Genes Not Annotated in the Current Assemblies: Difference between revisions

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


''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>The ORF is located in the minus strand of scaffold 21 (Spur v5.0).</p>


ORF:ATGCCTGATAAGAAAGAAATTGAAGGTTCCGTGAATGGAGAGGGGGATGCAAAGCCCAAGTTGAAGCCGTGTTGTGCTTGTCCAGAAACGAAGAAAGTTCGAGATGCATG|CATAATGGAGAATGGAGAAGCAGAGTGTGGTGACCTTATTGAAGCGCATAAAGAATGCATGAGGTCTCTGGGGTTCAACATCTGA
<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>


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


Gene Location: The ORF is located in the minus strand of scaffold 21 (in 5.0 version)
<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 style="margin-left: 20px">*The exon junction is marked with a bar "|" (TG|C to code for a cysteine residue).</p>
 
<p>Primers were designed to amplify, from cDNA, 290 bp encompassing the entire 195 bp ORF.</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>The amplicon was sequenced and confirmed the predicted ORF sequence.</p>


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


[[File:PCR_24hpf_cox17.jpg]]


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

Latest revision as of 10:57, 5 April 2024

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.

The ORF is located in the minus strand of scaffold 21 (Spur v5.0).

Coding region of Exon 1: 25740048-25739939

Coding region of Exon 2: 25735568-25735484

A hypothetical ORF was constructed from this location information.

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

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

Primers were designed to amplify, from cDNA, 290 bp encompassing the entire 195 bp ORF.

This gel shows in lane 1, 100 bp molecular weight ladder, lane 2, NTC (no RT) and lane 3, 24 hpf cDNA.

The amplicon was sequenced and confirmed the predicted ORF sequence.


L. variegatus

P. miniata

A. planci

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