Schema for Structure - UniProt Protein Primary/Secondary Structure Annotations
  Database: wuhCor1    Primary Table: unipCov2Struct Data last updated: 2022-07-21
Big Bed File: /gbdb/wuhCor1/uniprot/unipStructCov2.bb
Item Count: 755
Format description: Browser extensible data (12 fields), eight fields for bigGenePred support, plus extra fields (dbName-pmids, not used by all UniProt subtracks) with UniProt-specific information
fieldexampledescription
chromNC_045512v2Chromosome (or contig, scaffold, etc.)
chromStart19893Start position in chromosome
chromEnd19908End position in chromosome
namebetaName of item
score1000Score from 0-1000
strand++ or -
thickStart19893Start of where display should be thick (start codon)
thickEnd19908End of where display should be thick (stop codon)
reserved12,12,120Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes15Comma separated list of block sizes
chromStarts0Start positions relative to chromStart
name2Alternative/human readable name
cdsStartStatcmplStatus of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStatcmplStatus of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames0Exon frame {0,1,2}, or -1 if no frame for exon
typeswissprotTranscript type
geneNamePrimary identifier for gene
geneName2Alternative/human-readable gene name
geneTypeGene type
statusManually reviewed (Swiss-Prot)Status
annotationTypebeta strandAnnotation Type
positionamino acids 6544-6548 on protein P0DTD1Position
longNameLong Name
synsSynonyms
subCellLocSubcell. Location
commentsComment
uniProtIdP0DTD1UniProt record
pmidsSource articles

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneTypestatusannotationTypepositionlongNamesynssubCellLoccommentsuniProtIdpmids
NC_045512v21989319908beta1000+198931990812,12,1201150cmplcmpl0swissprotManually reviewed (Swiss-Prot)beta strandamino acids 6544-6548 on protein P0DTD1P0DTD1
NC_045512v21991119923beta1000+199111992312,12,1201120cmplcmpl0swissprotManually reviewed (Swiss-Prot)beta strandamino acids 6550-6553 on protein P0DTD1P0DTD1
NC_045512v21992619935turn1000+199261993512,12,120190cmplcmpl0swissprotManually reviewed (Swiss-Prot)turnamino acids 6555-6557 on protein P0DTD1P0DTD1
NC_045512v21993519950beta1000+199351995012,12,1201150cmplcmpl0swissprotManually reviewed (Swiss-Prot)beta strandamino acids 6558-6562 on protein P0DTD1P0DTD1
NC_045512v21995919968helix1000+199591996812,12,120190cmplcmpl0swissprotManually reviewed (Swiss-Prot)helixamino acids 6566-6568 on protein P0DTD1P0DTD1
NC_045512v21996819977beta1000+199681997712,12,120190cmplcmpl0swissprotManually reviewed (Swiss-Prot)beta strandamino acids 6569-6571 on protein P0DTD1P0DTD1
NC_045512v21998019992beta1000+199801999212,12,1201120cmplcmpl0swissprotManually reviewed (Swiss-Prot)beta strandamino acids 6573-6576 on protein P0DTD1P0DTD1
NC_045512v22000720028helix1000+200072002812,12,1201210cmplcmpl0swissprotManually reviewed (Swiss-Prot)helixamino acids 6582-6588 on protein P0DTD1P0DTD1
NC_045512v22003120058beta1000+200312005812,12,1201270cmplcmpl0swissprotManually reviewed (Swiss-Prot)beta strandamino acids 6590-6598 on protein P0DTD1P0DTD1
NC_045512v22009720106beta1000+200972010612,12,120190cmplcmpl0swissprotManually reviewed (Swiss-Prot)beta strandamino acids 6612-6614 on protein P0DTD1P0DTD1

Structure (unipCov2Struct) Track Description
 

Description

This track shows protein sequence annotations from the UniProt/SwissProt database, mapped to genomic coordinates. The data has been curated from scientific publications by the UniProt/SwissProt staff. The annotations are spread over multiple tracks, based on their "feature type" in UniProt:

Track Name Description
UCSC Alignment, SwissProt Protein sequences from SwissProt mapped onto the genome. All other tracks are (start,end) annotations mapped using this track.
UCSC Alignment, TrEMBL Protein sequences from TrEMBL mapped onto the genome. All other tracks are (start,end) annotations mapped using this track. This track is hidden by default. To show it, click its checkbox on the track description page.
UniProt Signal Peptides Regions found in proteins destined to be secreted, generally cleaved from mature protein.
UniProt Extracellular Domains Protein domains with the comment "Extracellular".
UniProt Transmembrane Domains Protein domains of the type "Transmembrane".
UniProt Cytoplasmic Domains Protein domains with the comment "Cytoplasmic".
UniProt Polypeptide Chains Polypeptide chain in mature protein after post-processing.
UniProt Domains Protein domains, zinc finger regions and topological domains.
UniProt Disulfide Bonds Disulfide bonds.
UniProt Amino Acid Modifications Glycosylation sites, modified residues and lipid moiety-binding regions.
UniProt Amino Acid Mutations Mutagenesis sites and sequence variants.
UniProt Protein Primary/Secondary Structure Annotations Beta strands, helices, coiled-coil regions and turns.
UniProt Sequence Conflicts Differences between Genbank sequences and the UniProt sequence.
UniProt Repeats Regions of repeated sequence motifs or repeated domains.
UniProt Other Annotations All other annotations

Display Conventions and Configuration

Genomic locations of UniProt/SwissProt annotations are labeled with a short name for the type of annotation (e.g. "glyco", "disulf bond", "Signal peptide" etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt record for more details. TrEMBL annotations are always shown in light blue, except in the Signal Peptides, Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.

Mouse-over a feature to see the full UniProt annotation comment. For variants, the mouse-over will show the full name of the UniProt disease acronym.

The subtracks for domains related to subcellular location are sorted from outside to inside of the cell: Signal peptide, extracellular, transmembrane, and cytoplasmic.

In the "UniProt Modifications" track, lipoification sites are highlighted in dark blue, glycosylation sites in dark green, and phosphorylation in light green.

Methods

UniProt sequences were aligned to UCSC/Gencode transcript sequences first with BLAT, filtered with pslReps (93% query coverage, within top 1% score), lifted to genome positions with pslMap and filtered again. UniProt annotations were obtained from the UniProt XML file. The annotations were then mapped to the genome through the alignment using the pslMap program. This mapping approach draws heavily on the LS-SNP pipeline by Mark Diekhans. Like all Genome Browser source code, the main script used to build this track can be found on GitHub.

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server. The exact filenames can be found in the track configuration file. Annotations can be converted to ASCII text by our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/uniprot/unipStructCov2.bb -chrom=NC_045512v2 -start=0 -end=29903 stdout

Please refer to our mailing list archives for questions or our Data Access FAQ for more information.

Credits

This track was created by Maximilian Haeussler at UCSC, with help from Chris Lee, Mark Diekhans and Brian Raney, feedback from the UniProt staff and Phil Berman, UCSC. Thanks to UniProt for making all data available for download.

References

UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. PMID: 22102590; PMC: PMC3245120

Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat. 2004 May;23(5):464-70. PMID: 15108278