Genes Not Annotated in the Current Assemblies - Revision history

Ctelmer at 17:57, 5 April 2024

2024-04-05T17:57:30Z

← Older revision		Revision as of 17:57, 5 April 2024
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	<p>The ''P. miniata'' protein sequence, XP_038076971.1, was then BLASTed against ''S. purpuratus'' with a hit to scaffold 21, NW_022145607.1.</p>		<p>The ''P. miniata'' protein sequence, XP_038076971.1, was then BLASTed against ''S. purpuratus'' with a hit to scaffold 21, NW_022145607.1.</p>
	<p>The ''H. sapiens'' protein sequence, AAF82569.1, hit 2 regions of scaffold 21, NW_022145607.1.</p>		<p>The ''H. sapiens'' protein sequence, AAF82569.1, hit 2 regions of scaffold 21, NW_022145607.1.</p>
	<p>~~A hypothetical~~ ORF ~~was constructed from this location information, and then PCR amplified it from cDNA~~.</p>		<p>The ORF is located in the minus strand of scaffold 21 (Spur v5.0).</p>

	<p>~~ORF~~:ATG CCT GAT AAG AAA GAA ATT GAA GGT TCC GTG AAT GGA GAG GGG GAT GCA AAG CCC AAG TTG AAG CCG TGT TGT GCT TGT CCA GAA ACG AAG AAA GTT CGA GAT GCA TG\|C ATA ATG GAG AAT GGA GAA GCA GAG TGT GGT GAC CTT ATT GAA GCG CAT AAA GAA TGC ATG AGG TCT CTG GGG TTC AAC ATC TGA</p>		<p style="margin-left: 20px">Coding region of Exon 1: 25740048-25739939</p>
			<p style="margin-left: 20px">Coding region of Exon 2: 25735568-25735484</p>

	<p>*The exon junction is marked with "\|" (TG\|C to code for a cysteine residue).</p>		<p>A hypothetical ORF was constructed from this location information.</p>

	<p>~~'''Gene Location''' </p>~~		<p style="margin-left: 20px">ORF:ATG CCT GAT AAG AAA GAA ATT GAA GGT TCC GTG AAT GGA GAG GGG GAT GCA AAG CCC AAG TTG AAG CCG TGT TGT GCT TGT CCA GAA ACG AAG AAA GTT CGA GAT GCA TG\|C ATA ATG GAG AAT GGA GAA GCA GAG TGT GGT GAC CTT ATT GAA GCG CAT AAA GAA TGC ATG AGG TCT CTG GGG TTC AAC ATC TGA</p>
	~~<p>The~~ ORF ~~is located in the minus strand of scaffold 21 (in 5.0 version)~~</p>

	<p~~>Coding region of Exon 1~~: ~~25740048-25739939</p>~~		<p style="margin-left: 20px">*The exon junction is marked with a bar "\|" (TG\|C to code for a cysteine residue).</p>
	<p>~~Coding region of Exon 2: 25735568-25735484~~</p>

	<p>Primers were designed to amplify a 290 bp ~~amplicon~~ encompassing the entire 195 bp ORF. </p>		<p>Primers were designed to amplify, from cDNA, 290 bp encompassing the entire 195 bp ORF.</p>
	<p>This gel shows in lane 1, 100 bp molecular weight ladder, lane 2, NTC (no RT) and lane 3, 24 hpf cDNA. </p>		<p style="margin-left: 20px">This gel shows in lane 1, 100 bp molecular weight ladder, lane 2, NTC (no RT) and lane 3, 24 hpf cDNA.</p>

	<p style="margin-left: 20px">[[File:PCR_24hpf_cox17.jpg\|frameless\|400px]]</p>		<p style="margin-left: 20px">[[File:PCR_24hpf_cox17.jpg\|frameless\|400px]]</p>

Ctelmer at 17:38, 5 April 2024

2024-04-05T17:38:02Z

← Older revision		Revision as of 17:38, 5 April 2024
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	'''''S. purpuratus'''''		'''''S. purpuratus'''''

