Question: UNIPROT missing values
gravatar for julie.chevalier
9 weeks ago by
julie.chevalier0 wrote:


I'm working with the latest version of AnnotationDbi(1.38.2) and (3.4.1) in R 3.3.3.

I've tried to retrieve matching SYMBOL with UNIPROT ID with this command :


I've obtained this error :

Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'UNIPROT'. Please use the keys method to see a listing of valid arguments.


It seems that this UNIPROT (verified by printing all UNIPROT of with this command : keys(,keytype="UNIPROT") doesn't exist in the database while this UNIPROT ID exists for mouse and correspond to the "Sox3" gene.

When I try the same command with sox3 gene as entry, I obtain this result :

'select()' returned 1:many mapping between keys and columns
1   Sox3  A2AM37
2   Sox3  Q5RKW0

The status of these two UNIPROT ID is "unreviewed" inthe UNIPROTKB website while the uniprot P53784 is "reviewed" but not contained in the DB!

I have the same problem with several UNIPROT ID, is it normal ? is there an other version of the database containing all UNIPROT ID ?

Thanks in advance



ADD COMMENTlink modified 9 weeks ago by Mike Smith2.1k • written 9 weeks ago by julie.chevalier0
gravatar for Mike Smith
9 weeks ago by
Mike Smith2.1k
EMBL Heidelberg / de.NBI
Mike Smith2.1k wrote:

If you take a look at the manual pages for it gives the following details on how the Uniprot mappings are derived: 

"This object is a simple mapping of Entrez Gene identifiers entrez/query.fcgi?db=gene to Uniprot Accession Numbers"

So we can take a look at the NCBI entry for Sox-3 at to try and understand a little more.

If you jump to the RefSeq section of that page (here) you'll see two values listed next to UniProtKB/TrEMBL: A2AM37 & Q5RKW0.  There are the two reported in the package.

P53784 is mentioned further down the pages as a "related sequence".  This doesn't necessarily answer the question as to which mapping you want to use, but it at least explains why you find the discrepancy in

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Mike Smith2.1k
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