bdc608599794265b358bd23b9dcfc00f89392923
max
  Mon Nov 29 06:17:47 2021 -0800
adding more colors to uniprot, refs #28560

diff --git src/hg/makeDb/trackDb/uniprot.ra src/hg/makeDb/trackDb/uniprot.ra
index 58991df..43448c9 100644
--- src/hg/makeDb/trackDb/uniprot.ra
+++ src/hg/makeDb/trackDb/uniprot.ra
@@ -1,226 +1,226 @@
 # if you modify this file, make sure that you also modify /hive/data/outside/otto/uniprot/uniprot.ra
 # which is the template for the hub in the archive/ on hgdownload. This hub is build for every release,
 # so users can open old versions of UniProt
 
 track uniprot
 shortLabel UniProt
 longLabel UniProt SwissProt/TrEMBL Protein Annotations
 group genes
 visibility hide
 type bigBed 12 +
 exonNumbers off
 compositeTrack on
 allButtonPair on
 mouseOverField comments
 urls uniProtId="http://www.uniprot.org/uniprot/$$#section_features" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"
 itemRgb on
 dataVersion /gbdb/$D/uniprot/version.txt
 html uniprotAlpha.html
 hideEmptySubtracks on
 
         track unipAliSwissprot
         shortLabel SwissProt Aln.
         longLabel UCSC alignment of SwissProt proteins to genome
         priority 1
         parent uniprot
         visibility hide
         type bigPsl
         bigDataUrl /gbdb/$D/uniprot/unipAliSwissprot.bb
         searchIndex name,acc
         urls acc="https://www.uniprot.org/uniprot/$$" hgncId="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" refSeq="https://www.ncbi.nlm.nih.gov/nuccore/$$" refSeqProt="https://www.ncbi.nlm.nih.gov/protein/$$" ncbiGene="https://www.ncbi.nlm.nih.gov/gene/$$" entrezGene="https://www.ncbi.nlm.nih.gov/gene/$$" ensGene="https://www.ensembl.org/Gene/Summary?g=$$"
         labelFields name,acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt
         mouseOverField protFullNames
-        itemRgb off
+        itemRgb on
         color 2,12,120
         indelDoubleInsert on
         indelQueryInsert on
         baseColorTickColor contrastingColor
         baseColorUseCds given
         baseColorDefault genomicCodons
         showDiffBasesAllScales on
 
         track unipAliTrembl
         shortLabel TrEMBL Aln.
         longLabel UCSC alignment of TrEMBL proteins to genome
         priority 2
         parent uniprot off
         visibility hide
         type bigPsl
         bigDataUrl /gbdb/$D/uniprot/unipAliTrembl.bb
         searchIndex name,acc
         urls acc="https://www.uniprot.org/uniprot/$$" hgncId="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" refseq="https://www.ncbi.nlm.nih.gov/nuccore/$$" refSeqProt="https://www.ncbi.nlm.nih.gov/protein/$$" ncbiGene="https://www.ncbi.nlm.nih.gov/gene/$$" entrezGene="https://www.ncbi.nlm.nih.gov/gene/$$" ensGene="https://www.ensembl.org/Gene/Summary?g=$$"
         labelFields name,acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt
         mouseOverField protFullNames
-        itemRgb off
+        itemRgb on
         color 0,150,250
         indelDoubleInsert on
         indelQueryInsert on
         baseColorTickColor contrastingColor
         baseColorUseCds given
         baseColorDefault genomicCodons
         showDiffBasesAllScales on
 
         track unipLocSignal
         shortLabel Signal Peptide
         longLabel UniProt Signal Peptides
         priority 3
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipLocSignal.bb
         color 255,0,150
         itemRgb off
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipLocExtra
         shortLabel Extracellular
         longLabel UniProt Extracellular Domain
         priority 4
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipLocExtra.bb
         color 0,150,255
         itemRgb off
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipLocTransMemb
         shortLabel Transmembrane
         longLabel UniProt Transmembrane Domains
         priority 5
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipLocTransMemb.bb
         color 0,150,0
         itemRgb off
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipLocCytopl
         shortLabel Cytoplasmic
         longLabel UniProt Cytoplasmic Domains
         priority 6
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipLocCytopl.bb
         color 255,150,0
         itemRgb off
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipChain
         shortLabel Chains
         longLabel UniProt Mature Protein Products (Polypeptide Chains)
         priority 7
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipChain.bb
         urls uniProtId="http://www.uniprot.org/uniprot/$$#ptm_processing" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipInterest
         shortLabel Interest
         longLabel UniProt Regions of Interest
         priority 4
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipInterest.bb
         itemRgb off
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipDomain
         shortLabel Domains
         longLabel UniProt Domains
         priority 8
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipDomain.bb
         urls uniProtId="http://www.uniprot.org/uniprot/$$#family_and_domains" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipDisulfBond
         shortLabel Disulf. Bonds
         longLabel UniProt Disulfide Bonds
         priority 8
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipDisulfBond.bb
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipModif
         shortLabel AA Modifications
         longLabel UniProt Amino Acid Modifications
         priority 9
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipModif.bb
         urls uniProtId="http://www.uniprot.org/uniprot/$$#aaMod_section" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipMut
         shortLabel Mutations
         longLabel UniProt Amino Acid Mutations
         priority 10
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipMut.bb
         urls uniProtId="http://www.uniprot.org/uniprot/$$#pathology_and_biotech" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" variationId="http://www.uniprot.org/uniprot/$$"
 
         track unipStruct
         shortLabel Structure
         longLabel UniProt Protein Primary/Secondary Structure Annotations
         priority 11
         parent uniprot
         group genes
         visibility hide
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipStruct.bb
         urls uniProtId="http://www.uniprot.org/uniprot/$$#structure" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipOther
         shortLabel Other Annot.
         longLabel UniProt Other Annotations
         priority 11
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipOther.bb
         urls uniProtId="http://www.uniprot.org/uniprot/$$#family_and_domains" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipRepeat
         shortLabel Repeats
         longLabel UniProt Repeats
         priority 12
         parent uniprot
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipRepeat.bb
         urls uniProtId="http://www.uniprot.org/uniprot/$$#family_and_domains" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
         track unipConflict
         shortLabel Seq. Conflicts
         longLabel UniProt Sequence Conflicts
         priority 13
         parent uniprot off
         visibility dense
         type bigBed 12 +
         bigDataUrl /gbdb/$D/uniprot/unipConflict.bb
         urls uniProtId="http://www.uniprot.org/uniprot/$$#Sequence_conflict_section" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"
         filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)
 
 searchTable unipAliSwissprot
 searchType bigBed
 searchDescription UniProt/SwissProt manually curated Proteins mapped to the genome by UCSC
 
 searchTable unipAliTrembl
 searchType bigBed
 searchDescription UniProt/TrEMBL predicted Proteins mapped to the genome by UCSC