Schema for Highlights - UniProt highlighted "Regions of Interest"
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Database: wuhCor1 Primary Table: unipCov2Interest Data last updated: 2023-06-21
Big Bed File Download: /gbdb/wuhCor1/uniprot/unipInterestCov2.bb Item Count: 58 The data is stored in the binary BigBed format.
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
field | example | description |
chrom | NC_045512v2 | Chromosome (or contig, scaffold, etc.) | chromStart | 21562 | Start position in chromosome | chromEnd | 21640 | End position in chromosome | name | Disordered | Name of item | score | 1000 | Score from 0-1000 | strand | + | + or - | thickStart | 21562 | Start of where display should be thick (start codon) | thickEnd | 21640 | End of where display should be thick (stop codon) | reserved | 12,12,120 | Used as itemRgb as of 2004-11-22 | blockCount | 1 | Number of blocks | blockSizes | 78 | Comma separated list of block sizes | chromStarts | 0 | Start positions relative to chromStart | name2 | | Alternative/human readable name | cdsStartStat | cmpl | Status of CDS start annotation (none, unknown, incomplete, or complete) | cdsEndStat | cmpl | Status of CDS end annotation (none, unknown, incomplete, or complete) | exonFrames | 0 | Exon frame {0,1,2}, or -1 if no frame for exon | type | swissprot | Transcript type | geneName | | Primary identifier for gene | geneName2 | | Alternative/human-readable gene name | geneType | | Gene type | status | Manually reviewed (Swiss-Prot) | Status | annotationType | region of interest | Annotation Type | position | amino acids 1-26 on protein P0DTC2 | Position | longName | | Long Name | syns | | Synonyms | subCellLoc | | Subcell. Location | comments | Disordered | Comment | uniProtId | P0DTC2 | UniProt record | pmids | 35108439 | Source articles |
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Sample Rows
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chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | name2 | cdsStartStat | cdsEndStat | exonFrames | type | geneName | geneName2 | geneType | status | annotationType | position | longName | syns | subCellLoc | comments | uniProtId | pmids |
NC_045512v2 | 21562 | 21640 | Disordered | 1000 | + | 21562 | 21640 | 12,12,120 | 1 | 78 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | region of interest | amino acids 1-26 on protein P0DTC2 | | | | Disordered | P0DTC2 | 35108439 |
NC_045512v2 | 21760 | 21802 | Disordered | 1000 | + | 21760 | 21802 | 12,12,120 | 1 | 42 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | region of interest | amino acids 67-80 on protein P0DTC2 | | | | Disordered | P0DTC2 | 35108439 |
NC_045512v2 | 21985 | 22054 | Disordered | 1000 | + | 21985 | 22054 | 12,12,120 | 1 | 69 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | region of interest | amino acids 142-164 on protein P0DTC2 | | | | Disordered | P0DTC2 | 35108439 |
NC_045512v2 | 22078 | 22117 | Disordered | 1000 | + | 22078 | 22117 | 12,12,120 | 1 | 39 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | region of interest | amino acids 173-185 on protein P0DTC2 | | | | Disordered | P0DTC2 | 35108439 |
NC_045512v2 | 22297 | 22348 | Disordered | 1000 | + | 22297 | 22348 | 12,12,120 | 1 | 51 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | region of interest | amino acids 246-262 on protein P0DTC2 | | | | Disordered | P0DTC2 | 35108439 |
NC_045512v2 | 22399 | 22465 | Putative super... | 1000 | + | 22399 | 22465 | 12,12,120 | 1 | 66 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | region of interest | amino acids 280-301 on protein P0DTC2 | | | | Putative superantigen; may bind T-cell receptor alpha/TRAC | P0DTC2 | 32989130 |
NC_045512v2 | 22516 | 23185 | Receptor-bindi... | 1000 | + | 22516 | 23185 | 12,12,120 | 1 | 669 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | region of interest | amino acids 319-541 on protein P0DTC2 | | | | Receptor-binding domain (RBD | P0DTC2 | 32132184 |
NC_045512v2 | 22516 | 22567 | Disordered | 1000 | + | 22516 | 22567 | 12,12,120 | 1 | 51 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | region of interest | amino acids 319-335 on protein P0DTC2 | | | | Disordered | P0DTC2 | 35108439 |
NC_045512v2 | 22768 | 22777 | Integrin-bindi... | 1000 | + | 22768 | 22777 | 12,12,120 | 1 | 9 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | region of interest | amino acids 403-405 on protein P0DTC2 | | | | Integrin-binding motif; | P0DTC2 | 33102950 |
NC_045512v2 | 22870 | 23086 | binds ACE2 | 1000 | + | 22870 | 23086 | 12,12,120 | 1 | 216 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | region of interest | amino acids 437-508 on protein P0DTC2 | | | | Receptor-binding motif; binding to human ACE2 | P0DTC2 | |
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Highlights (unipCov2Interest) Track Description
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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
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