fa8c5189bd70f63e4e4570a6abca89ce453f4cc7
hiram
  Wed Jun 18 15:01:06 2025 -0700
initial trackDb from GenArk refs #35898

diff --git src/hg/makeDb/trackDb/zebrafish/danRer12/genArk.trackDb.ra src/hg/makeDb/trackDb/zebrafish/danRer12/genArk.trackDb.ra
new file mode 100644
index 00000000000..b79329fa2a4
--- /dev/null
+++ src/hg/makeDb/trackDb/zebrafish/danRer12/genArk.trackDb.ra
@@ -0,0 +1,249 @@
+track assembly
+longLabel Assembly
+shortLabel Assembly
+visibility hide
+colorByStrand 150,100,30 230,170,40
+color 150,100,30
+altColor 230,170,40
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.assembly.bb
+type bigBed 6
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.assembly
+searchIndex name
+searchTrix /gbdb/genark/GCF/049/306/965/GCF_049306965.1/ixIxx/GCF_049306965.1_GRCz12tu.assembly.ix
+url https://www.ncbi.nlm.nih.gov/nuccore/$$
+urlLabel NCBI Nucleotide database:
+group map
+
+track cytoBandIdeo
+shortLabel Chromosome Band (Ideogram)
+longLabel Ideogram for Orientation
+group map
+visibility dense
+type bigBed 4 +
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.cytoBand.bb
+
+track gc5Base
+shortLabel GC Percent
+longLabel GC Percent in 5-Base Windows
+group map
+visibility dense
+autoScale Off
+maxHeightPixels 128:36:16
+graphTypeDefault Bar
+gridDefault OFF
+windowingFunction Mean
+color 0,0,0
+altColor 128,128,128
+viewLimits 30:70
+type bigWig 0 100
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.gc5Base.bw
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.gc5Base
+
+track tanDups
+shortLabel Tandem Dups
+longLabel Paired identical sequences
+compositeTrack on
+visibility hide
+type bigBed 12
+group map
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.tanDups
+
+track gapOverlap
+parent tanDups on
+shortLabel Gap Overlaps
+longLabel Paired exactly identical sequence on each side of a gap
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.gapOverlap.bb
+type bigBed 12
+
+track tandemDups
+parent tanDups on
+shortLabel Tandem Dups
+longLabel Paired exactly identical sequence survey over entire genome assembly
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.tandemDups.bb
+type bigBed 12
+
+track repeatMasker
+shortLabel RepeatMasker
+longLabel RepeatMasker Repetitive Elements
+type bigRmsk 9 +
+visibility pack
+group varRep
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.rmsk.bb
+maxWindowToDraw 5000000
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.repeatMasker
+
+track simpleRepeat
+shortLabel Simple Repeats
+longLabel Simple Tandem Repeats by TRF
+group varRep
+visibility dense
+type bigBed 4 +
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.simpleRepeat.bb
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.simpleRepeat
+
+track refSeqComposite
+compositeTrack on
+shortLabel NCBI RefSeq
+longLabel RefSeq gene predictions from NCBI
+group genes
+visibility pack
+type bigBed
+dragAndDrop subTracks
+allButtonPair on
+dataVersion NCBI RefSeq GCF_049306965.1-RS_2025_04 (2025-05-13)
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.refSeqComposite
+priority 2
+
+track ncbiRefSeq
+parent refSeqComposite on
+color 12,12,120
+shortLabel RefSeq All
+type bigGenePred
+urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
+labelFields name,geneName,geneName2
+defaultLabelFields geneName2
+searchIndex name
+searchTrix /gbdb/genark/GCF/049/306/965/GCF_049306965.1/ixIxx/GCF_049306965.1_GRCz12tu.ncbiRefSeq.ix
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.ncbiRefSeq.bb
+longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)
+idXref ncbiRefSeqLink mrnaAcc name
+baseColorUseCds given
+baseColorDefault genomicCodons
+priority 1
+
+track ncbiRefSeqCurated
+color 12,12,120
+parent refSeqComposite on
+shortLabel RefSeq Curated
+longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
+type bigGenePred
+urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
+labelFields name,geneName,geneName2
+defaultLabelFields geneName2
+searchIndex name