	''cox17''		'''''cox17'''''
	<p>This gene has been characterized in the lab of Kate Buckley by Nick Kraieski.</p>		<p>This gene has been characterized in the lab of Kate Buckley by Nick Kraieski.</p>
	<p>The ''cox17'' protein sequence was identified using BLAST of the human COX17 protein sequence against Echinoderm protein which returned a hit to ''P. miniata'' LOC119744863/XP_038076971.1 with the description cytochrome c oxidase copper chaperone-like.</p>		<p>The ''cox17'' protein sequence was identified using BLAST of the human COX17 protein sequence against Echinoderm protein which returned a hit to ''P. miniata'' LOC119744863/XP_038076971.1 with the description cytochrome c oxidase copper chaperone-like.</p>

Ctelmer at 17:37, 5 April 2024

2024-04-05T17:37:31Z

← Older revision		Revision as of 17:37, 5 April 2024
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	<p>Primers were designed to amplify a 290 bp amplicon encompassing the entire 195 bp ORF. </p>		<p>Primers were designed to amplify a 290 bp amplicon encompassing the entire 195 bp ORF. </p>
	<p>This gel shows in lane 1, 100 bp molecular weight ladder, lane 2, NTC and lane 3, 24 hpf cDNA. </p>		<p>This gel shows in lane 1, 100 bp molecular weight ladder, lane 2, NTC (no RT) and lane 3, 24 hpf cDNA. </p>

	<p style="margin-left: 20px">[[File:PCR_24hpf_cox17.jpg\|frameless\|400px]]</p>		<p style="margin-left: 20px">[[File:PCR_24hpf_cox17.jpg\|frameless\|400px]]</p>

Ctelmer at 17:35, 5 April 2024

2024-04-05T17:35:28Z

← Older revision		Revision as of 17:35, 5 April 2024
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	<p>Coding region of Exon 2: 25735568-25735484</p>		<p>Coding region of Exon 2: 25735568-25735484</p>

	Primers were designed to amplify a 290 bp amplicon encompassing the entire 195 bp ORF.		<p>Primers were designed to amplify a 290 bp amplicon encompassing the entire 195 bp ORF. </p>
	This gel shows in lane 1, 100 bp molecular weight ladder, lane 2, NTC and lane 3, 24 hpf cDNA		<p>This gel shows in lane 1, 100 bp molecular weight ladder, lane 2, NTC and lane 3, 24 hpf cDNA. </p>

	<p style="margin-left: 20px">[[File:PCR_24hpf_cox17.jpg\|frameless\|400px]]</p>		<p style="margin-left: 20px">[[File:PCR_24hpf_cox17.jpg\|frameless\|400px]]</p>

			<p>The amplicon was sequenced and confirmed the predicted ORF sequence.</p>

Ctelmer at 17:31, 5 April 2024

2024-04-05T17:31:24Z

← Older revision		Revision as of 17:31, 5 April 2024
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	<p>A hypothetical ORF was constructed from this location information, and then PCR amplified it from cDNA.</p>		<p>A hypothetical ORF was constructed from this location information, and then PCR amplified it from cDNA.</p>

	<p>ORF:~~ATGCCTGATAAGAAAGAAATTGAAGGTTCCGTGAATGGAGAGGGGGATGCAAAGCCCAAGTTGAAGCCGTGTTGTGCTTGTCCAGAAACGAAGAAAGTTCGAGATGCATG~~\|~~CATAATGGAGAATGGAGAAGCAGAGTGTGGTGACCTTATTGAAGCGCATAAAGAATGCATGAGGTCTCTGGGGTTCAACATCTGA~~		<p>ORF:ATG CCT GAT AAG AAA GAA ATT GAA GGT TCC GTG AAT GGA GAG GGG GAT GCA AAG CCC AAG TTG AAG CCG TGT TGT GCT TGT CCA GAA ACG AAG AAA GTT CGA GAT GCA TG\|C ATA ATG GAG AAT GGA GAA GCA GAG TGT GGT GAC CTT ATT GAA GCG CAT AAA GAA TGC ATG AGG TCT CTG GGG TTC AAC ATC TGA</p>

