Thank you Sean. You are right there is no annotation of this gene in GenBank or Ensemble. But if we dig into more, you can see that both GenBank (section "Reference sequence information" on the right panel)

and EMBL ("Ensemble Genes" in the "Navigation" section) point to the gene Pannexin 3 (PANX3) for this clone, and BLAST confirms that this clone aligns 100% to PANX3.

Is there a package/function in bioconductor that still allows me to retrieve the gene information for this ID? I have a bunch of GenBank/EMBL IDs in this situation, just want to automate the retrieval if possible.

Thanks

John





________________________________
 From: Sean Davis <sdavis2@mail.nih.gov>

Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> 
Sent: Wednesday, April 18, 2012 12:16 PM
Subject: Re: [BioC] retrieve gene symbol/description


> Hi, I am trying to retrieve gene symbol/description with GenBank/EMBL IDs using biomaRt. I was successful with some IDs, but not with others. For example:
>
>> library(biomaRt)
>
>> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
>
>
>> getBM(attributes=c('embl', 'description','hgnc_symbol'),   filters = 'embl', values = c('AF133587','AA456140'), mart = ensembl)
>
>       embl                                                          description hgnc_symbol
> 1 AF133587 rhabdoid tumor deletion region gene 1 [Source:HGNC Symbol;Acc:13437]       RTDR1
>
>
> As you can see, the first ID returns gene symbol/description successfully, but the 2nd one did not. What is the reason for the 2nd one not working? Is there other ways to get it to work?
>

Hi, John.

This query is working as expected.  The genbank accession "AA456140"
is not associated with any gene in the Ensembl gene collection.  Try
typing your two accessions into the ensembl search box.  You'll note
that one the first is associated with a gene while the second is
simply a genomic alignment (and not associated with a gene).

Sean
	[[alternative HTML version deleted]]

