# this file is used for building the archive track hub, it is template, not the final file.
# doUniprot builds the final file.
# if you modify this file, make sure that you also modify the original of the native track in trackDb/uniprot.ra

track uniprot13-Dec-2021
shortLabel UniProt 13-Dec-2021
longLabel UniProt SwissProt/TrEMBL Protein Annotations, release 13-Dec-2021
#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 unipAliSwissprot13-Dec-2021
        shortLabel SwissProt Aln.
        longLabel UCSC alignment of SwissProt proteins to genome - 13-Dec-2021
        priority 1
        parent uniprot13-Dec-2021
        visibility hide
        type bigPsl
        bigDataUrl 13-Dec-2021/unipAliSwissprot.bb
        searchIndex name,acc
        urls acc="http://www.uniprot.org/uniprot/$$" hgncId="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" 
        labelFields acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt,uniprotName
        mouseOverField protFullNames
        itemRgb off
        color 2,12,120
        indelDoubleInsert on
        indelQueryInsert on
        baseColorTickColor contrastingColor
        baseColorUseCds given
        baseColorDefault genomicCodons
        showDiffBasesAllScales on

        track unipAliTrembl13-Dec-2021
        shortLabel TrEMBL Aln.
        longLabel UCSC alignment of TrEMBL proteins to genome - 13-Dec-2021
        priority 2
        parent uniprot13-Dec-2021
        visibility dense
        type bigPsl
        bigDataUrl 13-Dec-2021/unipAliTrembl.bb
        searchIndex name,acc
        urls acc="http://www.uniprot.org/uniprot/$$" hgncId="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" 
        labelFields acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt,uniprotName
        mouseOverField protFullNames
        itemRgb off
        color 0,150,250
        indelDoubleInsert on
        indelQueryInsert on
        baseColorTickColor contrastingColor
        baseColorUseCds given
        baseColorDefault genomicCodons
        showDiffBasesAllScales on

        track unipLocSignal13-Dec-2021
        shortLabel Signal Peptide
        longLabel UniProt Signal Peptides - 13-Dec-2021
        priority 3
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/unipLocSignal.bb
        color 255,0,150
        itemRgb off
        filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)

        track unipLocExtra13-Dec-2021
        shortLabel Extracellular
        longLabel UniProt Extracellular Domain - 13-Dec-2021
        priority 4
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/unipLocExtra.bb
        color 0,150,255
        itemRgb off
        filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)

        track unipLocTransMemb13-Dec-2021
        shortLabel Transmembrane
        longLabel UniProt Transmembrane Domains - 13-Dec-2021
        priority 5
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/unipLocTransMemb.bb
        color 0,150,0
        itemRgb off
        filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)

        track unipLocCytopl13-Dec-2021
        shortLabel Cytoplasmic
        longLabel UniProt Cytoplasmic Domains - 13-Dec-2021
        priority 6
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/unipLocCytopl.bb
        color 255,150,0
        itemRgb off
        filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)

        track unipChain13-Dec-2021
        shortLabel Chains
        longLabel UniProt Mature Protein Products (Polypeptide Chains) - 13-Dec-2021
        priority 7
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/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 unipInterest13-Dec-2021
        shortLabel Interest
        longLabel UniProt Regions of Interest - 13-Dec-2021
        priority 4
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/unipInterest.bb
        itemRgb off
        filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)

        track unipDomain13-Dec-2021
        shortLabel Domains
        longLabel UniProt Domains - 13-Dec-2021
        priority 8
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/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 unipDisulfBond13-Dec-2021
        shortLabel Disulf. Bonds
        longLabel UniProt Disulfide Bonds - 13-Dec-2021
        priority 8
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/unipDisulfBond.bb
        filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)

        track unipModif13-Dec-2021
        shortLabel AA Modifications
        longLabel UniProt Amino Acid Modifications - 13-Dec-2021
        priority 9
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/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 unipMut13-Dec-2021
        shortLabel Mutations
        longLabel UniProt Amino Acid Mutations - 13-Dec-2021
        priority 10
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/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 unipStruct13-Dec-2021
        shortLabel Structure
        longLabel UniProt Protein Primary/Secondary Structure Annotations - 13-Dec-2021
        priority 11
        parent uniprot13-Dec-2021
        visibility hide
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/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 unipOther13-Dec-2021
        shortLabel Other Annot.
        longLabel UniProt Other Annotations - 13-Dec-2021
        priority 11
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/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 unipRepeat13-Dec-2021
        shortLabel Repeats
        longLabel UniProt Repeats - 13-Dec-2021
        priority 12
        parent uniprot13-Dec-2021
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/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 unipConflict13-Dec-2021
        shortLabel Seq. Conflicts
        longLabel UniProt Sequence Conflicts - 13-Dec-2021
        priority 13
        parent uniprot13-Dec-2021 off
        visibility dense
        type bigBed 12 +
        bigDataUrl 13-Dec-2021/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