3972ba54c468ace338d4a5578de1d20bf6c1f9ec
lrnassar
  Mon Apr 20 15:39:26 2026 -0700
Adding Rule 4 (long-exon rule, Lindeboom 2016) to NMD Escape tracks and releasing on Apr. 22, 2026. refs #33737

Script: added a fourth rule to genePredNmdEsc. Coding exons longer than
400 bp (excluding the last coding exon, which is already covered by the
50 bp rule) are flagged as NMD-escape regions. Rebuilt the Gencode and
NCBI RefSeq bigBed files.

trackDb:
- nmd.ra: appended "/400nt" to the nmdEsc longLabels, set nmdEscGencode
default visibility to dense so the track is visible in cart-reset
views, changed all four NMDetective subtracks from "visibility full"
to "visibility hide", updated pennantIcon to the Apr. 22, 2026
release date and anchor.
- nmd.html: mention long internal exons in the overview description,
update the rule count from three to four.
- nmdEscTranscripts.html: add the long-exon rule to the rule list and
color legend (gold, #FFD700), expand the Background section with
mechanisms for the intronless, start-proximal, and long-exon rules,
correct the 50 bp rule description to include the entire last coding
exon, fix Lindeboom 2016 author initials (RG -> RGH).

News:
- newsarch.html: add the 2026-04-22 NMD Escape news entry covering all
four rules, with acknowledgements to Guido Neidhardt and Andreas
Lahner for suggesting the track and the Decipher Genome Browser team
for inspiring the visualization.
- indexNews.html: add the front-page news link.

makedoc:
- nmd.txt: dated note for the Rule 4 rebuild.

diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html
index b717aa320d2..258c8360477 100755
--- src/hg/htdocs/indexNews.html
+++ src/hg/htdocs/indexNews.html
@@ -1,55 +1,55 @@
 <!-- News item template:
 
   <div class="jwNewsItem jwSingleLineRightColumn">
   __DATE__ -
   <a href="goldenPath/newsarch.html#__MMDDYY__">
   __HEADLINE__
   </a></div>
 
   1. Replace __DATE__ with something like 'Apr. 29, 2016'
   2. Replace __MMDDYY__ with something like '042916'
   3. Replace __HEADLINE__ with the news item's headline like 'Awesome New Feature'
      Be sure to follow the CORRECT STYLE for the headline: 
         - capitalize first letter of headline - no other caps except for proper nouns and acronyms
         - check that headline char count doesn't exceed the line length (otherwise will truncate)
         - approx 50 characters
   4. Drop the bottom item from the list (limit of 6 items at a time)
 
                                                 | <- Cutoff point
 -->
+  <div class="jwNewsItem jwSingleLineRightColumn">
+  Apr. 22, 2026 -
+  <a href="goldenPath/newsarch.html#042226">
+  New NMD Escape tracks on hg38
+  </a></div>
+
   <div class="jwNewsItem jwSingleLineRightColumn">
   Apr. 10, 2026 -
   <a href="goldenPath/newsarch.html#041026">
   New Short Tandem Repeat (STR) tracks on hg38
   </a></div>
 
   <div class="jwNewsItem jwSingleLineRightColumn">
   Apr. 3, 2026 -
   <a href="goldenPath/newsarch.html#040326">
   New heatmap display mode for bigBed tracks
   </a></div>
 
   <div class="jwNewsItem jwSingleLineRightColumn">
   Mar. 28, 2026 -
   <a href="goldenPath/newsarch.html#032826">
   New UCSC Genome Browser glossary page
   </a></div>
 
   <div class="jwNewsItem jwSingleLineRightColumn">
   Mar. 17, 2026 -
   <a href="goldenPath/newsarch.html#031726">
   Updated superTrack configuration page
   </a></div>
 
   <div class="jwNewsItem jwSingleLineRightColumn">
   Mar. 16, 2026 -
   <a href="goldenPath/newsarch.html#031626">
   Human Methylation Atlas Summary and Signals tracks for hg38/hg19
   </a></div>
 
-  <div class="jwNewsItem jwSingleLineRightColumn">
-  Mar. 13, 2026 -
-  <a href="goldenPath/newsarch.html#031326">
-  gnomAD v4 Exome and v3 Genome coverage tracks for hg38
-  </a></div>
-