Schema for Highlights - UniProt highlighted "Regions of Interest"
  Database: wuhCor1    Primary Table: unipCov2Interest Data last updated: 2022-07-21
Big Bed File: /gbdb/wuhCor1/uniprot/unipInterestCov2.bb
Item Count: 26
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.)
chromStart22399Start position in chromosome
chromEnd22465End position in chromosome
namePutative super...Name of item
score1000Score from 0-1000
strand++ or -
thickStart22399Start of where display should be thick (start codon)
thickEnd22465End of where display should be thick (stop codon)
reserved12,12,120Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes66Comma 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
annotationTyperegion of interestAnnotation Type
positionamino acids 280-301 on protein P0DTC2Position
longNameLong Name
synsSynonyms
subCellLocSubcell. Location
commentsPutative superantigen; may bind T-cell receptor alpha/TRACComment
uniProtIdP0DTC2UniProt record
pmids32989130Source articles

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneTypestatusannotationTypepositionlongNamesynssubCellLoccommentsuniProtIdpmids
NC_045512v22239922465Putative super...1000+223992246512,12,1201660cmplcmpl0swissprotManually reviewed (Swiss-Prot)region of interestamino acids 280-301 on protein P0DTC2Putative superantigen; may bind T-cell receptor alpha/TRACP0DTC232989130
NC_045512v22251623185Receptor-bindi...1000+225162318512,12,12016690cmplcmpl0swissprotManually reviewed (Swiss-Prot)region of interestamino acids 319-541 on protein P0DTC2Receptor-binding domain (RBDP0DTC232132184
NC_045512v22276822777Integrin-bindi...1000+227682277712,12,120190cmplcmpl0swissprotManually reviewed (Swiss-Prot)region of interestamino acids 403-405 on protein P0DTC2Integrin-binding motif;P0DTC233102950
NC_045512v22287023086binds ACE21000+228702308612,12,12012160cmplcmpl0swissprotManually reviewed (Swiss-Prot)region of interestamino acids 437-508 on protein P0DTC2Receptor-binding motif; binding to human ACE2P0DTC2
NC_045512v22290322930Immunodominant...1000+229032293012,12,1201270cmplcmpl0swissprotManually reviewed (Swiss-Prot)region of interestamino acids 448-456 on protein P0DTC2Immunodominant HLA epitope recognized by the CD8+; called NF9 peptideP0DTC234171266
NC_045512v22360223614Putative super...1000+236022361412,12,1201120cmplcmpl0swissprotManually reviewed (Swiss-Prot)region of interestamino acids 681-684 on protein P0DTC2Putative superantigen; may bind T-cell receptor beta/TRBC1P0DTC232989130
NC_045512v22400724073Fusion peptide 11000+240072407312,12,1201660cmplcmpl0swissprotManually reviewed (Swiss-Prot)region of interestamino acids 816-837 on protein P0DTC2Fusion peptide 1P0DTC2
NC_045512v22406424127Fusion peptide 21000+240642412712,12,1201630cmplcmpl0swissprotManually reviewed (Swiss-Prot)region of interestamino acids 835-855 on protein P0DTC2Fusion peptide 2P0DTC2
NC_045512v22431924472Heptad repeat 11000+243192447212,12,12011530cmplcmpl0swissprotManually reviewed (Swiss-Prot)region of interestamino acids 920-970 on protein P0DTC2Heptad repeat 1P0DTC2
NC_045512v22504825168Heptad repeat 21000+250482516812,12,12011200cmplcmpl0swissprotManually reviewed (Swiss-Prot)region of interestamino acids 1163-1202 on protein P0DTC2Heptad repeat 2P0DTC2

Highlights (unipCov2Interest) Track Description
 

Description

This track shows protein sequence annotations defined as "regions of interest" from the UniProt/SwissProt database, mapped to genomic coordinates. The data has been curated from scientific publications by the UniProt/SwissProt staff.

Display Conventions and Configuration

Genomic locations of UniProt/SwissProt annotations are labeled with a short name. A click on the item shows additional annotation deltails.

Mouse-over a feature to see the full UniProt annotation comment.

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/unipInterestCov2.bb -chrom=NC_045512v2 -start=0 -end=29903 stdout

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 Alejo Mujica, Regeneron Pharmaceuticals. 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