	<p>*The exon junction is marked with "\|" (TG\|C to code for a cysteine residue).		<p>*The exon junction is marked with "\|" (TG\|C to code for a cysteine residue).</p>

	Gene Location: The ORF is located in the minus strand of scaffold 21 (in 5.0 version)		<p>'''Gene Location''' </p>
			<p>The ORF is located in the minus strand of scaffold 21 (in 5.0 version)</p>

	Coding region of Exon 1: 25740048-25739939		<p>Coding region of Exon 1: 25740048-25739939</p>
	Coding region of Exon 2: 25735568-25735484		<p>Coding region of Exon 2: 25735568-25735484</p>

			Primers were designed to amplify a 290 bp amplicon encompassing the entire 195 bp ORF.
			This gel shows in lane 1, 100 bp molecular weight ladder, lane 2, NTC and lane 3, 24 hpf cDNA

	<p style="margin-left: 20px">[[File:PCR_24hpf_cox17.jpg\|frameless\|400px]]</p>		<p style="margin-left: 20px">[[File:PCR_24hpf_cox17.jpg\|frameless\|400px]]</p>

Ctelmer at 17:21, 5 April 2024

2024-04-05T17:21:00Z

Ctelmer at 17:17, 5 April 2024

2024-04-05T17:17:11Z

← Older revision		Revision as of 17:17, 5 April 2024
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	Coding region of Exon 2: 25735568-25735484		Coding region of Exon 2: 25735568-25735484

			[[File:PCR_24hpf_cox17.jpg]]

	'''''L. variegatus'''''		'''''L. variegatus'''''

Ctelmer at 17:10, 5 April 2024

2024-04-05T17:10:41Z

← Older revision		Revision as of 17:10, 5 April 2024
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	Coding region of Exon 1: 25740048-25739939		Coding region of Exon 1: 25740048-25739939
	Coding region of Exon 2: 25735568-25735484		Coding region of Exon 2: 25735568-25735484



	'''''L. variegatus'''''		'''''L. variegatus'''''

Ctelmer at 17:04, 5 April 2024

2024-04-05T17:04:46Z

← Older revision		Revision as of 17:04, 5 April 2024
Line 1:		Line 1:
	'''''S. purpuratus'''''		'''''S. purpuratus'''''

			''cox17''
			This gene has been characterized in the lab of Kate Buckley by Nick Kraieski.
			The ''cox17'' protein sequence was identified using BLAST of the human COX17 protein sequence against Echinoderm protein which returned a hit to ''P. miniata'' LOC119744863/XP_038076971.1 with the description cytochrome c oxidase copper chaperone-like.
			The ''P. miniata'' protein sequence, XP_038076971.1, was then BLASTed against ''S. purpuratus'' with a hit to scaffold 21, NW_022145607.1.
			The ''H. sapiens'' protein sequence, AAF82569.1, hit 2 regions of scaffold 21, NW_022145607.1.
			A hypothetical ORF was constructed from this location information, and then PCR amplified it from cDNA.

			ORF:ATGCCTGATAAGAAAGAAATTGAAGGTTCCGTGAATGGAGAGGGGGATGCAAAGCCCAAGTTGAAGCCGTGTTGTGCTTGTCCAGAAACGAAGAAAGTTCGAGATGCATG\|CATAATGGAGAATGGAGAAGCAGAGTGTGGTGACCTTATTGAAGCGCATAAAGAATGCATGAGGTCTCTGGGGTTCAACATCTGA

			*The exon junction is marked with "\|" (TG\|C to code for a cysteine residue).

