This track shows protein sequences and annotations on them from the UniProt/SwissProt database,
mapped to genomic coordinates.
UniProt/SwissProt data has been curated from scientific publications by the UniProt staff,
UniProt/TrEMBL data has been predicted by various computational algorithms.
The annotations are divided into multiple subtracks, based on their "feature type" in UniProt.
The first two subtracks below - one for SwissProt, one for TrEMBL - show the
alignments of protein sequences to the genome, all other tracks below are the protein annotations
mapped through these alignments to the genome.
|UCSC Alignment, SwissProt = curated protein sequences
||Protein sequences from SwissProt mapped to the genome. All other
tracks are (start,end) SwissProt annotations on these sequences mapped
through this alignment. Even protein sequences without a single curated
annotation (splice isoforms) are visible in this track. Each UniProt protein
has one main isoform, which is colored in dark. Alternative isoforms are
sequences that do not have annotations on them and are colored in light-blue.
They can be hidden with the TrEMBL/Isoform filter (see below). |
|UCSC Alignment, TrEMBL = predicted protein sequences
||Protein sequences from TrEMBL mapped to the genome. All other tracks
below are (start,end) TrEMBL annotations mapped to the genome using
this track. This track is hidden by default. To show it, click its
checkbox on the track configuration 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 Regions of Interest
||Regions that have been experimentally defined, such as the role of a region in mediating protein-protein interactions or some other biological process.
||Protein domains, zinc finger regions and topological domains.
|UniProt 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.
||Regions of repeated sequence motifs or repeated domains.
|UniProt Other Annotations
||All other annotations, e.g. compositional bias
For consistency and convenience for users of mutation-related tracks,
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,
transmembrane, and cytoplasmic.
In the "UniProt Modifications" track, lipoification sites are highlighted in
dark blue, glycosylation sites in
dark green, and phosphorylation in
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 protein sequence alignments but with the same genome
coordinates are only shown once.
On the configuration page of this track, you can choose to hide any TrEMBL annotations.
This filter will also hide the UniProt alternative isoform protein sequences because
both types of information are less relevant to most users. Please contact us if you
want more detailed filtering features.
Note that for the human hg38 assembly and SwissProt annotations, there
also is a public
track hub prepared by UniProt itself, with
genome annotations maintained by UniProt using their own mapping
method based on those Gencode/Ensembl gene models that are annotated in UniProt
for a given protein. For proteins that differ from the genome, UniProt's mapping method
will, in most cases, map a protein and its annotations to an unexpected location
(see below for details on UCSC's mapping method).
Briefly, UniProt protein sequences were aligned to the transcripts associated
with the protein, the top-scoring alignments were retained, and the result was
projected to the genome through a transcript-to-genome alignment.
Depending on the genome, the transcript-genome alignments was either
provided by the source database (NBCI RefSeq), created at UCSC (UCSC RefSeq) or
derived from the transcripts (Ensembl/Augustus). The transcript set is NCBI
RefSeq for hg38, UCSC RefSeq for hg19 (due to alt/fix haplotype misplacements
in the NCBI RefSeq set on hg19). For other genomes, RefSeq, Ensembl and Augustus
are tried, in this order. The resulting protein-genome alignments of this process
are available in the file formats for liftOver or pslMap from our data archive
(see "Data Access" section below).
An important step of the mapping process protein -> transcript ->
genome is filtering the alignment from protein to transcript. Due to
differences between the UniProt proteins and the transcripts (proteins were
made many years before the transcripts were made, and human genomes have
variants), the transcript with the highest BLAST score when aligning the
protein to all transcripts is not always the correct transcript for a protein
sequence. Therefore, the protein sequence is aligned to only a very short list
of one or sometimes more transcripts, selected by a three-step procedure:
- Use transcripts directly annotated by UniProt: for organisms that have a RefSeq transcript track,
proteins are aligned to the RefSeq transcripts that are annotated
by UniProt for this particular protein.
- Use transcripts for NCBI Gene ID annotated by UniProt: If no transcripts are annotated on the
protein, or the annotated ones have been deprecated by NCBI, but a NCBI Gene ID is
annotated, the RefSeq transcripts for this Gene ID are used. This can result in multiple matching transcripts for a protein.
