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/makeDb/trackDb/human/hg38/nmd.ra src/hg/makeDb/trackDb/human/hg38/nmd.ra
index ec025b59342..3c92e8c8ec8 100644
--- src/hg/makeDb/trackDb/human/hg38/nmd.ra
+++ src/hg/makeDb/trackDb/human/hg38/nmd.ra
@@ -1,102 +1,103 @@
 track nmd
 shortLabel NMD Escape
 longLabel NMD Escape: Predicted regions where premature termination codons escape NMD
 group genes
 type bed 4
 visibility hide
 superTrack on
+pennantIcon New red ../goldenPath/newsarch.html#042226 "Released Apr. 22, 2026"
 
         #track nmdGencode
         #shortLabel NMD escape 50bp-100bp rule: Gencode transcripts
         #longLabel NMD escape 50bp-100bp rule: Gencode transcripts
         #parent nmd on
         #bigDataUrl /gbdb/hg38/nmd/knownGeneNmdProt.bb
         #visibility pack
         #type bigBed
         #dataVersion Gencode V49
         #skipFields decoratedItem,style,fillColor,glyph,mouseover
         #mouseOverField mouseover
         #priority 1
 
         track nmdEscGencode
         shortLabel NMD Escape Gencode
-        longLabel NMD escape 50bp/100bp/intronless ruleset: Gencode transcripts
+        longLabel NMD escape 50bp/100bp/intronless/400nt ruleset: Gencode transcripts
         parent nmd on
         bigDataUrl /gbdb/hg38/nmd/nmdEscRegions.bb
-        visibility pack
+        visibility dense
         type bigBed 9 +
         mouseOverField mouseover
         html nmdEscTranscripts
         # this could use a text file one day with the version
         dataVersion Gencode V49
         priority 1.5
 
         track nmdEscNcbiRefSeq
         shortLabel NMD Escape RefSeq
-        longLabel NMD escape 50bp/100bp/intronless ruleset: NCBI RefSeq transcripts
+        longLabel NMD escape 50bp/100bp/intronless/400nt ruleset: NCBI RefSeq transcripts
         parent nmd on
         bigDataUrl /gbdb/hg38/nmd/nmdEscNcbiRefSeq.bb
         visibility pack
         type bigBed 9 +
         mouseOverField mouseover
         html nmdEscTranscripts
         # this could use a text file one day with the version
         dataVersion GCF_000001405.40-RS_2025_08
         priority 1.6
 
         track nmdDetectiveA
         shortLabel NMDetective-A
         longLabel NMDetective-A: Random forest prediction of NMD efficiency (Lindeboom 2016)
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/NMDetectiveA.bw
         type bigWig
-        visibility full
+        visibility hide
         color 0,128,255
         autoScale off
         viewLimits -1:1
         maxHeightPixels 128:32:8
         html nmdDetective
         priority 2
 
         track nmdDetectiveB
         shortLabel NMDetective-B
         longLabel NMDetective-B: Decision tree prediction of NMD efficiency (Lindeboom 2016)
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/NMDetectiveB.bw
         type bigWig
-        visibility full
+        visibility hide
         color 0,128,255
         autoScale off
         viewLimits -1:1
         maxHeightPixels 128:32:8
         html nmdDetective
         priority 3
 
         track nmdDetectiveA_ptc
         shortLabel NMDetective-A PTC
         longLabel NMDetective-A: Random forest NMD efficiency for first out-of-frame PTC
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/nmdDectA-ptc.bw
         type bigWig
-        visibility full
+        visibility hide
         color 0,153,102
         autoScale off
         viewLimits -1:1
         maxHeightPixels 128:32:8
         html nmdDetective
         priority 4
 
         track nmdDetectiveB_ptc
         shortLabel NMDetective-B PTC
         longLabel NMDetective-B: Decision tree NMD efficiency for first out-of-frame PTC
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/nmdDectB-ptc.bw
         type bigWig
-        visibility full
+        visibility hide
         color 0,153,102
         autoScale off
         viewLimits -1:1
         maxHeightPixels 128:32:8
         html nmdDetective
         priority 5