d10aba5d8ac8abc3655c599b9e421538a8a7e32e
lrnassar
  Wed Jul 22 10:56:04 2026 -0700
Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39).

Promote knownGene from the alpha-gated staging file to the released trackDb: bump
shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the
include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files.
refs #37395 #37393 #37391

diff --git src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
index bf38812bc29..7a6386aaa84 100644
--- src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
+++ src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
@@ -1,66 +1,65 @@
 include mouseDevTimecourse.ra
 
 # Local declaration so that local gold.html is picked up.
 track gold override
 html gold
 
 # Local declaration so that local gap.html is picked up.
 track gap override
 html gap
 
 #track chainNetCalJac4 override
 #chainMinScore 3000
 
 #track ensGene override
 #priority 2.02
 
 track xenoRefGene override
 visibility hide
 #priority 2.03
 
 track mrna override
 priority 2.1
 
 searchTable gold
 shortCircuit 1
 termRegex [ABCFLM][ACEFGHLNOPQRTUXY][AEKJQR0-9]+(\.[0-9_]+)?
 query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
 searchPriority 8
 
 #include evaSnp.ra
 include xenoRefGene.ra
 include trackDb.35way.ra
 include trackDb.chainNet.ra
 include trackDb.syntenicNet.ra alpha
 include trackDb.rbestNet.ra alpha
 include trackDb.gencode.ra
-include knownGene.ra beta,public
-include knownGene.alpha.ra alpha
+include knownGene.ra
 include knownGeneArchive.ra
 include reMap.ra
 
 include liftOverMm10.ra
 
 track vistaEnhancersBb
 shortLabel VISTA Enhancers
 longLabel VISTA Enhancers
 group regulation
 url https://enhancer.lbl.gov/vista/element?vistaId=$$
 type bigBed 9 +
 mouseOverField patternExpression
 urlLabel View on the VISTA Enhancer Browser
 bigDataUrl /gbdb/mm39/vistaEnhancers/vistaEnhancers.bb
 itemRgb on
 
 include ../refSeqComposite.mm10.mm39.ra
 
 include cytoBand.ra
 
 track ucscGenePfam override
 shortLabel Pfam in GENCODE
 longLabel Pfam Domains in GENCODE Genes
 html gencodePfam
 
 include vgp577way.trackDb.ra alpha
 
 include tad.ra alpha