0b88e0fa63875f67aaf77a4fefc4038ee6caee58
hiram
  Fri Sep 11 16:09:16 2026 -0700
meat puppet here, claude didn't like the name mismatch, oh well, whatever, it isn't important what the name is here refs #38224

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+<h2>Description</h2>
+
+<p>
+This track represents fixed retrocopies identified and annotated by
+<a href="https://www.rcpediadb.org/" target="_blank">RCPedia pipeline</a>.
+Retrocopies are genomic copies generated by reverse transcription and
+reintegration of processed messenger RNAs (mRNAs). Because they originate
+from processed transcripts, retrocopies generally lack introns and may
+retain complete or partial open reading frames from their parental genes.
+</p>
+
+<p>
+RCPedia contains more than 219,000 fixed retrocopies across 44 eukaryotic
+species, providing information on genomic coordinates, parental genes,
+genomic context, sequence, conservation and expression.
+</p>
+
+<h2>Display Conventions and Configuration</h2>
+
+<p>
+Each feature represents a fixed retrocopy locus in the corresponding
+reference genome. The track coordinates follow the
+<a href="https://genome.ucsc.edu/" target="_blank">UCSC Genome Browser</a>
+0-based coordinate system.
+</p>
+
+<ul>
+    <li><b>Retrocopy:</b> genomic location of the fixed retrocopy.</li>
+</ul>
+
+<h2>Methods</h2>
+
+<p>
+Fixed retrocopies were identified by aligning RefSeq mRNAs to reference
+genomes using LAST, followed by filtering based on alignment quality,
+genomic distance from the parental gene, exon-exon junctions and repetitive
+sequence content. Candidate loci were further filtered to reduce false
+positives arising from duplicated genes and large gene families.
+</p>
+
+<p>
+For detailed methodology, please refer to the
+<a href="https://www.rcpediadb.org/pages/faq" target="_blank">
+RCPedia FAQ</a>.
+</p>
+
+<h2>Credits</h2>
+
+<p>
+RCPedia pipeline was developed by the Galante Lab and collaborators.
+</p>
+
+<p>
+For questions or additional information, please visit the
+<a href="https://www.rcpediadb.org/pages/contact" target="_blank">
+RCPedia Contact &amp; Credits</a> page.
+</p>
+
+<h2>References</h2>
+
+<p>
+Conceição HB, Mercuri RLV, de Castro MPM, Ohara DT, Guardia GDA,
+Galante PAF. RCPedia: A global resource for studying and exploring
+retrocopies in diverse species. <i>Bioinformatics</i>. 2024;40(9):btae530.
+<a href="https://doi.org/10.1093/bioinformatics/btae530" target="_blank">
+doi:10.1093/bioinformatics/btae530</a>.
+</p>