XB-FEAT-5768883 - Revision history

Christina: /* orthology analysis */

2023-04-26T18:14:51Z

orthology analysis

← Older revision		Revision as of 18:14, 26 April 2023
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	NCBI/COBALT alignment of the human, model ~~vertebrates~~ and these ''Xenopus'' proteins shows that X.laevis and X.trop proteins [NP_001087818.1 and XP_002933698.2] are much shorter and have no significant similarity to the other vertebrate NEFH genes, although they are almost identical to each other.		NCBI/COBALT alignment of the human, Xtrop and model vertebrate NEFH genes and these uncharacterized ''Xenopus'' proteins shows that X.laevis and X.trop proteins [NP_001087818.1 and XP_002933698.2] are much shorter and have no significant similarity to the other vertebrate NEFH genes, although they are almost identical to each other.

	Accessions used in COBALT MSA:		Accessions used in COBALT MSA:

	NP_066554.2 neurofilament heavy polypeptide [Homo sapiens]		NP_066554.2 neurofilament heavy polypeptide [Homo sapiens] (1020aa)

	XP_002933698.2 neurofilament heavy polypeptide [Xenopus tropicalis]		XP_002933698.2 neurofilament heavy polypeptide [Xenopus tropicalis] (626aa)

	NP_001087818.1 uncharacterized protein LOC447642 [Xenopus laevis]		NP_001087818.1 uncharacterized protein LOC447642 [Xenopus laevis](644aa)

	NP_035034.2 neurofilament heavy polypeptide [Mus musculus]		NP_035034.2 neurofilament heavy polypeptide [Mus musculus] (1090aa)

	NP_036739.2 neurofilament heavy polypeptide [Rattus norvegicus]		NP_036739.2 neurofilament heavy polypeptide [Rattus norvegicus] (1064aa)

	XP_040541104.1 neurofilament heavy polypeptide isoform X2 [Gallus gallus]		XP_040541104.1 neurofilament heavy polypeptide isoform X2 [Gallus gallus] (939aa)

	XP_002934335.2 neurofilament heavy polypeptide [Xenopus tropicalis]		XP_002934335.2 neurofilament heavy polypeptide [Xenopus tropicalis] (1125aa)

	=Human NEFH protein=		=Human NEFH protein=

Christina: /* orthology analysis */

2023-04-26T18:11:23Z

orthology analysis

← Older revision		Revision as of 18:11, 26 April 2023
Line 12:		Line 12:


	NCBI/COBALT alignment of the human and these ''Xenopus'' proteins shows that X.laevis and X.trop proteins [NP_001087818.1 and XP_002933698.2] are much shorter and have no significant similarity to the other vertebrate NEFH genes, although they are almost identical to each other.		NCBI/COBALT alignment of the human, model vertebrates and these ''Xenopus'' proteins shows that X.laevis and X.trop proteins [NP_001087818.1 and XP_002933698.2] are much shorter and have no significant similarity to the other vertebrate NEFH genes, although they are almost identical to each other.

			Accessions used in COBALT MSA:

			NP_066554.2 neurofilament heavy polypeptide [Homo sapiens]

			XP_002933698.2 neurofilament heavy polypeptide [Xenopus tropicalis]

			NP_001087818.1 uncharacterized protein LOC447642 [Xenopus laevis]

			NP_035034.2 neurofilament heavy polypeptide [Mus musculus]

			NP_036739.2 neurofilament heavy polypeptide [Rattus norvegicus]

			XP_040541104.1 neurofilament heavy polypeptide isoform X2 [Gallus gallus]

			XP_002934335.2 neurofilament heavy polypeptide [Xenopus tropicalis]

	=Human NEFH protein=		=Human NEFH protein=

Christina: /* orthology analysis */

2023-04-26T18:08:52Z

orthology analysis

← Older revision		Revision as of 18:08, 26 April 2023
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	=orthology analysis=		=orthology analysis=
	DIOPT/EggNog analysis finds no matches/homology groups for the X.laevis and X.trop proteins [NP_001087818.1 and XP_002933698.2] ~~but matches the human NEFH to 100+ other species proteins with high confidence.~~		DIOPT/EggNog analysis finds no matches/homology groups for the X.laevis and X.trop proteins [NP_001087818.1 and XP_002933698.2]

	~~Human gene [Gene ID: 4744] is called~~ NEFH ~~neurofilament heavy chain~~.		DIOPT/EggNog matches the human NEFH to 100+ other species proteins with high confidence.

