00e086afbcb8296c6aef946c13eeb777f34bac02
max
  Mon May 11 07:03:10 2026 -0700
mei: new track for HGSVC3 mobile element insertions on hg38 and hs1

12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon
et al. 2025). Single shared trackDb stanza in human/mei.ra with $D
substitution. Okabe-Ito colors, INS-svLen:carrierCount item names,
inserted DNA in an insertSeq field. Cross-link to lrSv via
relatedTracks.ra. refs #37524

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+<h2>Description</h2>
+<p>
+This track collection shows <b>Mobile Element Insertions (MEIs)</b> in the
+human genome. Mobile elements are stretches of DNA that have copied themselves
+into new genomic locations during evolution, and a few families remain
+active enough to keep producing new insertions in the human population
+today. The three element classes responsible for almost all MEIs in
+humans are <b>Alu</b> (~300 bp SINE retrotransposons), <b>L1/LINE-1</b>
+(typically 6 kb autonomous retrotransposons) and <b>SVA</b> (composite
+elements of ~700-3000 bp). Polymorphic MEIs - sites where some individuals
+carry the inserted element while others do not - are an important source
+of structural variation, can disrupt or alter gene expression, and have
+been implicated in a number of human diseases.
+</p>
+
+<p>
+Tracks in this collection report MEI calls assembled from long-read
+genome sequencing. Items are colored by element class.
+</p>
+
+<h3>Available subtracks</h3>
+<ul>
+  <li><a href="hgTrackUi?g=meiHgsvc3">HGSVC3 65 MEIs</a> -
+      mobile element insertions identified in 65 diverse long-read
+      assembled samples relative to the reference assembly
+      (HGSVC3, Logsdon et al. 2025, <em>Nature</em>). Available on
+      both GRCh38/hg38 (12,642 MEIs) and T2T-CHM13/hs1 (12,919 MEIs).</li>
+</ul>
+
+<p>
+Related: <a href="hgTrackUi?g=lrSv">Long-read Structural Variants</a>
+contains the parent SV callsets from which several of these MEI tracks
+are derived. <a href="hgTrackUi?g=rmsk">RepeatMasker</a> shows
+all annotated mobile elements in the reference genome (regardless of
+whether they are polymorphic).
+</p>
+
+<h2>Display Conventions and Configuration</h2>
+<p>
+Each MEI is shown as a 1-bp anchor block at the position where the
+insertion attaches to the reference. Items are colored by element class:
+</p>
+<ul>
+  <li><span style="display:inline-block;background-color:#0072B2;width:18px;height:12px;vertical-align:middle;"></span> <b>Alu</b> &mdash; SINE (Short INterspersed Element)</li>
+  <li><span style="display:inline-block;background-color:#D55E00;width:18px;height:12px;vertical-align:middle;"></span> <b>L1</b> &mdash; LINE-1 (Long INterspersed Element-1)</li>
+  <li><span style="display:inline-block;background-color:#009E73;width:18px;height:12px;vertical-align:middle;"></span> <b>SVA</b> (SINE-VNTR-Alu) &mdash; composite retrotransposon</li>
+  <li><span style="display:inline-block;background-color:#CC79A7;width:18px;height:12px;vertical-align:middle;"></span> <b>HERVK</b> (Human Endogenous Retrovirus K) &mdash; endogenous retrovirus</li>
+  <li><span style="display:inline-block;background-color:#000000;width:18px;height:12px;vertical-align:middle;"></span> <b>snRNA</b> &mdash; small nuclear RNA</li>
+</ul>
+
+<p>
+Filters available on the subtrack configuration page allow restricting
+the displayed items by element class, insertion length, allele frequency,
+number of carrier samples, the number of MEI callers that supported the
+call, validation by L1ME-AID or PALMER, and overlap with reference
+segmental duplications and tandem repeats.
+</p>
+
+<h2>Data Access</h2>
+<p>
+Each subtrack has its own description page with details on file location,
+the autoSql schema, citation and download instructions.
+</p>
+
+<h2>References</h2>
+<p>
+Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo
+D <em>et al</em>.
+<a href="https://doi.org/10.1038/s41586-025-09140-6" target="_blank">
+Complex genetic variation in nearly complete human genomes</a>.
+<em>Nature</em>. 2025 Aug;644(8076):430-441.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40702183" target="_blank">40702183</a>; PMC: <a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12350169/" target="_blank">PMC12350169</a>
+</p>