Schema for Structure - UniProt Protein Primary/Secondary Structure Annotations |
|---|
| |
Database: wuhCor1 Primary Table: unipCov2Struct Data last updated: 2023-06-21
Big Bed File Download: /gbdb/wuhCor1/uniprot/unipStructCov2.bb
Item Count: 793
The data is stored in the binary BigBed format.
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
| field | example | description |
|---|
| chrom | NC_045512v2 | Chromosome (or contig, scaffold, etc.) | | chromStart | 19893 | Start position in chromosome | | chromEnd | 19908 | End position in chromosome | | name | beta | Name of item | | score | 1000 | Score from 0-1000 | | strand | + | + or - | | thickStart | 19893 | Start of where display should be thick (start codon) | | thickEnd | 19908 | End of where display should be thick (stop codon) | | reserved | 12,12,120 | Used as itemRgb as of 2004-11-22 | | blockCount | 1 | Number of blocks | | blockSizes | 15 | Comma separated list of block sizes | | chromStarts | 0 | Start positions relative to chromStart | | name2 | | Alternative/human readable name | | cdsStartStat | cmpl | Status of CDS start annotation (none, unknown, incomplete, or complete) | | cdsEndStat | cmpl | Status of CDS end annotation (none, unknown, incomplete, or complete) | | exonFrames | 0 | Exon frame {0,1,2}, or -1 if no frame for exon | | type | swissprot | Transcript type | | geneName | | Primary identifier for gene | | geneName2 | | Alternative/human-readable gene name | | geneType | | Gene type | | status | Manually reviewed (Swiss-Prot) | Status | | annotationType | beta strand | Annotation Type | | position | amino acids 6544-6548 on protein P0DTD1 | Position | | longName | | Long Name | | syns | | Synonyms | | subCellLoc | | Subcell. Location | | comments | | Comment | | uniProtId | P0DTD1 | UniProt record | | pmids | | Source articles |
|
| |
|
|
|
Sample Rows
|
|---|
| |
| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | name2 | cdsStartStat | cdsEndStat | exonFrames | type | geneName | geneName2 | geneType | status | annotationType | position | longName | syns | subCellLoc | comments | uniProtId | pmids |
|---|
| NC_045512v2 | 19893 | 19908 | beta | 1000 | + | 19893 | 19908 | 12,12,120 | 1 | 15 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | beta strand | amino acids 6544-6548 on protein P0DTD1 | | | | | P0DTD1 | |
| NC_045512v2 | 19911 | 19923 | beta | 1000 | + | 19911 | 19923 | 12,12,120 | 1 | 12 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | beta strand | amino acids 6550-6553 on protein P0DTD1 | | | | | P0DTD1 | |
| NC_045512v2 | 19926 | 19935 | turn | 1000 | + | 19926 | 19935 | 12,12,120 | 1 | 9 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | turn | amino acids 6555-6557 on protein P0DTD1 | | | | | P0DTD1 | |
| NC_045512v2 | 19935 | 19950 | beta | 1000 | + | 19935 | 19950 | 12,12,120 | 1 | 15 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | beta strand | amino acids 6558-6562 on protein P0DTD1 | | | | | P0DTD1 | |
| NC_045512v2 | 19959 | 19968 | helix | 1000 | + | 19959 | 19968 | 12,12,120 | 1 | 9 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | helix | amino acids 6566-6568 on protein P0DTD1 | | | | | P0DTD1 | |
| NC_045512v2 | 19968 | 19977 | beta | 1000 | + | 19968 | 19977 | 12,12,120 | 1 | 9 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | beta strand | amino acids 6569-6571 on protein P0DTD1 | | | | | P0DTD1 | |
| NC_045512v2 | 19980 | 19992 | beta | 1000 | + | 19980 | 19992 | 12,12,120 | 1 | 12 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | beta strand | amino acids 6573-6576 on protein P0DTD1 | | | | | P0DTD1 | |
| NC_045512v2 | 19992 | 20001 | beta | 1000 | + | 19992 | 20001 | 12,12,120 | 1 | 9 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | beta strand | amino acids 6577-6579 on protein P0DTD1 | | | | | P0DTD1 | |
| NC_045512v2 | 20007 | 20028 | helix | 1000 | + | 20007 | 20028 | 12,12,120 | 1 | 21 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | helix | amino acids 6582-6588 on protein P0DTD1 | | | | | P0DTD1 | |
| NC_045512v2 | 20031 | 20058 | beta | 1000 | + | 20031 | 20058 | 12,12,120 | 1 | 27 | 0 | | cmpl | cmpl | 0 | swissprot | | | | Manually reviewed (Swiss-Prot) | beta strand | amino acids 6590-6598 on protein P0DTD1 | | | | | P0DTD1 | |
|
| |
|
|
|
Structure (unipCov2Struct) 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
| |
|
|
|
US Server