			Gene Location: The ORF is located in the minus strand of scaffold 21 (in 5.0 version)

			Coding region of Exon 1: 25740048-25739939
			Coding region of Exon 2: 25735568-25735484

	'''''L. variegatus'''''		'''''L. variegatus'''''

Ctelmer: Created page with "'''''S. purpuratus''''' '''''L. variegatus''''' '''''P. miniata''''' '''''A. planci'''''"

2024-04-05T16:39:00Z

Created page with "'''''S. purpuratus''''' '''''L. variegatus''''' '''''P. miniata''''' '''''A. planci'''''"

New page

'''''S. purpuratus'''''

'''''L. variegatus'''''

'''''P. miniata'''''

'''''A. planci'''''

← Older revision		Revision as of 17:21, 5 April 2024
Line 2:		Line 2:

	''cox17''		''cox17''
	This gene has been characterized in the lab of Kate Buckley by Nick Kraieski.		<p>This gene has been characterized in the lab of Kate Buckley by Nick Kraieski.</p>
	The ''cox17'' protein sequence was identified using BLAST of the human COX17 protein sequence against Echinoderm protein which returned a hit to ''P. miniata'' LOC119744863/XP_038076971.1 with the description cytochrome c oxidase copper chaperone-like.		<p>The ''cox17'' protein sequence was identified using BLAST of the human COX17 protein sequence against Echinoderm protein which returned a hit to ''P. miniata'' LOC119744863/XP_038076971.1 with the description cytochrome c oxidase copper chaperone-like.</p>
	The ''P. miniata'' protein sequence, XP_038076971.1, was then BLASTed against ''S. purpuratus'' with a hit to scaffold 21, NW_022145607.1.		<p>The ''P. miniata'' protein sequence, XP_038076971.1, was then BLASTed against ''S. purpuratus'' with a hit to scaffold 21, NW_022145607.1.</p>
	The ''H. sapiens'' protein sequence, AAF82569.1, hit 2 regions of scaffold 21, NW_022145607.1.		<p>The ''H. sapiens'' protein sequence, AAF82569.1, hit 2 regions of scaffold 21, NW_022145607.1.</p>
	A hypothetical ORF was constructed from this location information, and then PCR amplified it from cDNA.		<p>A hypothetical ORF was constructed from this location information, and then PCR amplified it from cDNA.</p>

	ORF:ATGCCTGATAAGAAAGAAATTGAAGGTTCCGTGAATGGAGAGGGGGATGCAAAGCCCAAGTTGAAGCCGTGTTGTGCTTGTCCAGAAACGAAGAAAGTTCGAGATGCATG\|CATAATGGAGAATGGAGAAGCAGAGTGTGGTGACCTTATTGAAGCGCATAAAGAATGCATGAGGTCTCTGGGGTTCAACATCTGA		<p>ORF:ATGCCTGATAAGAAAGAAATTGAAGGTTCCGTGAATGGAGAGGGGGATGCAAAGCCCAAGTTGAAGCCGTGTTGTGCTTGTCCAGAAACGAAGAAAGTTCGAGATGCATG\|CATAATGGAGAATGGAGAAGCAGAGTGTGGTGACCTTATTGAAGCGCATAAAGAATGCATGAGGTCTCTGGGGTTCAACATCTGA

	*The exon junction is marked with "\|" (TG\|C to code for a cysteine residue).		<p>*The exon junction is marked with "\|" (TG\|C to code for a cysteine residue).

	Gene Location: The ORF is located in the minus strand of scaffold 21 (in 5.0 version)		Gene Location: The ORF is located in the minus strand of scaffold 21 (in 5.0 version)
Line 17:		Line 17:
	Coding region of Exon 2: 25735568-25735484		Coding region of Exon 2: 25735568-25735484

	[[File:PCR_24hpf_cox17.jpg]]		<p style="margin-left: 20px">[[File:PCR_24hpf_cox17.jpg\|frameless\|400px]]</p>



	'''''L. variegatus'''''		'''''L. variegatus'''''