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Search Genomic Coordinates of UniProt entries

Source: R/uniprot_coordinates.R
rba_uniprot_coordinates_search.Rd

Search genomic coordinates associated with UniProt entries by accession, chromosome, Ensembl identifier, gene, protein, taxonomy, or genomic range.

Usage

rba_uniprot_coordinates_search(
  accession = NULL,
  chromosome = NULL,
  ensembl_id = NULL,
  gene = NULL,
  protein = NULL,
  taxid = NULL,
  location = NULL,
  ...
)

Arguments

accession

Character: (optional) UniProtKB primary or secondary accession(s). You can supply up to 100 accession numbers.

chromosome

Character or Numeric: (optional) Chromosome name, such as "X", "Y", 1, or 20. You can supply up to 20 values.

ensembl_id

Character: (optional) Ensembl stable gene ID, transcript ID, or translation ID. You can supply up to 20 IDs.

gene

Character: (optional) UniProt gene name(s). You can supply up to 20 gene names.

protein

Character: (optional) UniProt protein name.

taxid

Numeric: (optional) NIH-NCBI Taxon ID. You can supply up to 20 taxon IDs.

location

Character: (optional) Genome location range, such as "58205437-58219305".

...

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

Value

A list named by accession. Each element contains one matching protein's genomic-coordinate information.

Details

At least one search criterion is required.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/coordinates"

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_location_protein()

Examples

# \donttest{
rba_uniprot_coordinates_search(taxid = 9606, chromosome = "y")
# }