06d7be056190c14b85e71bc12523f18ea6815b5e
markd
  Mon Dec 7 00:50:29 2020 -0800
BLAT mmap index support merge with master

diff --git src/hg/makeDb/trackDb/mouse/trackDb.ra src/hg/makeDb/trackDb/mouse/trackDb.ra
index c86b04e..eaf133c 100644
--- src/hg/makeDb/trackDb/mouse/trackDb.ra
+++ src/hg/makeDb/trackDb/mouse/trackDb.ra
@@ -1,18 +1,35 @@
 # chainNet tracks
 include trackDb.chainNet.ra
 
+track knownGene
+shortLabel UCSC Genes
+longLabel UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics)
+group genes
+visibility pack
+color 12,12,120
+type genePred knownGenePep knownGeneMrna
+exonNumbers on
+idXref kgAlias kgID alias
+hgGene on
+hgsid on
+directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s
+baseColorUseCds given
+baseColorDefault genomicCodons
+defaultLinkedTables kgXref
+intronGap 12
+
 track cytoBandIdeo
 shortLabel Chromosome Band (Ideogram)
 longLabel Chromosome Bands Based on Microscopy (for Ideogram)
 group map
 visibility dense
 altColor 150,50,50
 type bed 4 +
 
 track cytoBand
 shortLabel Chromosome Band
 longLabel Chromosome Bands Based On Microscopy
 group map
 visibility hide
 altColor 150,50,50
 type bed 4 +
@@ -89,30 +106,31 @@
 type bed 12
 noScoreFilter .
 itemRgb on
 urlLabel KOMP Data Coordination Center: 
 url http://www.mousephenotype.org/data/genes/$$
 mgiUrlLabel MGI Report: 
 mgiUrl http://www.informatics.jax.org/marker/$$
 
 track acembly
 shortLabel AceView Genes
 longLabel AceView Gene Models With Alt-Splicing
 group genes
 visibility hide
 color 155,0,125
 type genePred acemblyPep acemblyMrna
+exonNumbers on
 autoTranslate 0
 url https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=mouse&l=$$
 itemClassTbl acemblyClass
 geneClasses main putative
 gClass_main 128,0,125
 gClass_putative 200,0,125
 urlLabel AceView Gene Summary:
 
 track slamHuman
 shortLabel Slam Human
 longLabel SLAM Gene Predictions Using Human/Mouse Homology
 group genes
 visibility hide
 color 100,50,0
 altColor 175,150,128
@@ -737,30 +755,33 @@
 group regulation
 visibility hide
 type expRatio
 expScale 4.0
 expStep 0.5
 url http://biogps.gnf.org/?query=$$
 urlLabel BioGPS:
 groupings gnfMouseAtlas3Groups
 
 track chainOtoGar1Best override
 priority 274.0
 
 track ensGene override
 visibility dense
 
+track uniprot override
+hideEmptySubtracks off
+
 #facebase microarray track
 track FaceBase24SampleTypesAvg
 shortLabel FaceBase 24STypes
 longLabel FaceBase 24 Sample Types Averaged
 #priority 79.1
 visibility hide
 type expRatio
 expScale 1.50
 expStep 0.1
 groupings facebase31_AllGroups
 group regulation
 
 #searchTable FaceBase_24Samp_Types_Averaged
 #searchType bed