UniProt highlighted "Regions of Interest" (binds ACE2)
 
Item: binds ACE2
Score: 1000
Position: NC_045512v2:22871-23086
Genomic Size: 216
Strand: +
View DNA for this feature (wuhCor1/SARS-CoV-2)

StatusManually reviewed (Swiss-Prot)
Annotation Typeregion of interest
Positionamino acids 437-508 on protein P0DTC2
Long Name
Synonyms
Subcell. Location
CommentReceptor-binding motif; binding to human ACE2
UniProt recordP0DTC2
Source articles
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Data version: Covid-19 pre-release 2-JUN-2020
Data last updated: 2020-06-05 06:12:13

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