-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". -
- --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.
- --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. -
- -
-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/$db/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.
-
-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. -
- --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 -