Schema for Protein Products - UniProt Protein Products (Polypeptide Chains, after cleavage)
  Database: wuhCor1    Primary Table: unipCov2Chain Data last updated: 2021-07-05
Big Bed File: /gbdb/wuhCor1/uniprot/unipChainCov2.bb
Item Count: 35
Format description: Browser extensible data (12 fields), eight fields for bigGenePred support, plus extra fields (dbName-pmids, not used by all UniProt subtracks) with UniProt-specific information
fieldexampledescription
chromNC_045512v2Chromosome (or contig, scaffold, etc.)
chromStart265Start position in chromosome
chromEnd21552End position in chromosome
namepp1abName of item
score1000Score from 0-1000
strand++ or -
thickStart265Start of where display should be thick (start codon)
thickEnd21552End of where display should be thick (stop codon)
reserved12,12,120Used as itemRgb as of 2004-11-22
blockCount2Number of blocks
blockSizes13200,8085Comma separated list of block sizes
chromStarts0,13202Start positions relative to chromStart
name2Alternative/human readable name
cdsStartStatcmplStatus of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStatcmplStatus of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames0,0Exon frame {0,1,2}, or -1 if no frame for exon
typeswissprotTranscript type
geneNamePrimary identifier for gene
geneName2Alternative/human-readable gene name
geneTypeGene type
statusManually reviewed (Swiss-Prot)Status
annotationTypechainAnnotation Type
positionamino acids 1-7096 on protein P0DTD1Position
longNameReplicase polyprotein 1abLong Name
synspp1ab; ORF1a-1b; ORF1ab polyprotein; Replicase polyprotein 1a; Replicase polyprotein 1abSynonyms
subCellLocSubcell. Location
commentsMultifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.Comment
uniProtIdP0DTD1UniProt record
pmidsSource articles

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneTypestatusannotationTypepositionlongNamesynssubCellLoccommentsuniProtIdpmids
NC_045512v226521552pp1ab1000+2652155212,12,120213200,80850,13202cmplcmpl0,0swissprotManually reviewed (Swiss-Prot)chainamino acids 1-7096 on protein P0DTD1Replicase polyprotein 1abpp1ab; ORF1a-1b; ORF1ab polyprotein; Replicase polyprotein 1a; Replicase polyprotein 1abMultifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for th ...P0DTD1
NC_045512v21962020658nsp151000+196202065812,12,120110380cmplcmpl0swissprotManually reviewed (Swiss-Prot)chainamino acids 6453-6798 on protein P0DTD1Uridylate-specific endoribonuclease nsp15Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.P0DTD1
NC_045512v22065821552nsp161000+206582155212,12,12018940cmplcmpl0swissprotManually reviewed (Swiss-Prot)chainamino acids 6799-7096 on protein P0DTD12'-O-methyltransferase nsp16Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs (By similarity). N7-meth ...P0DTD1
NC_045512v22159825381S glycoprotein1000+215982538112,12,120137830cmplcmpl0swissprotManually reviewed (Swiss-Prot)chainamino acids 13-1273 on protein P0DTC2Spike glycoproteinS glycoprotein; ORF2; E2; Peplomer proteinMay down-regulate host tetherin (BST2) by lysosomal degradation, thereby counteracting its antiviral activity.P0DTC2
NC_045512v22159823617Spike protein S11000+215982361712,12,120120190cmplcmpl0swissprotManually reviewed (Swiss-Prot)chainamino acids 13-685 on protein P0DTC2Spike protein S1attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 rece ...P0DTC2
NC_045512v22361725381Spike protein S21000+236172538112,12,120117640cmplcmpl0swissprotManually reviewed (Swiss-Prot)chainamino acids 686-1273 on protein P0DTC2Spike protein S2mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the p ...P0DTC2
NC_045512v22400725381Spike protein S2'1000+240072538112,12,120113740cmplcmpl0swissprotManually reviewed (Swiss-Prot)chainamino acids 816-1273 on protein P0DTC2Spike protein S2'Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.P0DTC2
NC_045512v22539226217ORF3a1000+253922621712,12,12018250cmplcmpl0swissprotManually reviewed (Swiss-Prot)chainamino acids 1-275 on protein P0DTC3ORF3a proteinORF3a; ORF3a; Protein 3a; Protein X1; Protein U274; Accessory protein 3aP0DTC3
NC_045512v22545625579ORF3c1000+254562557912,12,12011230cmplcmpl0swissprotManually reviewed (Swiss-Prot)chainamino acids 1-41 on protein P0DTG1ORF3c proteinORF3c; ORF3h; ORF3h proteinP0DTG1
NC_045512v22552325694ORF3d protein1000+255232569412,12,12011710cmplcmpl0swissprotManually reviewed (Swiss-Prot)chainamino acids 1-57 on protein P0DTG0ORF3d proteinP0DTG0

Protein Products (unipCov2Chain) 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