I am trying to retrieve the cDNA sequence based on the HGNC symbol.

ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")

getSequence(id = "BRCA1", type = "hgnc_symbol", seqType = "gene_exon", mart = ensembl)

The above code works fine. However, if I do this:

ensembl <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")

getSequence(id = "BRCA1", type = "hgnc_symbol", seqType = "gene_exon", mart = ensembl)

The output is an empty table with 0 rows.

What am I doing wrong? I've checked for typos but can't find any.

Session info:

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8      
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C             
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] biomaRt_2.28.0

loaded via a namespace (and not attached):
 [1] IRanges_2.6.1        parallel_3.3.1       DBI_0.5            
 [4] tools_3.3.1          RCurl_1.95-4.8       Biobase_2.32.0     
 [7] AnnotationDbi_1.34.4 RSQLite_1.0.0        S4Vectors_0.10.3   
[10] BiocGenerics_0.18.0  stats4_3.3.1         bitops_1.0-6       
[13] XML_3.98-1.4   

I don't believe hgnc_symbol is a valid filter for mouse, try using mgi_symbol instead. Also, for mouse symbols only the first character is uppercase, I would search for "Brca1".

cheers, jo