Get Genomic Coordinates of a Protein

Retrieve genomic coordinates for a protein using either its UniProt accession or its ID in a cross-reference database (Ensembl, CCDS, HGNC, or RefSeq). You should supply either accession alone or db_type and db_id together.

Usage

rba_uniprot_coordinates(accession = NULL, db_type = NULL, db_id = NULL, ...)

Arguments

accession: Character: (optional) UniProtKB primary or secondary accession.
db_type: Character: (optional) Cross-reference database name. One of "Ensembl", "CCDS", "HGNC", or "RefSeq".
db_id: Character: (optional) Protein identifier in the cross-reference database.
...: rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A list containing the requested protein's genomic coordinates.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/coordinates/{accession}"
"GET https://www.ebi.ac.uk/proteins/api/coordinates/{dbtype}:{dbid}"

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

Examples

# \donttest{
rba_uniprot_coordinates(accession = "P25942")
# }
# \donttest{
rba_uniprot_coordinates(db_type = "HGNC", db_id = "CD40")
# }