0f8c134e2fb577bb6cd39bc3d8233af4c3e0b122 lrnassar Mon May 4 08:52:48 2026 -0700 Fix unit spacing and entity encodings in NMD Escape descriptions per CR feedback. refs #33737 nmd.html / nmdEscTranscripts.html / newsarch.html (Apr. 22, 2026 entry): normalize 50bp/100bp/400nt to '50 bp' / '100 bp' / '400 nt' for consistent unit spacing; replace 3′UTR with plain 3'UTR; replace between numbers and units with a regular space. diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 590638ad2c8..0dd74d8cedd 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -166,40 +166,40 @@ 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.

The container track includes:

NMD escape ruleset tracks for MANE Select Plus Clinical, GENCODE V49, and NCBI RefSeq transcripts, applying four rules derived from Nagy & Maquat 1998 and Lindeboom et al. 2016:
- 50 bp rule – the entire last coding exon and the last - 50 bp of the penultimate coding exon. PTCs here have no downstream +
- 50 bp rule – the entire last coding exon and the last + 50 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.
- No-downstream-EJC rule – transcripts with a single coding - exon and no 3′UTR intron. No EJC is deposited downstream of the stop + exon and no 3'UTR intron. No EJC is deposited downstream of the stop codon, so any PTC in the coding sequence escapes NMD.
- Start-proximal 100 bp rule – the first 100 bp of +
- Start-proximal 100 bp rule – the first 100 bp of coding nucleotides. PTCs here escape NMD, likely through translation re-initiation at a downstream AUG codon.
- Long-exon rule – coding exons longer than 400 bp +
- Long-exon rule – coding exons longer than 400 bp (excluding the last coding exon). NMD efficiency drops in very long exons because the PTC is far from the downstream exon-exon junction.
NMDetective machine-learning prediction tracks from Lindeboom et al. 2016, providing continuous NMD efficiency scores for every possible PTC position.

We would like to thank Guido Neidhardt and Andreas Lahner for suggesting this track and providing feedback throughout its development, and the Decipher Genome Browser team for inspiring this type of visualization. We also would like to thank Max Haeussler and Lou Nassar for the creation and release of the UCSC Genome Browser tracks.