Description
UniProt is a resource of information on protein sequences and function.
Manual curation of high quality experimental protein data from the literature
describes the role of a protein, and regions or sites of interest such as functional
domains, binding and enzyme active sites, sequence structure, post-translational
modifications and variants associated with disease.
In order to support the genomics community in the interpretation and exploration of
the rat (mixed female BN/SsNHsdMCW and male SHR) genome, UniProt provides an up-to-date
mapping between specific genomic sequence coordinates and the corresponding protein
sequence annotations.
Methods
Rat protein sequences in the UniProt Knowledgebase (UniProtKB) have been mapped
to the Rat reference genome assembly (Rnor_6.0) via the Ensembl resource. For each
protein sequence in UniProtKB the corresponding peptide, transcript and genomic
coordinates in Ensembl are identified. These mappings are updated for each UniProt
release and specific tracks are provided for each UniProt sequence annotation
type e.g. binding site.
Display Conventions and Configuration
Track naming convention
Each track name consists of a unique proteome identifier followed by the species
NCBI taxonomy identifier and the specific UniProt sequence annotation name.
For example, for rat the UniProt unique proteome identifier is UP000002494
and the NCBI taxonomy identifier is 10116.
The list of sequence annotation names and their descriptions are provided below.
UP000002494_10116_proteome
The proteome is the set of proteins thought to be expressed by the organism.
UniProt proteomes include both manually reviewed (UniProtKB/Swiss-Prot)
and unreviewed (UniProtKB/TrEMBL) entries.
UP000002494_10116_site
Any interesting single amino acid site on the sequence.
UP000002494_10116_binding
Binding site for any chemical group (co-enzyme, prosthetic group, etc).
UP000002494_10116_ca_bind.bb
Position(s) of calcium binding region(s) within the protein.
UP000002494_10116_carbohyd.bb
Covalently attached glycan group(s).
UP000002494_10116_chain
Extent of a polypeptide chain in the mature protein.
UP000002494_10116_coiled
Positions of regions of coiled coil within the protein.
UP000002494_10116_crosslnk
Residues participating in covalent linkage(s) between proteins.
UP000002494_10116_disulfide
Cysteine residues participating in disulfide bonds.
UP000002494_10116_dna_bind
Position and type of a DNA-binding domain.
UP000002494_10116_domain
Position and type of each modular protein domain.
UP000002494_10116_intramem
Extent of a region located in a membrane without crossing it.
UP000002494_10116_lipid
Covalently attached lipid group(s).
UP000002494_10116_metal
Binding site for a metal ion.
UP000002494_10116_modres
Modified residues excluding lipids, glycans and protein cross-links.
UP000002494_10116_motif
Short (up to 20 amino acids) sequence motif of biological interest.
UP000002494_10116_np_bind
Nucleotide phosphate binding region.
UP000002494_10116_peptide
Extent of an active peptide in the mature protein.
UP000002494_10116_region
Region of interest in the sequence.
UP000002494_10116_repeat
Positions of repeated sequence motifs or repeated domains.
UP000002494_10116_signal
Sequence targeting proteins to the secretory pathway or periplasmic space.
UP000002494_10116_site
Any interesting single amino acid site on the sequence.
UP000002494_10116_topodomain
Location of non-membrane regions of membrane-spanning proteins.
UP000002494_10116_transit
Extent of a transit peptide for organelle targeting.
UP000002494_10116_transmem
Extent of a membrane-spanning region.
UP000002494_10116_variants
A natural variant in the protein.
UP000002494_10116_zn_fing
Position(s) and type(s) of zinc fingers within the protein.
Credits
UniProt is a collaboration between the EMBL-European Bioinformatics Institute (EMBL-EBI),
the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR).
UniProt is supported by the National Eye Institute (NEI), National Human Genome Research
Institute (NHGRI), National Heart, Lung, and Blood Institute (NHLBI), National Institute
of Allergy and Infectious Diseases (NIAID), National Institute of Diabetes and Digestive
and Kidney Diseases (NIDDK), National Institute of General Medical Sciences (NIGMS), and
National Institute of Mental Health (NIMH) of the National Institutes of Health (NIH)
under grant U24HG007822. Additional support for the EMBL-EBI’s involvement in UniProt
comes from European Molecular Biology Laboratory (EMBL), the British Heart Foundation
(BHF) (RG/13/5/30112), the Parkinson’s Disease United Kingdom (PDUK) GO grant G-1307, and
the NIH GO grant U41HG02273. UniProt activities at the SIB are additionally supported by
the Swiss Federal Government through the State Secretariat for Education, Research and
Innovation SERI. PIR’s UniProt activities are also supported by the NIH grants R01GM080646,
G08LM010720, and P20GM103446, and the National Science Foundation (NSF) grant DBI-1062520.
help@uniprot.org
References
https://academic.oup.com/nar/article/47/D1/D506/5160987
and
https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23738