Getting Uniprot accession number
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2.1 years ago

Hello,

I have a table full of Uniprot protein names and an uniprot identifier like this : ANTR6_ARATH. https://www.uniprot.org/uniprot/Q3E9A0&format=html

It is supposed to be the gene id, however when I use https://biodbnet-abcc.ncifcrf.gov/db/db2db.php with ANTR6_ARATH as a gene id input I have no output results (I have tried Uniprot info and Kegg info also as outputs).

Does anyone know how I could use this identifier on biodbnet ?

gene RNA-Seq • 800 views
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ANTR6_ARATH : ANTR6 is gene symbol (for bioDBnet entry) and ARATH = ARAbidopsis THaliana.

Using the gene symbol as input will give you output with UniProt selection.

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23 months ago

Note: assigning the "uniprot" tag to your post would have made it much more findable and we could have replied earlier.

ANTR6_ARATH is a mnemonic identifier for the UniProtKB entry, often also called "entry name", but it is not a stable identifier (see https://www.uniprot.org/help/entry_name). In contrast, we strongly recommend to use the accession number instead: An accession number (AC) is assigned to each sequence upon inclusion into UniProtKB. Accession numbers are stable from release to release. https://www.uniprot.org/help/difference_accession_entryname

The accession number of ANTR6_ARATH is Q3E9A0 (see https://www.uniprot.org/uniprot/Q3E9A0)

I recommend that you upload your list of mnemonics to the UniProt Batch retrieve/IDmapping tool at https://www.uniprot.org/uploadlists This will return the list of accession numbers - click on "Downloads" to obtain either the mapping table or the list of UniProtKB ACs. These are more widely used in other databases.

@GenoMax: The UniProtKB/Swiss-Prot entry name consists of up to 11 uppercase alphanumeric characters with a naming convention that can be symbolized as X_Y, where: X is a mnemonic protein identification code of at most 5 alphanumeric characters; The mnemonic code 'X' is an abbreviation of the protein/gene name, which does not necessarily correspond to the recommended protein name or to the gene name (https://www.uniprot.org/help/entry_name).

Please don't hesitate to contact the UniProt helpdesk if you have any addtional questions.

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My comment was showing OP what selections they needed to use with bioDBnet to get expected output.