36c22bace06f07f8d4f59ef8a18659e926f9d410
jcasper
  Thu Apr 10 10:30:30 2025 -0700
Gencode V48 knownGene trackDb

diff --git src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
index 41dddeb16fd..c9de593f762 100644
--- src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
+++ src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
@@ -1,59 +1,60 @@
 track knownGene
 table knownGene
-shortLabel GENCODE V47
-longLabel GENCODE V47
+shortLabel GENCODE V48
+longLabel GENCODE V48
 #parent knownGeneArchive
 priority 1
 #priority 5
 visibility pack
 type bigGenePred knownGenePep knownGeneMrna
-bigDataUrl /gbdb/hg38/gencode/gencodeV47.bb
+bigDataUrl /gbdb/hg38/gencode/gencodeV48.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 knownGeneV47
+#externalDb knownGeneV48
 maxItems 50000
-html knownGeneV47
+html knownGeneV48
 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
 
-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
+# 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/knownGeneFastV47.ix
+searchTrix /gbdb/hg38/knownGeneFastV48.ix
 searchTrixContext on
 doPage 1