LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome

MOTIVATION Despite the increasing notions of the functional importance of antisense transcripts in gene regulation, the genome-wide overview on the ontology of antisense genes has not been obtained. Therefore, we tried to find novel antisense genes genome-wide by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries. RESULTS We identified 1260 potential antisense genes, of which 1001 are not annotated in EnsEMBL, thereby being regarded as novel. Interestingly their sense counterparts were co-expressed in the majority of the cases. CONCLUSIONS The use of LongSAGE transcriptome data is extremely powerful in the identification of thus-far unknown antisense transcripts, even in the case of well-characterized organisms like the mouse. CONTACT [email protected].