diff --git a/modules/Bio/EnsEMBL/TranscriptMapper.pm b/modules/Bio/EnsEMBL/TranscriptMapper.pm
index a9a6f9e59f6db8b52e1c19278dc2ca182edf7993..78576a033f5347f2c6eec532971d2ca73c900cf6 100644
--- a/modules/Bio/EnsEMBL/TranscriptMapper.pm
+++ b/modules/Bio/EnsEMBL/TranscriptMapper.pm
@@ -157,8 +157,8 @@ sub _load_mapper {
 
 
   foreach my $ex (@{$transcript->get_all_Exons}) {
-    my $gen_start = $ex->start();
-    my $gen_end   = $ex->end();
+    my $gen_start = $ex->seq_region_start();
+    my $gen_end   = $ex->seq_region_end();
 
     $cdna_start = $cdna_end + 1;
     $cdna_end   = $cdna_start + $ex->length() - 1;