ee07d5a59eb7fb9bf1062741f44c77388e16c40a
lrnassar
  Mon Dec 4 15:11:41 2023 -0800
Restructuring the RefSeqComposite track to be at the mouse and human level so that we can add an override at the hg38/hg19/mm10/mm39 level. The motivation is to have the RefSeq all track on my default for non human and mouse assemblies, but keep only curated for human and mouse. Refs #32716

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index f293c98..249f3a4 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -5637,15 +5637,46 @@
 labelFields symbol, geneName, name, uniprot_ids, ensembl_gene_id, ucsc_id, refseq_accession
 defaultLabelFields symbol
 mouseOver Symbol:$symbol; $name, Alias symbol: $alias_symbol; Previous symbols:$prev_symbol
 filterValues.locus_type RNA Y,RNA cluster,RNA long non-coding,RNA micro,RNA misc,RNA ribosomal,RNA small nuclear,RNA small nucleolar,RNA transfer,RNA vault,T cell receptor gene,T cell receptor pseudogene,complex locus constituent,endogenous retrovirus,fragile site,gene with protein product,immunoglobulin gene,immunoglobulin pseudogene,locus_type,protocadherin,pseudogene,readthrough,region,unknown,virus integration site,
 group genes
 searchIndex name
 searchTrix /gbdb/$D/hgnc/search.ix
 skipEmptyFields on
 itemRgb on
 noScoreFilter on
 
 searchTable hgnc
 searchMethod exact
 searchType bigBed
 
+include ../refSeqComposite.ra
+
+track ncbiRefSeqSelect
+parent refSeqComposite off
+priority 8
+type genePred
+shortLabel RefSeq Select and MANE
+longLabel NCBI RefSeq Select and MANE subset: A single representative transcript
+trackHandler ncbiRefSeq
+idXref ncbiRefSeqLink mrnaAcc name
+color 20,20,160
+baseColorUseCds given
+baseColorDefault genomicCodons
+
+track ncbiRefSeqHistorical
+parent refSeqComposite off
+priority 10000
+type genePred
+shortLabel RefSeq Historical
+longLabel NCBI RefSeq Historical Transcript Versions
+color 12,12,120
+idXref ncbiRefSeqLinkHistorical mrnaAcc name
+baseColorUseCds given
+baseColorDefault genomicCodons
+
+searchTable ncbiRefSeqHistorical
+searchMethod exact
+searchType genePred
+semiShortCircuit 1
+termRegex [N][MR]_[0-9]{6}[0-9]*\.[0-9]+
+searchPriority 20