Get Genomic Coordinates of a Protein
Using this function you can retrieve genomic Coordinates of a Protein by either providing the protein's UniProt accession or it's ID in a cross-reference database (Ensembl, CCDC, HGNC or RefSeq). You should provide either 'accession' alone or 'db_type' and 'db_id' together.
rba_uniprot_coordinates(accession = NA, db_type = NA, db_id = NA, ...)
accession |
|
db_type |
cross-reference database name, Should be one of: "Ensembl", "CCDC", "HGNC" or "RefSeq". |
db_id |
Protein's ID in the cross-reference database |
... |
rbioapi option(s). Refer to |
For more information about how UniProt imports and calculates genomic
coordinates data, see:
McGarvey, P. B., Nightingale, A., Luo, J., Huang, H., Martin, M. J.,
Wu, C., & 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
A list with genome coordinates of your provided protein.
"GET https://ebi.ac.uk/proteins/api/coordinates/accession"
"GET https://ebi.ac.uk/proteins/api/coordinates/dbtype:dbid"
Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Martin, The Proteins API: accessing key integrated protein and genome information, Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W539–W544, https://doi.org/10.1093/nar/gkx237
Other "UniProt - Coordinates":
rba_uniprot_coordinates_location(),
rba_uniprot_coordinates_search(),
rba_uniprot_coordinates_sequence()
rba_uniprot_coordinates(accession = "P25942") rba_uniprot_coordinates(db_type = "HGNC", db_id = "CD40")
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