			DIOPT/EggNog confirms that the 3rd Xenopus accession, XP_002934335.2, is also quickly matched to the other vertebrate NEFH homolog groups.

	NCBI/COBALT alignment of the human and ''Xenopus'' proteins		NB: the Human gene [Gene ID: 4744] is called NEFH neurofilament heavy chain.


			NCBI/COBALT alignment of the human and these ''Xenopus'' proteins shows that X.laevis and X.trop proteins [NP_001087818.1 and XP_002933698.2] are much shorter and have no significant similarity to the other vertebrate NEFH genes, although they are almost identical to each other.

	=Human NEFH protein=		=Human NEFH protein=

Christina: /* NCBI protein accessions */

2023-04-26T18:04:39Z

NCBI protein accessions

← Older revision		Revision as of 18:04, 26 April 2023
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	ADVSGSAPLPIIEDKIESHVTLAEESVDEKIPSDVQIVDKHVTLNGLPSKEEIKVKENLENGSNHAISEL		ADVSGSAPLPIIEDKIESHVTLAEESVDEKIPSDVQIVDKHVTLNGLPSKEEIKVKENLENGSNHAISEL
	NGQNEKHEIEVCNE		NGQNEKHEIEVCNE

			neurofilament heavy polypeptide [Xenopus tropicalis]
			NCBI Reference Sequence: XP_002934335.2
			GenPept Identical Proteins Graphics
			>XP_002934335.2 neurofilament heavy polypeptide [Xenopus tropicalis]
			MLSFSLERSMGPVTYRRPPGDHYLRSSSVSLTHSGSSSFQSHSRSRRSAPSYSESPEPSNGPRDEKEALQ
			GLNERFAGYIEKVRRLEEQNRSLQQEATALRKQQAGISAIGQLYEREIRDMRNQLLKINSENGQEQLERD
			RLSEDIELLRLKTQEEERLKEEALNSERALRQFLQECSLDREQLGRKVQSLEDEAAHLCKCHQEDVEEMI
			QQIHGSQVTTQQMGEVPSLELASALKDIRSQLEGHIGKNNLQTQGWFQAQLNKLNEASQVNTQAIRSASD
			EITNYRHQLQSQVTQLEVLKSSQQSLERQCLDMEDRHQAEMASYQDTLQQLDNELRTTKWEMAAQIREYQ
			DLLNVKMALDIEIAAYRKLLEGEECRLGSGFDPFSFDEKIPRGPSTPKHIKVKKEEKIKIVEKSDKETVI
			VEKQTEETHVTEEVTEEDEVVGSPEEEQEEEKEKTPSEEQEEIESKEEEQGEEKDEENEEEHDTVEEEEE
			TKDKQGEDSADTEEGEGEKAGETKDEELDKKEEKKPTKATDKGPELKIKEGEPKEKSDKEEGKGEQKSKE
			DKPVKKEEKEEPAKKEDKAYKEGKGEATKTEDEAAVKKEKKGEPTKKEEKEPAKKNEQTGIEEKPEPAKK
			KEKEEPKKEEKKEAAKTEDKKEQTRADEKPEPAKKEEKGEQIKKDQKEPAKKEEKVDSKKKEEKDAAKKE
			EKMEQTKTVEKPDLAKKGEKGESKTEEKPKEDEPTKKEPASKEEKKEQAKTEEKPEPVKKEEKGEPKAKE
			QKEPVKKEEKTEPVKKDEGKESSKKDVPKKEESAKKDDKEIAKKEEKGAAQKDEELSKKDEPMKKEEKQE
			PAKKEEPSKKEEKKEPSTKVVPTEEEQNLPEKVEKKESAKKEEKKQPVTEEKKEAPKKEVAADKKEDKET
			TKKETKESTKKEDKPESAKKEDSPKIDEKKETPKKEEKKEPTKKEEPSKQEEKTEPPKKEVKDQVKDDKE
			PAKKEEKSPKAEVKTPSKEPEKQPKLDGKPAKDDVKKSAKVEESKPATDEEKIPSKVEKPPKTEEKKESS
			KDNEPLKKAEKEPTKKITEVTKIEEKSKEDSQKITKKDPVGGNTQNVKPKTEKIEKSSGTDQLESESTQG
			AKSEK

