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.
The data has been curated from scientific publications by the UniProt/SwissProt staff.
Note that the data is not online at UniProt itself yet, so the Genome
Browser is the only place where you can see it, at the time of release of this Genome Browser. It will be
released on April 22nd.
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.
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
The raw data can be explored interactively with the
Table Browser or the
For automated analysis, the genome annotation is stored in a bigBed file that
can be downloaded from the
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
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.
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.