df8c8dcd64bc7d71f9711df629b6d0178d6fa26f
max
  Tue Feb 25 13:33:12 2020 -0800
trying to reduce the confusion in docs between refseq select and MANE, refs #24787

diff --git src/hg/makeDb/trackDb/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra
index 134f5c1..55c0213 100644
--- src/hg/makeDb/trackDb/refSeqComposite.ra
+++ src/hg/makeDb/trackDb/refSeqComposite.ra
@@ -78,73 +78,63 @@
         baseColorUseCds table ncbiRefSeqCds
         idXref ncbiRefSeqLink mrnaAcc name
         color 0,0,0
         pepTable ncbiRefSeqPepTable
 
         track ncbiRefSeqGenomicDiff
         parent refSeqComposite off
         priority 6
         type bigBed 9 +
         skipEmptyFields on
         shortLabel RefSeq Diffs
         longLabel Differences between NCBI RefSeq Transcripts and the Reference Genome
         bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb
         itemRgb on
 
-        track ncbiRefSeqSelect
+        track refGene override
         parent refSeqComposite off
+        shortLabel UCSC RefSeq
+        longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*)
+        color 12,12,120
+        type genePred refPep refMrna
+        idXref hgFixed.refLink mrnaAcc name
+        dataVersion 
         priority 7
-        type genePred
-        shortLabel RefSeq Select/MANE
-        longLabel NCBI RefSeq Select/MANE: One representative transcript per protein-coding gene
-        trackHandler ncbiRefSeq
-        idXref ncbiRefSeqLink mrnaAcc name
-        color 20,20,160
         baseColorUseCds given
         baseColorDefault genomicCodons
 
-        track ncbiRefSeqHgmd
+        track ncbiRefSeqSelect
         parent refSeqComposite off
-        priority 7
+        priority 8
         type genePred
-        shortLabel RefSeq HGMD
-        longLabel NCBI RefSeq curated and annotated by HGMD, usually one per clinically relevant gene
+        shortLabel RefSeq Select+MANE
+        longLabel NCBI RefSeq Select+MANE subset: one representative transcript per protein-coding gene
         trackHandler ncbiRefSeq
         idXref ncbiRefSeqLink mrnaAcc name
         color 20,20,160
         baseColorUseCds given
         baseColorDefault genomicCodons
 
-        track ncbiRefSeqMane
+        track ncbiRefSeqHgmd
         parent refSeqComposite off
-        priority 8
+        priority 9
         type genePred
-        shortLabel RefSeq MANE
-        longLabel RefSeq selected representative transcript for each gene, MANE 0.5
+        shortLabel RefSeq HGMD
+        longLabel NCBI RefSeq HGMD subset: transcripts with clinical variants in HGMD
         trackHandler ncbiRefSeq
-        baseColorUseCds given
-        baseColorDefault genomicCodons
-
-        track refGene override
-        parent refSeqComposite off
-        shortLabel UCSC RefSeq
-        longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*)
-        color 12,12,120
-        type genePred refPep refMrna
-        idXref hgFixed.refLink mrnaAcc name
-        dataVersion 
-        priority 9
+        idXref ncbiRefSeqLink mrnaAcc name
+        color 20,20,160
         baseColorUseCds given
         baseColorDefault genomicCodons
 
 searchName ncbiRefSeqCuratedName2
 searchTable ncbiRefSeqCurated
 searchMethod prefix
 query select chrom, txStart,txEnd, name from %s where name2 like '%s%%'
 searchPriority 1.07200
 
 searchName ncbiRefSeqPredictedName2
 searchTable ncbiRefSeqPredicted
 searchMethod prefix
 query select chrom, txStart,txEnd, name from %s where name2 like '%s%%'
 searchPriority 1.07201