e53713685bee07a91be62ffb8354d7478ce2ce7a
lrnassar
  Wed Apr 29 15:05:45 2026 -0700
NMD Escape: switch default to MANE+Gencode, add MANE to descriptions and news. refs #33737

- nmd.ra: nmdEscMane on/pack and nmdEscGencode on/dense as the new defaults;
nmdEscNcbiRefSeq off/hide. Fix "FIlter" typo in the RefSeq filterLabel.
- nmd.html and nmdEscTranscripts.html: list MANE alongside Gencode and RefSeq
("Three transcript sets" / "Three versions"), with a short description of
the MANE Select Plus Clinical set.
- newsarch.html (Apr. 22, 2026 entry): add MANE Select Plus Clinical to the
list of NMD escape ruleset tracks.

diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html
index 3a55fb9ae89..ad9d7a8b43c 100755
--- src/hg/htdocs/goldenPath/newsarch.html
+++ src/hg/htdocs/goldenPath/newsarch.html
@@ -69,31 +69,32 @@
 <p>
 We are pleased to announce a new
 <a href="/cgi-bin/hgTrackUi?db=hg38&g=nmd" target="_blank"><b>NMD Escape</b></a>
 track on the human genome assembly (GRCh38/hg38). This track collection displays
 regions where premature termination codons (PTCs) are predicted to escape
 nonsense-mediated mRNA decay (NMD), a cellular quality control mechanism that normally
 degrades transcripts with premature stop codons. Identifying NMD escape regions is
 important for interpreting the clinical significance of truncating variants under the
 ACMG/AMP PVS1 criterion.
 </p>
 <p>
 The container track includes:
 </p>
 <ul>
   <li><b>NMD escape ruleset</b> tracks for
-  <a href="/cgi-bin/hgTrackUi?db=hg38&g=nmdEscGencode" target="_blank">GENCODE V49</a> and
+  <a href="/cgi-bin/hgTrackUi?db=hg38&g=nmdEscMane" target="_blank">MANE Select Plus Clinical</a>,
+  <a href="/cgi-bin/hgTrackUi?db=hg38&g=nmdEscGencode" target="_blank">GENCODE V49</a>, and
   <a href="/cgi-bin/hgTrackUi?db=hg38&g=nmdEscNcbiRefSeq" target="_blank">NCBI RefSeq</a>
   transcripts, applying four rules derived from Nagy &amp; Maquat 1998 and Lindeboom
   et al. 2016:
     <ul>
       <li><b>50&nbsp;bp rule</b> &ndash; the entire last coding exon and the last
       50&nbsp;bp of the penultimate coding exon. PTCs here have no downstream
       exon-exon junction, or are too close to it, for NMD to be triggered.</li>
       <li><b>No-downstream-EJC rule</b> &ndash; transcripts with a single coding
       exon and no 3&#8242;UTR intron. No EJC is deposited downstream of the stop
       codon, so any PTC in the coding sequence escapes NMD.</li>
       <li><b>Start-proximal 100&nbsp;bp rule</b> &ndash; the first 100&nbsp;bp of
       coding nucleotides. PTCs here escape NMD, likely through translation
       re-initiation at a downstream AUG codon.</li>
       <li><b>Long-exon rule</b> &ndash; coding exons longer than 400&nbsp;bp
       (excluding the last coding exon). NMD efficiency drops in very long exons