Convert Uniprot ID to Ensembl Protein ID

[Brian Smith]

Hi,

How do I convert a uniprot ID (e.g. Q06787-1) to it's corresponding Ensembl Protein ID.

thanks!

[Matthew Speir]

Hi Brian,

Thank you for your question! You can find the UniProt ID and its corresponding Ensembl ID for most genes in the UCSC Genes track for hg19 using the Table Browser tool (genome.ucsc.edu/cgi-bin/hgTables).

Once there select:

Group: Genes and Gene Prediction Tracks
Track: UCSC Genes
Table: kgXref
Output format: selected fields from primary and related tables

If you have a list of specific UniProt IDs for which you want the corresponding Ensembl ID, you can paste or upload your list by using the buttons under the "identifiers" section on the main table browser page.

On the next page select the following fields:

First select the knownToEnsembl table, scroll to the bottom of the page and then click the "allow selection from checked tables" button.
After the page refreshes, then select the ensGtp table, scroll to the bottom of the page and then click the "allow selection from checked tables".

From ensGtp: protein
From kgXref: spID

Hit "get output" and you should see a table of Ensembl protein IDs and a column of UniProt IDs. It should look something like this:

#hg19.kgXref.spID    hg19.ensGtp.protein
Q8NH21    ENSP00000334393
...

Alternatively, UniProt's website has an ID Mapping tool (http://www.uniprot.org/?tab=mapping) that allows you to paste or upload a list of identifiers from one database and see the corresponding identifiers from another database. UniProt's mappings may differ slightly from those that you get through the Table Browser, since they may have directly mapped UniProt IDs to Ensembl Protein IDs, while the instructions outlined above are the result of mapping UniProt IDs and Ensembl IDs separately to UCSC Genes.

I hope this information is helpful. If you have further questions, please contact us again at gen...@soe.ucsc.edu.

-Matt Speir

UCSC Genome Bioinformatics Group

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