse:

			17 seqs 8364.ENSXETP00000057169, 8364.ENSXETP00000015664, 8364.ENSXETP00000048888, 8364.ENSXETP00000021658, 8364.ENSXETP00000062384, 8364.ENSXETP00000023728, 8364.ENSXETP00000064034, 8364.ENSXETP00000063506, 8364.ENSXETP00000014000, 8364.ENSXETP00000023716, 8364.ENSXETP00000035701, 8364.ENSXETP00000009033, 8364.ENSXETP00000001012, 8364.ENSXETP00000034708, 8364.ENSXETP00000061262, 8364.ENSXETP00000017352, 8364.ENSXETP00000058282 ccni, 8364.ENSXETP00000015664, ccnb3, 8364.ENSXETP00000021658, 8364.ENSXETP00000062384, ccnb2, 8364.ENSXETP00000064034, 8364.ENSXETP00000063506, ccng2, LOC394448, ccnb1.2, ccni2, ccnb1, cntd2, 8364.ENSXETP00000061262, ccng1, ccno

			It also matches these Chicken/Gallus proteins: 7 seqs 9031.ENSGALP00000018658, 9031.ENSGALP00000039111, 9031.ENSGALP00000002633, 9031.ENSGALP00000016827, 9031.ENSGALP00000041819, 9031.ENSGALP00000041991, 9031.ENSGALP00000006605 CCNI, CCNI2, CCNG1, CCNG2, CCNB3, CCNO, CCNB2.

			and these proteinsin Mouse and rat.

			Mus musculus 4 seqs 10090.ENSMUSP00000029270, 10090.ENSMUSP00000058111, 10090.ENSMUSP00000111048, 10090.ENSMUSP00000029368 Ccna2, Ccnjl, Ccnf, Ccna1

			Rattus norvegicus 5 seqs 10116.ENSRNOP00000021156, 10116.ENSRNOP00000060445, 10116.ENSRNOP00000039931, 10116.ENSRNOP00000005171, 10116.ENSRNOP00000039779 Ccna2, Ccnf, Ccna1, Ccnjl, Apob


			note that:
			Ccna2, is cylin A2
			Ccnf, is cyclin F
			Ccna1,is cylin A1
			Ccng1, i s cyclin G1
			Ccno is cyclin O

			SO we can confidently say this is another cyclin gene. The cyclins consist of 8 classes of cell cycle regulators, designated A-G, also Q & S in invertebates, that regulate cyclin dependent kinases (CDKs), so further phylogenetic assessment is required to classify this protein.

			=protein accession=
			uncharacterized protein LOC100127658 [Xenopus tropicalis]

			NCBI Reference Sequence: NP_001106473.2

			>NP_001106473.2 uncharacterized protein LOC100127658 [Xenopus tropicalis]

			MEILSVGMRKRRREEEEEQEEEIISPGCSPEFKRAKPQGDLRGTSTPTAEEPVPEGEPWNTLTNLADALQ
			TFREYGEECYLYKKGLEGGYQLENFLENQKDINPTSWNHITTLMINVHRYLRLDFQTLCLGINFLERYVS
			CTPTNPDTLTRVGATCLYMAYKVAELRYPLPPKLFLPLFDYRMTPAEMRHLERTILRKLLFRLGVPTIDF
			FLEHFSLLRLTNQEECSPAQLKRAAKSLTAARGIAALCLNQHQDFYMHKPSLMALCCLNVADKIYSYNNP
			VKVAPTDYPEHQIEECMEKICHLVSIGHYFLHPLLPGVYPAIFPAFNPPTTRPAATPTNQHLPEGRERTP
			EVASTSRDTAGSQHLEMAERSSHSQDMEGAGYVLHNTYWPTDPYRQVYMHPYMPTPPYWHPYMPPVSYWH
			PYMHTLPYLHPYGYIFPY

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