Schema for UniProt - UniProt SwissProt/TrEMBL Protein Annotations

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts	dbName	annotationType	position	comments	uniProtId
chr2L	16173503	16175833	repeat	1000	+	16173503	16175833	12,12,120	7	41,106,140,107,153,182,117	0,214,553,912,1351,1931,2213	Manually reviewed (Swiss-Prot)	repeat	amino acids 602-883 on protein Q24270	I	Q24270
chr2L	16176094	16177026	repeat	1000	+	16176094	16177026	12,12,120	4	142,226,211,162	0,205,497,770	Manually reviewed (Swiss-Prot)	repeat	amino acids 971-1217 on protein Q24270	II	Q24270
chr2L	16178487	16183254	repeat	1000	+	16178487	16183254	12,12,120	8	5,130,167,88,108,53,147,151	0,419,713,971,1651,4291,4405,4616	Manually reviewed (Swiss-Prot)	repeat	amino acids 1331-1613 on protein Q24270	III	Q24270
chr2L	16183356	16184485	repeat	1000	+	16183356	16184485	12,12,120	6	219,84,66,189,249,39	0,273,412,533,781,1090	Manually reviewed (Swiss-Prot)	repeat	amino acids 1648-1929 on protein Q24270	IV	Q24270
chr2L	16262235	16262421	repeat	0	+	16262235	16262421	0,150,250	2	43,83	0,103	Unreviewed (TrEMBL)	repeat	amino acids 13-54 on protein Q9VJL9	WD	Q9VJL9
chr2L	16262421	16262666	repeat	0	+	16262421	16262666	0,150,250	3	36,73,17	0,99,228	Unreviewed (TrEMBL)	repeat	amino acids 55-96 on protein Q9VJL9	WD	Q9VJL9
chr2L	16262666	16262792	repeat	0	+	16262666	16262792	0,150,250	1	126	0	Unreviewed (TrEMBL)	repeat	amino acids 97-138 on protein Q9VJL9	WD	Q9VJL9
chr2L	16312233	16312344	repeat	0	+	16312233	16312344	0,150,250	1	111	0	Unreviewed (TrEMBL)	repeat	amino acids 330-366 on protein Q24044	WD	Q24044
chr2L	16312641	16312740	repeat	0	+	16312641	16312740	0,150,250	1	99	0	Unreviewed (TrEMBL)	repeat	amino acids 466-498 on protein Q24044	WD	Q24044
chr2L	16314600	16314699	repeat	0	-	16314600	16314699	0,150,250	1	99	0	Unreviewed (TrEMBL)	repeat	amino acids 395-427 on protein C1C5B1	ANK	C1C5B1

UniProt (uniprot) Track Description

Description

This track was produced by the Genome Bioinformatics Group at the UCSC Genomics Institute. It shows protein sequence annotations from the UniProt/SwissProt database, mapped to genomic coordinates. It also shows how the protein sequences in this database map to the genome. The data has been curated from scientific publications by the UniProt/SwissProt staff. The annotations are divided into multiple subtracks, 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

For consistency, the subtrack "UniProt/SwissProt Variants" is a copy of the track "UniProt Variants" in the track group "Phenotype and Literature", or "Variation and Repeats", depending on the assembly.

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.

Duplicate annotations are removed as far as possible: if a TrEMBL annotation has the same genome position and same feature type, comment, disease and mutated amino acids as a SwissProt annotation, it is not shown again. Two annotations mapped through different transcripts but with the same genome coordinates are only shown once.

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. For human and mouse, the alignments were filtered by retaining only proteins annotated with a given transcript in the Genome Browser table kgXref. 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/dm6/uniprot/unipStruct.bb -chrom=chr6 -start=0 -end=1000000 stdout
This track is updated every month. The MySQL table hgFixed.trackVersion contains the name of the currently available data on the website. Older versions of the data files can be downloaded from the archive folder of our downloads server.
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 Alejo Mujica, Regeneron Pharmaceuticals. 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