This track shows protein sequence annotations from the UniProt/SwissProt database, mapped to genomic coordinates. It shows how the protein sequences in this database map to the genome. This mapping was used to "lift" the UniProt protein annotations to the SARS-CoV-2 genome. The protein annotation themselves have been curated from scientific publications by the UniProt/SwissProt staff.
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.
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.
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. For human and mouse, the alignments were filtered by retaining only proteins annotated with a given transcript in the Genome Browser table kgXref. Like all Genome Browser source code, the main script used to build this track can be found on GitHub.
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/unipAliSwissprotCov2.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.
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.
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