395a8efc6994c18a3b0bdfcee82217ff9d78b739 lrnassar Wed Apr 22 12:54:59 2026 -0700 Expand NMD Escape newsarch rules into sub-bullets. refs #33737 Break the four-rule summary into individual sub-bullets under the ruleset line so each rule is visible at a glance. diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 1e6d0beaeed..3a55fb9ae89 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -72,35 +72,46 @@ 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.

The container track includes:

NMD escape ruleset tracks for GENCODE V49 and NCBI RefSeq transcripts, applying four rules derived from Nagy & Maquat 1998 and Lindeboom - et al. 2016: the 50 bp last-junction rule, the no-downstream-EJC rule - (transcripts with a single coding exon and no 3′UTR intron), the - start-proximal 100 bp rule, and the long-exon rule (PTCs in coding exons - longer than 400 bp, which show reduced NMD efficiency due to the large - distance between the stalled ribosome and the downstream EJC).

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 + codon, so any PTC in the coding sequence escapes NMD.
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 + (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.

Apr. 10, 2026 New Short Tandem Repeat (STR) tracks on hg38

We are pleased to announce several new Short Tandem Repeat (STR) tracks on the