[ensembl-dev] upstream API question

[Rami Al-Ouran]

Hello,

I am trying to extract gene promoters from the Ensembl data base using the Perl API . I am using the Bio::EnsEMBL::Upstream->new function to get the upstream regions, and from there get the promoter region. When I give it a gene (gene Gvin1 from Mouse latest build) the upstream region returned is still within the gene range not upstream of it. When I try using UCSC genome browser server it does give me the region upstream the gene.

More details:
Gene: Gvin1
Gene range: Chromosome 7: 113,300,049-113,358,854
output from my $upstream = Bio::EnsEMBL::Upstream->new(
     -transcript =>  $inTranscript,
     -length     =>  1000           # bp
   );

my $upstream_region_start = $upstream->upstart; # this returns 113308775
my $upstream_region_end   = $upstream->upend; #this returns 113308775

Am I misunderstanding something? (I am a computer science major) or is there a more accurate way to get promoters?

Thank you very much,
Rami