Schema for Mutations - UniProt Amino Acid Mutations
  Database: wuhCor1    Primary Table: unipCov2Mut Data last updated: 2021-07-05
Big Bed File: /gbdb/wuhCor1/uniprot/unipMutCov2.bb
Item Count: 88
Format description: Browser extensible data (12 fields) plus information about uniProt mutation
fieldexampledescription
chromNC_045512v2Chromosome (or contig, scaffold, etc.)
chromStart21574Start position in chromosome
chromEnd21577End position in chromosome
nameL5FName of item
score1000Score from 0-1000
strand++ or -
thickStart21574Start of where display should be thick (start codon)
thickEnd21577End of where display should be thick (stop codon)
reserved0Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes3Comma separated list of block sizes
chromStarts0Start positions relative to chromStart
statusManually reviewed (Swiss-Prot)Status
varTypeNaturally occurring sequence variantVariant Type
diseasesstrain: B.1.526Diseases
mutationposition 5, Leu changed to PheCoding seq. mutation
commentsstrain: B.1.526; Comment
variationIdUniProt variant
dbSnpIddbSNP
uniProtIdP0DTC2UniProt record
pmidsSource articles

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsstatusvarTypediseasesmutationcommentsvariationIddbSnpIduniProtIdpmids
NC_045512v22157421577L5F1000+21574215770130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: B.1.526position 5, Leu changed to Phestrain: B.1.526;P0DTC2
NC_045512v22159821601S13I1000+21598216010130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: B.1.429position 13, Ser changed to Ilestrain: B.1.429;P0DTC2
NC_045512v22161321616L18F1000+21613216160130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: B.1.351, P1, 19B/501Yposition 18, Leu changed to Phestrain: B.1.351, P1, 19B/501Y;P0DTC233690265
NC_045512v22161921622T20N1000+21619216220130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: P1position 20, Thr changed to Asnstrain: P1;P0DTC2
NC_045512v22163721640P26S1000+21637216400130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: P1position 26, Pro changed to Serstrain: P1;P0DTC2
NC_045512v22171521718Q52R1000+21715217180130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: B.1.525position 52, Gln changed to Argstrain: B.1.525;P0DTC2
NC_045512v2217662177269-71del1000+21766217720160Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: B.1.1.7, 19B/501Tposition 69-71, removal of amino acidsstrain: B.1.1.7, 19B/501T;P0DTC233413740
NC_045512v22179921802D80A1000+21799218020130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: B.1.351position 80, Asp changed to Alastrain: B.1.351;P0DTC233690265
NC_045512v22184421847T95I1000+21844218470130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: B.1.526, B.1.1.318position 95, Thr changed to Ilestrain: B.1.526, B.1.1.318;P0DTC2
NC_045512v22186521868R102I1000+21865218680130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: A23.1position 102, Arg changed to Ilestrain: A23.1;P0DTC2

Mutations (unipCov2Mut) Track Description
 

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/SwissProt staff. The annotations are spread over multiple tracks, based on their "feature type" in UniProt:

Track Name Description
UCSC Alignment, SwissProt Protein sequences from SwissProt mapped onto the genome. All other tracks are (start,end) annotations mapped using this track.
UCSC Alignment, TrEMBL Protein sequences from TrEMBL mapped onto the genome. All other tracks are (start,end) annotations mapped using this track. This track is hidden by default. To show it, click its checkbox on the track description page.
UniProt Signal Peptides Regions found in proteins destined to be secreted, generally cleaved from mature protein.
UniProt Extracellular Domains Protein domains with the comment "Extracellular".
UniProt Transmembrane Domains Protein domains of the type "Transmembrane".
UniProt Cytoplasmic Domains Protein domains with the comment "Cytoplasmic".
UniProt Polypeptide Chains Polypeptide chain in mature protein after post-processing.
UniProt Domains Protein domains, zinc finger regions and topological domains.
UniProt Disulfide Bonds Disulfide bonds.
UniProt Amino Acid Modifications Glycosylation sites, modified residues and lipid moiety-binding regions.
UniProt Amino Acid Mutations Mutagenesis sites and sequence variants.
UniProt Protein Primary/Secondary Structure Annotations Beta strands, helices, coiled-coil regions and turns.
UniProt Sequence Conflicts Differences between Genbank sequences and the UniProt sequence.
UniProt Repeats Regions of repeated sequence motifs or repeated domains.
UniProt Other Annotations All other annotations

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. TrEMBL annotations are always shown in light blue, except in the Signal Peptides, Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.

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.

The subtracks for domains related to subcellular location are sorted from outside to inside of the cell: Signal peptide, extracellular, transmembrane, and cytoplasmic.

In the "UniProt Modifications" track, lipoification sites are highlighted in dark blue, glycosylation sites in dark green, and phosphorylation in light green.

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/unipStructCov2.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.

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 Phil Berman, UCSC. 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