Schema for Mutations - UniProt Amino Acid Mutations
  Database: wuhCor1    Primary Table: unipCov2Mut Data last updated: 2022-07-21
Big Bed File: /gbdb/wuhCor1/uniprot/unipMutCov2.bb
Item Count: 277
Format description: Browser extensible data (12 fields) plus information about uniProt mutation
fieldexampledescription
chromNC_045512v2Chromosome (or contig, scaffold, etc.)
chromStart19953Start position in chromosome
chromEnd19956End position in chromosome
nameT6564IName of item
score1000Score from 0-1000
strand++ or -
thickStart19953Start of where display should be thick (start codon)
thickEnd19956End 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: Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.4, Omicron/BA.5Diseases
mutationposition 6564, Thr changed to IleCoding seq. mutation
commentsstrain: Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.4, Omicron/BA.5; Comment
variationIdUniProt variant
dbSnpIddbSNP
uniProtIdP0DTD1UniProt record
pmidsSource articles

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsstatusvarTypediseasesmutationcommentsvariationIddbSnpIduniProtIdpmids
NC_045512v21995319956T6564I1000+19953199560130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.4, Omicron/BA.5position 6564, Thr changed to Ilestrain: Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.4, Omicron/BA.5;P0DTD1
NC_045512v22031920322H6686A1000+20319203220130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 6686, His changed to AlaComplete loss of NSP15 endonuclease activity.P0DTD133504779
NC_045512v22036420367H6701A1000+20364203670130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 6701, His changed to AlaComplete loss of NSP15 endonuclease activity.P0DTD133504779
NC_045512v22039420397K6711R1000+20394203970130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: Kappa/B.1.617.1position 6711, Lys changed to Argstrain: Kappa/B.1.617.1;P0DTD1
NC_045512v22157421577L5F1000+21574215770130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: Iota/B.1.526position 5, Leu changed to Phestrain: Iota/B.1.526;P0DTC2
NC_045512v22159821601S13I1000+21598216010130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: Epsilon/B.1.427/B.1.429position 13, Ser changed to Ilestrain: Epsilon/B.1.427/B.1.429; may change signal peptide cleavage to position 16-17P0DTC234210893
NC_045512v22161321616L18F1000+21613216160130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: Beta/B.1.351, Gamma/P.1, 19B/501Yposition 18, Leu changed to Phestrain: Beta/B.1.351, Gamma/P.1, 19B/501Y;P0DTC233690265
NC_045512v22161621619T19R1000+21616216190130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: Delta/B.1.617.2, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.4, Omicron/BA.5position 19, Thr changed to Argstrain: Delta/B.1.617.2, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.4, Omicron/BA.5;P0DTC2
NC_045512v22161921622T20N1000+21619216220130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: Gamma/P.1position 20, Thr changed to Asnstrain: Gamma/P.1;P0DTC2
NC_045512v22163121643LPPA24S1000+216312164301120Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.4, Omicron/BA.5position 24-28, Leu-Pro-Pro-Ala changed to Serstrain: Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.4, Omicron/BA.5;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