[BioC] [biomaRt] contradicting gene information

[Paul Theodor Pyl]

Hi Guys,

I observed the following in a dataset I'm working on:

> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> getBM( attributes = c("ensembl_gene_id", "chromosome_name", "strand",
"start_position", "end_position"), filters = "ensembl_gene_id", values =
c("ENSG00000002586"), mart = ensembl)
  ensembl_gene_id chromosome_name strand start_position end_position
1 ENSG00000002586               X      1        2609220      2659350
2 ENSG00000002586               Y      1        2559220      2609350
> sessionInfo()
R version 2.14.0 Under development (unstable) (2011-07-03 r56263)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] GenomicRanges_1.6.2 IRanges_1.12.1      biomaRt_2.10.0     

loaded via a namespace (and not attached):
[1] RCurl_1.7-0  tools_2.14.0 XML_3.4-3 

When I check the gene on the ensembl website
( http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=1;q=ENSG00000002586 ) or web-interface to ensembl biomart ( http://www.ensembl.org/biomart/martview )

I get the coordinates on chromosome X only.
Any idea as to what might cause this?

Cheers,
Paul
-- 
Paul Theodor Pyl
Predoctoral Fellow
Huber Group - Genome Biology Unit
EMBL Heidelberg
+49 6221 387-8676