Schema for Protein Domains - UniProt Domains
  Database: wuhCor1    Primary Table: unipCov2Domain Data last updated: 2021-07-05
Big Bed File: /gbdb/wuhCor1/uniprot/unipDomainCov2.bb
Item Count: 50
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.)
chromStart19803Start position in chromosome
chromEnd20181End position in chromosome
nameAV-Nsp11N/CoV-...Name of item
score1000Score from 0-1000
strand++ or -
thickStart19803Start of where display should be thick (start codon)
thickEnd20181End of where display should be thick (stop codon)
reserved12,12,120Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes378Comma separated list of block sizes
chromStarts0Start 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)
exonFrames0Exon 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
annotationTypedomainAnnotation Type
positionamino acids 6514-6639 on protein P0DTD1Position
longNameLong Name
synsSynonyms
subCellLocSubcell. Location
commentsAV-Nsp11N/CoV-Nsp15MComment
uniProtIdP0DTD1UniProt record
pmidsSource articles

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneTypestatusannotationTypepositionlongNamesynssubCellLoccommentsuniProtIdpmids
NC_045512v21980320181AV-Nsp11N/CoV-...1000+198032018112,12,12013780cmplcmpl0swissprotManually reviewed (Swiss-Prot)domainamino acids 6514-6639 on protein P0DTD1AV-Nsp11N/CoV-Nsp15MP0DTD1
NC_045512v22022920649NendoU1000+202292064912,12,12014200cmplcmpl0swissprotManually reviewed (Swiss-Prot)domainamino acids 6656-6795 on protein P0DTD1NendoUP0DTD1
NC_045512v22066121546Nidovirus-type...1000+206612154612,12,12018850cmplcmpl0swissprotManually reviewed (Swiss-Prot)domainamino acids 6800-7094 on protein P0DTD1Nidovirus-type SAM-dependent 2'-O-MTaseP0DTD1
NC_045512v22159822471BetaCoV S1-NTD1000+215982247112,12,12018730cmplcmpl0swissprotManually reviewed (Swiss-Prot)domainamino acids 13-303 on protein P0DTC2BetaCoV S1-NTDP0DTC2
NC_045512v22256123143BetaCoV S1-CTD1000+225612314312,12,12015820cmplcmpl0swissprotManually reviewed (Swiss-Prot)domainamino acids 334-527 on protein P0DTC2BetaCoV S1-CTDP0DTC232132184
NC_045512v22548825815CoV 3a-like vi...1000+254882581512,12,12013270cmplcmpl0swissprotManually reviewed (Swiss-Prot)domainamino acids 33-141 on protein P0DTC3CoV 3a-like viroporin TMP0DTC3
NC_045512v22582426103CoV 3a-like vi...1000+258242610312,12,12012790cmplcmpl0swissprotManually reviewed (Swiss-Prot)domainamino acids 145-237 on protein P0DTC3CoV 3a-like viroporin CDP0DTC3
NC_045512v22624426283Virion surface1000+2624426283100,0,01390cmplcmpl0swissprotManually reviewed (Swiss-Prot)topological domainamino acids 1-13 on protein P0DTC4Virion surfaceP0DTC432898469
NC_045512v22634626469Intravirion1000+2634626469100,0,011230cmplcmpl0swissprotManually reviewed (Swiss-Prot)topological domainamino acids 35-75 on protein P0DTC4IntravirionP0DTC432898469
NC_045512v22652526579Virion surface1000+2652526579100,0,01540cmplcmpl0swissprotManually reviewed (Swiss-Prot)topological domainamino acids 2-19 on protein P0DTC5Virion surfaceP0DTC5

Protein Domains (unipCov2Domain) 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