Description

This track shows protein sequence annotations from the UniProt/SwissProt database, mapped to genomic coordinates. The data has been curated from scientific publications by the UniProt staff. The annotations are divided into two subtracks, one for all secondary structure annotations and another one for all other annotations.

For the mutations curated by UniProt/SwissProt, please open the track "UniProt Variants" in the track group "Phenotype and Literature".

Display Conventions and Configuration

Genomic locations of UniProt/SwissProt annotations are labeled with a short name for the type of annotation (e.g. "glyco", "disul", "signal pep" 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.

Modified residues are highlighted in light blue, transmembrane regions in blue, glycosylation sites in yellow, disulfide bonds in grey, topological domains in red.

Note that for the human hg38 assembly, there also is a public track hub prepared by UniProt itself, with genome annotations produced and maintained by UniProt using their mapping method.

Methods

UniProt sequences were aligned to UCSC/Gencode transcript sequences first with BLAT, then lifted to genome positions with pslMap. UniProt variants were obtained from the UniProt XML file. The variants 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. The complete script is part of the kent source tree and is located in src/utils/uniprotLift. The exact commands that were 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 files for this track are called spAnnot.bb and spStruct.bb. Individual regions or the whole genome annotation can be obtained using 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/hg38/bbi/spStruct.bb -chrom=chr6 -start=0 -end=1000000 stdout
Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credits

This track was created by Maximilian Haeussler, with advice from Mark Diekhans and Brian Raney. 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