+searchTrix /gbdb/genark/GCF/049/306/965/GCF_049306965.1/ixIxx/GCF_049306965.1_GRCz12tu.ncbiRefSeqCurated.ix
+idXref ncbiRefSeqLink mrnaAcc name
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.ncbiRefSeqCurated.bb
+baseColorUseCds given
+baseColorDefault genomicCodons
+priority 2
+
+track ncbiRefSeqPredicted
+color 12,12,120
+parent refSeqComposite on
+shortLabel RefSeq Predicted
+longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
+type bigGenePred
+urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
+labelFields name,geneName,geneName2
+defaultLabelFields geneName2
+searchIndex name
+searchTrix /gbdb/genark/GCF/049/306/965/GCF_049306965.1/ixIxx/GCF_049306965.1_GRCz12tu.ncbiRefSeqPredicted.ix
+idXref ncbiRefSeqLink mrnaAcc name
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.ncbiRefSeqPredicted.bb
+baseColorUseCds given
+baseColorDefault genomicCodons
+priority 3
+
+track ncbiRefSeqOther
+color 32,32,32
+parent refSeqComposite on
+shortLabel RefSeq Other
+longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)
+priority 4
+searchIndex name
+searchTrix /gbdb/genark/GCF/049/306/965/GCF_049306965.1/ixIxx/GCF_049306965.1_GRCz12tu.ncbiRefSeqOther.ix
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.ncbiRefSeqOther.bb
+type bigBed 12 +
+labelFields name
+skipEmptyFields on
+urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$"
+
+track ncbiRefSeqPsl
+priority 5
+parent refSeqComposite off
+shortLabel RefSeq Alignments
+longLabel RefSeq Alignments of RNAs
+type bigPsl
+searchIndex name
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.bigPsl.bb
+indelDoubleInsert on
+indelQueryInsert on
+showDiffBasesAllScales .
+showDiffBasesMaxZoom 10000.0
+showCdsMaxZoom 10000.0
+showCdsAllScales .
+baseColorDefault diffCodons
+pslSequence no
+baseColorUseSequence lfExtra
+baseColorUseCds table given
+color 0,0,0
+
+track cpgIslands
+compositeTrack on
+shortLabel CpG Islands
+longLabel CpG Islands (Islands < 300 Bases are Light Green)
+group regulation
+visibility dense
+type bigBed 4 +
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.cpgIslands
+
+track cpgIslandExt
+parent cpgIslands off
+shortLabel CpG Islands
+longLabel CpG Islands (Islands < 300 Bases are Light Green)
+type bigBed 4 +
+priority 1
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.cpgIslandExt.bb
+
+track cpgIslandExtUnmasked
+parent cpgIslands on
+shortLabel Unmasked CpG
+longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
+type bigBed 4 +
+priority 2
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.cpgIslandExtUnmasked.bb
+
+track windowMasker
+shortLabel WM + SDust
+longLabel Genomic Intervals Masked by WindowMasker + SDust
+group varRep
+visibility dense
+type bigBed 3
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.windowMasker.bb
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.windowMasker
+
+track allGaps
+shortLabel All Gaps
+longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
+group map
+visibility hide
+type bigBed 3
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.allGaps.bb
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.allGaps
+
+track augustus
+shortLabel Augustus
+longLabel Augustus Gene Predictions
+group genes
+visibility dense
+color 180,0,0
+type bigGenePred
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.augustus.bb
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.augustus
+
+track xenoRefGene
+shortLabel RefSeq mRNAs
+longLabel RefSeq mRNAs mapped to this assembly
+group rna
+visibility pack
+color 180,0,0
+type bigGenePred
+bigDataUrl /gbdb/genark/GCF/049/306/965/GCF_049306965.1/bbi/GCF_049306965.1_GRCz12tu.xenoRefGene.bb
+url https://www.ncbi.nlm.nih.gov/nuccore/$$
+urlLabel NCBI Nucleotide database:
+labelFields name,geneName,geneName2
+defaultLabelFields geneName
+searchIndex name
+searchTrix /gbdb/genark/GCF/049/306/965/GCF_049306965.1/ixIxx/GCF_049306965.1_GRCz12tu.xenoRefGene.ix
+html /gbdb/genark/GCF/049/306/965/GCF_049306965.1/html/GCF_049306965.1_GRCz12tu.xenoRefGene