0967c36677fccbce9d80eb6e2aa21eed04759ebe
gperez2
Fri Dec 20 17:42:53 2024 -0800
Announcing the release of the NCBI Gene Orthologs track, refs #30262
diff --git src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
index 09b02ab..2f7cff5 100644
--- src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
+++ src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
@@ -1,226 +1,227 @@
track refSeqComposite
compositeTrack on
shortLabel NCBI RefSeq
longLabel RefSeq genes from NCBI
group genes
visibility dense
type genePred
dragAndDrop subTracks
noInherit on
#subGroup1 view Views aNcbiRefSeq=NCBI_RefSeq zUcscRefSeq=UCSC_RefSeq
allButtonPair on
dataVersion /gbdb/$D/ncbiRefSeq/ncbiRefSeqVersion.txt
priority 2
dbPrefixUrls hg="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" dm="http://flybase.org/reports/$$" ce="http://www.wormbase.org/db/gene/gene?name=$$" rn="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" sacCer="https://www.yeastgenome.org/locus/$$" danRer="https://zfin.org/$$" mm="https://www.informatics.jax.org//marker/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$"
dbPrefixLabels hg="HGNC" dm="FlyBase" ce="WormBase" rn="RGD" sacCer="SGD" danRer="ZFIN" mm="MGI" xenTro="XenBase"
+pennantIcon Updated red ../goldenPath/newsarch.html#122024 "December 20, 2024"
track ncbiRefSeq
parent refSeqComposite off
color 12,12,120
shortLabel RefSeq All
longLabel NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, 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_*)
idXref ncbiRefSeqLink mrnaAcc name
baseColorUseCds given
baseColorDefault genomicCodons
priority 2
track ncbiRefSeqPredicted
color 12,12,120
parent refSeqComposite off
shortLabel RefSeq Predicted
longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
idXref ncbiRefSeqLink mrnaAcc name
baseColorUseCds given
baseColorDefault genomicCodons
priority 3
track ncbiRefSeqOther
color 32,32,32
parent refSeqComposite off
shortLabel RefSeq Other
longLabel NCBI RefSeq Other Annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)
priority 4
searchIndex name
searchTrix /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.ix
bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.bb
type bigBed 12 +
labelFields gene
skipEmptyFields on
urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/612091" HGNC="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" 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="https://www.informatics.jax.org//marker/$$"
track ncbiRefSeqPsl
priority 5
parent refSeqComposite off
shortLabel RefSeq Alignments
longLabel RefSeq Alignments of RNAs
type psl
indelDoubleInsert on
indelQueryInsert on
showDiffBasesAllScales .
showDiffBasesMaxZoom 10000.0
showCdsMaxZoom 10000.0
showCdsAllScales .
baseColorDefault diffCodons
pslSequence no
baseColorUseSequence extFile seqNcbiRefSeq extNcbiRefSeq
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/$D/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb
itemRgb on
track refGene override
parent refSeqComposite off
shortLabel UCSC RefSeq
longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*)
color 12,12,120
type genePred refPep refMrna
idXref hgFixed.refLink mrnaAcc name
priority 7
baseColorUseCds given
baseColorDefault genomicCodons
track ncbiRefSeqHgmd
parent refSeqComposite off
priority 9
type genePred
shortLabel RefSeq HGMD
longLabel NCBI RefSeq HGMD subset: transcripts with clinical variants in HGMD
trackHandler ncbiRefSeq
idXref ncbiRefSeqLink mrnaAcc name
color 20,20,160
baseColorUseCds given
baseColorDefault genomicCodons
track ncbiRefSeqSelect
parent refSeqComposite off
priority 8
type genePred
shortLabel RefSeq Select
longLabel NCBI RefSeq Select: One representative transcript per protein-coding gene
trackHandler ncbiRefSeq
idXref ncbiRefSeqLink mrnaAcc name
color 20,20,160
baseColorUseCds given
baseColorDefault genomicCodons
track ncbiOrtho
parent refSeqComposite off
shortLabel NCBI Orthologs
longLabel NCBI Gene Orthologs
type bigBed 9 +
bigDataUrl /gbdb/$D/ncbiOrtho/ncbiOrtho.bb
visibility hide
labelFields hugo,name
searchIndex hugo,name
searchTrix /gbdb/$D/ncbiOrtho/ncbiOrtho.ix
defaultLabelFields hugo
color 136,0,204
priority 9
mouseOver $url
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
searchName ncbiRefSeqCuratedProtAcc
searchTable ncbiRefSeqCurated
searchType genePred
searchMethod prefix
xrefTable ncbiRefSeqLink
xrefQuery select id,protAcc from %s where protAcc like '%s%%'
termRegex [NY]P_[0-9]+(\.[0-9]+)?
dontCheck XP_[0-9]+(\.[0-9]+)?
searchPriority 2.07201
searchName ncbiRefSeqPredictedProtAcc
searchTable ncbiRefSeqPredicted
searchType genePred
searchMethod prefix
xrefTable ncbiRefSeqLink
xrefQuery select id,protAcc from %s where protAcc like '%s%%'
termRegex XP_[0-9]+(\.[0-9]+)?
dontCheck [NY]P_[0-9]+(\.[0-9]+)?
searchPriority 2.07203
searchName ncbiRefSeqCuratedProduct
searchTable ncbiRefSeqCurated
searchType genePred
searchMethod fuzzy
xrefTable ncbiRefSeqLink
xrefQuery select id,product from %s where product like '%%%s%%'
searchPriority 2.07201
searchName ncbiRefSeqPredictedProduct
searchTable ncbiRefSeqPredicted
searchType genePred
searchMethod fuzzy
xrefTable ncbiRefSeqLink
xrefQuery select id,product from %s where product like '%%%s%%'
searchPriority 2.07203
searchTable ncbiRefSeqCurated
searchMethod exact
searchType genePred
semiShortCircuit 1
termRegex [NY][MRP]_[0-9]{6}[0-9]*\.[0-9]+
searchPriority 2.07202
searchName ncbiRefSeqCuratedNoVersion
searchTable ncbiRefSeqCurated
query select chrom,txStart,txEnd,name from %s where name like '%s.%%'
semiShortCircuit 1
termRegex [NY][MRP]_[0-9]{6}[0-9]*
dontCheck [NY][MRP]_[0-9]{6}[0-9]*\.[0-9]+
searchPriority 2.07202
searchTable ncbiRefSeqPredicted
searchMethod exact
searchType genePred
semiShortCircuit 1
termRegex X[MR]_[0-9]{6}[0-9]*\.[0-9]+
searchPriority 2.07204
searchName ncbiRefSeqPredictedNoVersion
searchTable ncbiRefSeqPredicted
query select chrom,txStart,txEnd,name from %s where name like '%s.%%'
semiShortCircuit 1
termRegex X[MR]_[0-9]{6}[0-9]*
dontCheck X[MR]_[0-9]{6}[0-9]*\.[0-9]+
searchPriority 2.07204
searchTable ncbiRefSeqOther
searchPriority 2.07207
searchType bigBed
searchName ncbiOrtho
searchTable ncbiOrtho
searchType bigBed
searchPriority 21