c15a59c6ddc7428025519ec671af0a7d4649d7be
gperez2
  Thu Oct 30 16:50:26 2025 -0700
Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165

diff --git src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
deleted file mode 100644
index e1bddb9ca62..00000000000
--- src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
+++ /dev/null
@@ -1,60 +0,0 @@
-track knownGene
-table knownGene
-shortLabel GENCODE V49
-longLabel GENCODE V49
-#parent knownGeneArchive
-priority 1
-#priority 5
-visibility pack
-type bigGenePred knownGenePep knownGeneMrna
-bigDataUrl /gbdb/hg38/gencode/gencodeV49.bb
-downloadUrl.1 "GFF Format" https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.knownGene.gtf.gz
-baseColorDefault genomicCodons
-group genes
-isGencode3 on
-directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s
-labelFields geneName,name,geneName2,name2
-defaultLabelFields geneName
-itemRgb on
-#externalDb knownGeneV49
-maxItems 50000
-html knownGeneV49
-searchIndex name
-idXref kgAlias kgID alias
-intronGap 12
-defaultLinkedTables kgXref
-squishyPackPoint 1
-squishyPackField rank
-squishyPackLabel Number of transcripts shown at full height (ranked by <A href="#squishyPack">GENCODE transcript ranking</A>)
-
-searchName knownGeneAcc
-searchTable knownGene
-searchMethod exact
-searchType knownGene
-shortCircuit 1
-semiShortCircuit 1
-termRegex ENST[0-9.]+
-searchPriority 9
-
-# Note: Planning to remove the Previous track now that we have the Archive track set
-#track knownGeneOldV45
-#shortLabel Old UCSC Genes
-#longLabel Previous Version of UCSC Genes
-#group genes
-#visibility hide
-#color 82,82,160
-#type genePred
-#hgsid on
-#oldToNew kgV45ToKgV46
-#baseColorUseCds given
-#baseColorDefault genomicCodons
-
-searchName knownGeneFast
-searchTable knownGene
-searchType knownGeneFast
-shortCircuit 1
-searchPriority 1001
-searchTrix /gbdb/hg38/knownGeneFastV49.ix
-searchTrixContext on
-doPage 1
-