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Map Protein Sequence Positions to Genomic Coordinates

Source: R/uniprot_coordinates.R
rba_uniprot_coordinates_location_protein.Rd

Map an amino-acid position or range in a UniProt protein sequence to its corresponding genomic coordinates. A protein sequence location may have more than one genomic mapping. Supply p_position alone, or supply p_start and p_end together.

Usage

rba_uniprot_coordinates_location_protein(
  accession,
  p_position = NULL,
  p_start = NULL,
  p_end = NULL,
  ...
)

Arguments

accession

Character: UniProtKB primary or secondary accession.

p_position

Numeric: (optional) Protein sequence position. Supply this alone, or supply both p_start and p_end.

p_start

Numeric: (optional) Protein sequence range start.

p_end

Numeric: (optional) Protein sequence range end.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A list with a locations element containing the mapped protein and genomic boundaries. Records can include chromosome, strand, genome assembly, nucleotide and Ensembl identifiers, amino acids, and mapped sequence features.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/coordinates/location/{accession}:{pPosition}"
"GET https://www.ebi.ac.uk/proteins/api/coordinates/location/{accession}:{pStart}-{pEnd}"

References

  • The UniProt Consortium. (2025). UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Research, 53(D1), D609–D617. https://doi.org/10.1093/nar/gkae1010

  • Nightingale, A., Antunes, R., Alpi, E., Bursteinas, B., Gonzales, L., Liu, W., Luo, J., Qi, G., Turner, E., & Martin, M. (2017). The Proteins API: Accessing key integrated protein and genome information. Nucleic Acids Research, 45(W1), W539–W544. https://doi.org/10.1093/nar/gkx237

  • McGarvey, P. B., Nightingale, A., Luo, J., Huang, H., Martin, M. J., Wu, C., & The UniProt Consortium. (2019). UniProt genomic mapping for deciphering functional effects of missense variants. Human Mutation, 40(6), 694–705. https://doi.org/10.1002/humu.23738

  • Proteins API Documentation

  • Citations note on UniProt website

See also

Other "UniProt - Coordinates": rba_uniprot_coordinates(), rba_uniprot_coordinates_location(), rba_uniprot_coordinates_location_genome(), rba_uniprot_coordinates_search()

Examples

# \donttest{
rba_uniprot_coordinates_location_protein(accession = "P25942", p_position = 1)
# }
# \donttest{
rba_uniprot_coordinates_location_protein(accession = "P25942",
    p_start = 1, p_end = 277)
# }