Schema for Repeats - UniProt Repeats
  Database: wuhCor1    Primary Table: unipCov2Repeat Data last updated: 2022-07-21
Big Bed File: /gbdb/wuhCor1/uniprot/unipRepeatCov2.bb
Item Count: 9
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.)
chromStart1897Start position in chromosome
chromEnd1972End position in chromosome
namerepeatName of item
score1000Score from 0-1000
strand++ or -
thickStart1897Start of where display should be thick (start codon)
thickEnd1972End of where display should be thick (stop codon)
reserved12,12,120Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes75Comma 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
annotationTyperepeatAnnotation Type
positionamino acids 545-569 on protein P0DTD1Position
longNameLong Name
synsSynonyms
subCellLocSubcell. Location
commentsLRR 1Comment
uniProtIdP0DTD1UniProt record
pmidsSource articles

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneTypestatusannotationTypepositionlongNamesynssubCellLoccommentsuniProtIdpmids
NC_045512v218971972repeat1000+1897197212,12,1201750cmplcmpl0swissprotManually reviewed (Swiss-Prot)repeatamino acids 545-569 on protein P0DTD1LRR 1P0DTD1
NC_045512v223532422repeat1000+2353242212,12,1201690cmplcmpl0swissprotManually reviewed (Swiss-Prot)repeatamino acids 697-719 on protein P0DTD1LRR 2P0DTD1
NC_045512v253025371repeat1000+5302537112,12,1201690cmplcmpl0swissprotManually reviewed (Swiss-Prot)repeatamino acids 1680-1702 on protein P0DTD1LRR 3P0DTD1
NC_045512v298179883repeat1000+9817988312,12,1201660cmplcmpl0swissprotManually reviewed (Swiss-Prot)repeatamino acids 3185-3206 on protein P0DTD1LRR 4P0DTD1
NC_045512v21206712142repeat1000+120671214212,12,1201750cmplcmpl0swissprotManually reviewed (Swiss-Prot)repeatamino acids 3935-3959 on protein P0DTD1LRR 5P0DTD1
NC_045512v21219312277repeat1000+121931227712,12,1201840cmplcmpl0swissprotManually reviewed (Swiss-Prot)repeatamino acids 3977-4004 on protein P0DTD1LRR 6P0DTD1
NC_045512v21403414112repeat1000+140341411212,12,1201780cmplcmpl0swissprotManually reviewed (Swiss-Prot)repeatamino acids 4591-4616 on protein P0DTD1LRR 7P0DTD1
NC_045512v21691716980repeat1000+169171698012,12,1201630cmplcmpl0swissprotManually reviewed (Swiss-Prot)repeatamino acids 5552-5572 on protein P0DTD1LRR 8P0DTD1
NC_045512v22071220787repeat1000+207122078712,12,1201750cmplcmpl0swissprotManually reviewed (Swiss-Prot)repeatamino acids 6817-6841 on protein P0DTD1LRR 9P0DTD1

Repeats (unipCov2Repeat) 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