- Use best matching transcript: If no NCBI Gene is
annotated, then BLAST scores are used to pick the transcripts. There can be multiple transcripts for one
protein, as their coding sequences can be identical. All transcripts within 1% of the highest observed BLAST score are used.
For strategy 2 and 3, many of the transcripts found do not differ in coding
sequence, so the resulting alignments on the genome will be identical.
Therefore, any identical alignments are removed in a final filtering step. The
details page of these alignments will contain a list of all transcripts that
result in the same protein-genome alignment. On hg38, only a handful of edge
cases (pseudogenes, very recently added proteins) remain in 2023 where strategy
3 has to be used.
In other words, when an NCBI or UCSC RefSeq track is used for the mapping and to align a
protein sequence to the correct transcript, we use a three stage process:
- If UniProt has annotated a given RefSeq transcript for a given protein
sequence, the protein is aligned to this transcript. Any difference in the
version suffix is tolerated in this comparison.
- If no transcript is annotated or the transcript cannot be found in the
NCBI/UCSC RefSeq track, the UniProt-annotated NCBI Gene ID is resolved to a
set of NCBI RefSeq transcript IDs via the most current version of NCBI
genes tables. Only the top match of the resulting alignments and all
others within 1% of its score are used for the mapping.
- If no transcript can be found after step (2), the protein is aligned to all transcripts,
the top match, and all others within 1% of its score are used.
This system was designed to resolve the problem of incorrect mappings of
proteins, mostly on hg38, due to differences between the SwissProt
sequences and the genome reference sequence, which has changed since the
proteins were defined. The problem is most pronounced for gene families
composed of either very repetitive or very similar proteins. To make sure that
the alignments always go to the best chromosome location, all _alt and _fix
reference patch sequences are ignored for the alignment, so the patches are
entirely free of UniProt annotations. Please contact us if you have feedback on
this process or example edge cases. We are not aware of a way to evaluate the
results completely and in an automated manner.
Proteins were aligned to transcripts with TBLASTN, converted to PSL, filtered
with pslReps (93% query coverage, keep alignments within top 1% score), lifted to genome
positions with pslMap and filtered again with pslReps. UniProt annotations were
obtained from the UniProt XML file. The UniProt annotations were then mapped to the
genome through the alignment described above using the pslMap program. This 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.
This track is automatically updated on an ongoing basis, every 2-3 months.
The current version name is always shown on the track details page, it includes the
release of UniProt, the version of the transcript set and a unique MD5 that is
based on the protein sequences, the transcript sequences, the mapping file
between both and the transcript-genome alignment. The exact transcript
that was used for the alignment is shown when clicking a protein alignment
in one of the two alignment tracks.
For reproducibility of older analysis results and for manual inspection, previous versions of this track
are available for browsing in the form of the UCSC UniProt Archive Track Hub (click this link to connect the hub now). The underlying data of
all releases of this track (past and current) can be obtained from our downloads server, including the UniProt
The raw data of the current track can be explored interactively with the
Table Browser, or the
For automated analysis, the genome annotation is stored in a bigBed file that
can be downloaded from the
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
The tool can also be used to obtain only features within a given range, for example:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/cavPor3/uniprot/unipStruct.bb -chrom=chr6 -start=0 -end=1000000 stdout
Please refer to our
mailing list archives
for questions, or our
Data Access FAQ
for more information.
Lifting from UniProt to genome coordinates in pipelines
To facilitate mapping protein coordinates to the genome, we provide the
alignment files in formats that are suitable for our command line tools. Our
command line programs liftOver or pslMap can be used to map
coordinates on protein sequences to genome coordinates. The filenames are
unipToGenome.over.chain.gz (liftOver) and unipToGenomeLift.psl.gz (pslMap).
wget -q https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/uniprot/2022_03/unipToGenome.over.chain.gz
wget -q https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver
chmod a+x liftOver
echo 'Q99697 1 10 annotationOnProtein' > prot.bed
liftOver prot.bed unipToGenome.over.chain.gz genome.bed
This track was created by Maximilian Haeussler at UCSC, with a lot of input from Chris
Lee, Mark Diekhans and Brian Raney, feedback from the UniProt staff, Alejo
Mujica, Regeneron Pharmaceuticals and Pia Riestra, GeneDx. Thanks to UniProt for making all data
available for download.
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.