Christina: /* orthology analysis */

2023-04-26T18:00:13Z

orthology analysis

← Older revision		Revision as of 18:00, 26 April 2023
Line 3:		Line 3:

	=orthology analysis=		=orthology analysis=
	DIOPT/EggNog analysis finds no matches/homology groups for the X.laevis and X.trop proteins [NP_001087818.1 and XP_002933698.2]		DIOPT/EggNog analysis finds no matches/homology groups for the X.laevis and X.trop proteins [NP_001087818.1 and XP_002933698.2] but matches the human NEFH to 100+ other species proteins with high confidence.

	Human gene [Gene ID: 4744] is called NEFH neurofilament heavy chain.		Human gene [Gene ID: 4744] is called NEFH neurofilament heavy chain.


			NCBI/COBALT alignment of the human and ''Xenopus'' proteins

	=Human NEFH protein=		=Human NEFH protein=

Christina: /* orthology analysis */

2023-04-26T17:57:24Z

orthology analysis

@@ Line 3: / Line 3: @@
 =orthology analysis=
-DIOPT/EggNog analysis finds no matches/homology groups for the X.laevis and  X.trop proteins [ XP_002933698.2]
+DIOPT/EggNog analysis finds no matches/homology groups for the X.laevis and  X.trop proteins [NP_001087818.1 and XP_002933698.2]
 Human gene [Gene ID: 4744] is called NEFH neurofilament heavy chain.
 =NCBI protein accessions=

Christina: /* orthology analysis */

2023-04-26T17:55:33Z

orthology analysis

← Older revision		Revision as of 17:55, 26 April 2023
Line 3:		Line 3:

	=orthology analysis=		=orthology analysis=
	DIOPT/EggNog analysis finds no matches/homology groups for the. ~~Xtrop protein~~ XP_002933698.2		DIOPT/EggNog analysis finds no matches/homology groups for the X.laevis and X.trop proteins [ XP_002933698.2]

	~~Human gene [Gene ID: 4744~~] ~~is called NEFH neurofilament heavy chain.~~

			Human gene [Gene ID: 4744] is called NEFH neurofilament heavy chain.

	=NCBI protein accessions=		=NCBI protein accessions=

Christina: /* X. tropicalis protein */

2023-04-26T17:54:54Z

X. tropicalis protein

← Older revision		Revision as of 17:54, 26 April 2023
Line 8:		Line 8:


	=~~X. tropicalis~~ protein=		=NCBI protein accessions=
	>XP_002933698.2 neurofilament heavy polypeptide [Xenopus tropicalis]		>XP_002933698.2 neurofilament heavy polypeptide '''[Xenopus tropicalis]
			'''
	MGAKFSKKKKSYCLGAGKDGESTETTEVEQKETETQSGQKDAVVPKEETPQPDKTVANGTSEEQNPQAEK		MGAKFSKKKKSYCLGAGKDGESTETTEVEQKETETQSGQKDAVVPKEETPQPDKTVANGTSEEQNPQAEK
	QLDLETKPDEPTKDDQNAGPVSENNLESNKAETDETPQEKAESNCLSAVQEQSSEVAKGDSSSKAQTAPP		QLDLETKPDEPTKDDQNAGPVSENNLESNKAETDETPQEKAESNCLSAVQEQSSEVAKGDSSSKAQTAPP
Line 20:		Line 20:
	DLESEDQSSDKHSLEQEKSVEEESKAVVDVVQETLNQEQRDSNHISSSPVDKQDISGSAPQPLTEDTIEN		DLESEDQSSDKHSLEQEKSVEEESKAVVDVVQETLNQEQRDSNHISSSPVDKQDISGSAPQPLTEDTIEN
	HATLAEESVHEKILADVQIVDKHVTLNGLPSKEEIKVKENVENGSNHSISDLNGQNENHEIEVCNE		HATLAEESVHEKILADVQIVDKHVTLNGLPSKEEIKVKENVENGSNHSISDLNGQNENHEIEVCNE

