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

diff --git src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
index 2819ba02dd1..ae7aa743fe9 100644
--- src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
+++ src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
@@ -1,190 +1,220 @@
 track knownGeneArchive
 superTrack on
 shortLabel GENCODE Archive
 longLabel GENCODE Archive
 group genes
 type bed 6 +
 html ../../knownGeneArchive
 
     track knownGeneV36
     #table knownGene
     shortLabel GENCODE V36
     longLabel GENCODE V36
     parent knownGeneArchive
     priority 8
     visibility hide
     type bigGenePred
     bigDataUrl /gbdb/hg38/gencode/gencodeV36.bb
     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 knownGeneV36
     maxItems 50000
     html knownGeneV36
     searchIndex name
     idXref kgAlias kgID alias
     intronGap 12
     defaultLinkedTables kgXref
 
 
     track knownGeneV38
     #table knownGene
     shortLabel GENCODE V38
     longLabel GENCODE V38
     parent knownGeneArchive
     priority 7
     visibility hide
     type bigGenePred
     bigDataUrl /gbdb/hg38/gencode/gencodeV38.bb
     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 knownGeneV38
     maxItems 50000
     html knownGeneV38
     searchIndex name
     idXref kgAlias kgID alias
     intronGap 12
     defaultLinkedTables kgXref
 
     track knownGeneV39
     #table knownGene
     shortLabel GENCODE V39
     longLabel GENCODE V39
     parent knownGeneArchive
     priority 6
     visibility hide
     type bigGenePred
     bigDataUrl /gbdb/hg38/gencode/gencodeV39.bb
     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 knownGeneV39
     maxItems 50000
     html knownGeneV39
     searchIndex name
     idXref kgAlias kgID alias
     intronGap 12
     defaultLinkedTables kgXref
 
     track knownGeneV43
     #table knownGene
     shortLabel GENCODE V43
     longLabel GENCODE V43
     parent knownGeneArchive
     priority 5
     visibility hide
     type bigGenePred
     bigDataUrl /gbdb/hg38/gencode/gencodeV43.bb
     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 knownGeneV43
     maxItems 50000
     html knownGeneV43
     searchIndex name
     idXref kgAlias kgID alias
     intronGap 12
     defaultLinkedTables kgXref
     squishyPackPoint 2
     squishyPackField rank
 
     track knownGeneV44
     #table knownGene
     shortLabel GENCODE V44
     longLabel GENCODE V44
     parent knownGeneArchive
     priority 4
     visibility hide
     type bigGenePred knownGenePep knownGeneMrna
     bigDataUrl /gbdb/hg38/gencode/gencodeV44.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 knownGeneV44
     maxItems 50000
     html knownGeneV44
     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>)
 
     track knownGeneV45
     #table knownGene
     shortLabel GENCODE V45
     longLabel GENCODE V45
     parent knownGeneArchive
     priority 3
     visibility pack
     type bigGenePred knownGenePep knownGeneMrna
     bigDataUrl /gbdb/hg38/gencode/gencodeV45.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 knownGeneV45
     maxItems 50000
     html knownGeneV45
     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>)
 
     track knownGeneV46
     #table knownGene
     shortLabel GENCODE V46
     longLabel GENCODE V46
     parent knownGeneArchive
     priority 2
     visibility pack
     type bigGenePred knownGenePep knownGeneMrna
     bigDataUrl /gbdb/hg38/gencode/gencodeV46.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 knownGeneV46
     maxItems 50000
     html knownGeneV46
     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>)
+
+    track knownGeneV47
+    release alpha
+    #table knownGene
+    shortLabel GENCODE V47
+    longLabel GENCODE V47
+    parent knownGeneArchive
+    priority 1.9
+    visibility pack
+    type bigGenePred knownGenePep knownGeneMrna
+    bigDataUrl /gbdb/hg38/gencode/gencodeV47.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
+    maxItems 50000
+    html knownGeneV47
+    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>)
+