https://wiki.echinobase.org/echinowiki/index.php?action=history&feed=atom&title=ECB-FEAT-23138504 2026-05-09T00:53:24Z Revision history for this page on the wiki MediaWiki 1.44.2 https://wiki.echinobase.org/echinowiki/index.php?title=ECB-FEAT-23138504&diff=3848&oldid=prev 2024-12-02T23:04:59Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:04, 2 December 2024</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>From Matt <del style="font-weight: bold; text-decoration: none;">Glasenappe</del>:</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>From Matt <ins style="font-weight: bold; text-decoration: none;">Glasenapp</ins>:</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The &#039;&#039;ebr1&#039;&#039; gene annotation in Spur_5.0 and Echinobase is 56,133 base pairs. The gene contains many (40+) exons spread across this region.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The &#039;&#039;ebr1&#039;&#039; gene annotation in Spur_5.0 and Echinobase is 56,133 base pairs. The gene contains many (40+) exons spread across this region.</div></td></tr> </table>

Ctelmer https://wiki.echinobase.org/echinowiki/index.php?title=ECB-FEAT-23138504&diff=3847&oldid=prev 2024-12-02T23:00:35Z

<p>Created page with &quot;From Matt Glasenappe: The &#039;&#039;ebr1&#039;&#039; gene annotation in Spur_5.0 and Echinobase is 56,133 base pairs. The gene contains many (40+) exons spread across this region. From previous cDNA sequencing, we know that the &#039;&#039;S. purpuratus&#039;&#039; &#039;&#039;ebr1&#039;&#039; mRNA is 12,074 base pairs (https://www.ncbi.nlm.nih.gov/nuccore/NM_214665.1) and the mature protein is 3,712 amino acids (11,136 base pairs) (https://www.ncbi.nlm.nih.gov/protein/47551295). However, looking at the Spur_5.0 gff/gtf anno...&quot;</p> <p><b>New page</b></p><div>From Matt Glasenappe:<br /> <br /> The &#039;&#039;ebr1&#039;&#039; gene annotation in Spur_5.0 and Echinobase is 56,133 base pairs. The gene contains many (40+) exons spread across this region.<br /> <br /> From previous cDNA sequencing, we know that the &#039;&#039;S. purpuratus&#039;&#039; &#039;&#039;ebr1&#039;&#039; mRNA is 12,074 base pairs (https://www.ncbi.nlm.nih.gov/nuccore/NM_214665.1) and the mature protein is 3,712 amino acids (11,136 base pairs) (https://www.ncbi.nlm.nih.gov/protein/47551295).<br /> <br /> However, looking at the Spur_5.0 gff/gtf annotation files, the sum of all the annotated exons is only 9,421 base pairs, and the combined length of all the annotated CDS is 8,486 base pairs.<br /> <br /> So, there appear to be many missing exons/CDS/bases in the Spur_5.0 gene prediction. The missing data appears to be at the 5&#039; end of the gene (&#039;&#039;ebr1&#039;&#039; is on the (-) strand). This is evident in the Echinobase CDS Gene Model, which does not begin with a start codon.</div>

Ctelmer