/
uniprot.ra
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uniprot.ra
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# 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/$D/uniprot/version.txt
hideEmptySubtracks on
track unipAliSwissprot
shortLabel SwissProt Aln.
longLabel UCSC alignment of SwissProt proteins to genome (dark blue: main isoform, light blue: alternative isoforms)
priority 1
parent uniprot
visibility pack
type bigPsl
bigDataUrl /gbdb/$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=$$"
labelFields name,acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt
mouseOverField protFullNames
itemRgb on
#color 2,12,120
indelDoubleInsert on
indelQueryInsert on
baseColorTickColor contrastingColor
baseColorUseCds given
baseColorDefault genomicCodons
showDiffBasesAllScales on
# this is only for filtering, no need to show it
skipFields isMain
track unipAliTrembl
shortLabel TrEMBL Aln.
longLabel UCSC alignment of TrEMBL proteins to genome
priority 2
parent uniprot off
visibility hide
type bigPsl
bigDataUrl /gbdb/$D/uniprot/unipAliTrembl.bb
searchIndex name,acc
urls acc="https://www.uniprot.org/uniprot/$$" 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 on
#color 0,150,250
indelDoubleInsert on
indelQueryInsert on
baseColorTickColor contrastingColor
baseColorUseCds given
baseColorDefault genomicCodons
showDiffBasesAllScales on
# this is only for filtering, no need to show it
skipFields isMain
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