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Mapping Uniprot IDs in Ensembl Plants

BioMart is a very handy tool when you want to map between different databases. The following is a list of IDs from the UniProtKB/Swiss-Prot database of Arabidopsis thaliana proteins that are supposedly involved in flavonoid metabolism: P42813, Q9LS08, Q9ZST4, Q9SYM2, P51102, Q9LPV9, Q9FE25, Q96323, Q9FKW3, P13114, P41088, Q9S818, Q96330, O22203, Q39224, O22264, Q9SD85, Q9LYT3, Q9FJA2, Q43128, P43254, O04153, Q43125, Q9S9P6, Q94C57, Q9LNE6, Q9FK25, Q9SYM5, Q9ZQ95

Using BioMart in Ensembl Plants a list that shows to which Ensembl Gene IDs these UniProtKB/Swiss-Prot IDs map. Also include the gene name and description.

  1. Go to BioMart in Ensembl Plants. Click the New button on the toolbar in the top left-hand corner to start a new query. Choose the Ensembl Plants Genes database. Choose the Arabidopsis thaliana genes dataset.

  2. Click on Filters in the left panel. Expand the GENE section. Select ID list limit – UniProt/Swissprot ID(s). Enter the list of IDs in the text box (either comma separated or as a list).

  3. Click on Attributes in the left panel. Expand the GENE section. Deselect Transcript Stable ID. Select Gene name and Gene description. Expand the EXTERNAL section. Select UniProtKB/SwissProt ID(s).

  4. Click the Results button on the toolbar. Select View: All rows as HTML or export all results to a file. Tick the box Unique results only.

    Your results should show 28 / 32833 genes.