			>NP_001087818.1 uncharacterized protein LOC447642 ['''Xenopus laevis]'''
			MGAKFSKKKKSYCLGAGKDGESTETTEVEQKGTETQNGQKDAVAPKEETPQPDKPVGNGTSEEQKPQVEK
			QSDPETKQDEPTKDEQNAISMPENNLESNKAEAEETPQEKTESNCSSAVQEHSSEVAKDDRSNLTQKAPP
			SHEPEKTEEEQLNKNLDSSSDPPCDAVAEPEVKQSSVEKHQVIVQPVDHLQEATVKEAAEEHPPASQLTA
			EKENQLVTDIDPIPENTVPLPEEVPEVVVTIADNNEKVTTPVIMTESSPMQMQTPNVAEISKLEEESKQS
			LEGQSPLPEHEIPEPVQTPQPIAQTEKPDELPVLATPEPVAEQLVPLVDPVSEEIESLEHPQAHMPLTTE
			PATEKELVDLEATPQELKSVAEPENPDHVAEPVTSEGLQQSQTETGKVCENETKQSVQEDEQPQPKTSEV
			PEQPAHDEVNTANQESSTFGNKESEVLCSQSSDVSSNDKPELISPKQEICTEIPSEVSPLQTLQDSAAEL
			PVPLEPNAHGMKLEDQSSDKHSVEQEKCVEEENKAEVDVVQETLNQEPIDGNHTASSPTAVQDTISDPST
			ADVSGSAPLPIIEDKIESHVTLAEESVDEKIPSDVQIVDKHVTLNGLPSKEEIKVKENLENGSNHAISEL
			NGQNEKHEIEVCNE

Christina: /* X. tropicalis protein */

2023-04-26T17:53:28Z

X. tropicalis protein

← Older revision		Revision as of 17:53, 26 April 2023
Line 8:		Line 8:


	=~~Xtropicalis~~ protein=		=X. tropicalis protein=
	>XP_002933698.2 neurofilament heavy polypeptide [Xenopus tropicalis]		>XP_002933698.2 neurofilament heavy polypeptide [Xenopus tropicalis]

Christina: /* loc100498624 */

2023-04-26T17:53:08Z

loc100498624

← Older revision		Revision as of 17:53, 26 April 2023
Line 1:		Line 1:
	=~~loc100498624~~=		= ''XB5768883'' =
	This is the community wiki page for the gene ''~~loc100498624~~'' 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 ''XB5768883'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

			=orthology analysis=
			DIOPT/EggNog analysis finds no matches/homology groups for the. Xtrop protein XP_002933698.2

			Human gene [Gene ID: 4744] is called NEFH neurofilament heavy chain.


			=Xtropicalis protein=
			>XP_002933698.2 neurofilament heavy polypeptide [Xenopus tropicalis]

			MGAKFSKKKKSYCLGAGKDGESTETTEVEQKETETQSGQKDAVVPKEETPQPDKTVANGTSEEQNPQAEK
			QLDLETKPDEPTKDDQNAGPVSENNLESNKAETDETPQEKAESNCLSAVQEQSSEVAKGDSSSKAQTAPP
			SQEPEKTGEEQLNKDLVSSSDPPCAAVAEPEVIQSVSVEQQVTVQQVDHLQEATVKEAAEELPPASKLAA
			EEENQLVTEHSMSENYVPLPEVVPEVVSNSEVDNKEKDTTPVFMPESSTKQIAANVPEIRISVEEPKQSF
			EDQGPLPETDIPEPVQTPQLTEEVEEPDEVPVLAASEPAAEQLVPLADTVSSETESLGHPQVHMPLTTVP
			AHEKDAESAPQELKSVAEPEDHIAEAVTSEAPQQSKSETEVCEKETKQDAQEDDQQAKTSEVPEQPAHDE
			KNNANQESTTFDNKEEALCPESSDVVSNEQPKLTSPEQQICTEIASEVTPLQNLQDCAAELSVPLEPNAN
			DLESEDQSSDKHSLEQEKSVEEESKAVVDVVQETLNQEQRDSNHISSSPVDKQDISGSAPQPLTEDTIEN
			HATLAEESVHEKILADVQIVDKHVTLNGLPSKEEIKVKENVENGSNHSISDLNGQNENHEIEVCNE