We used known alternatively spliced forms of mouse OPRM1 (MOR-1B, MOR-1F, MOR-1I, MOR-1J, MOR-1K and MOR-1L, MOR-1Q, MOR-1S, MOR-1T, MOR-1R, MOR-1P, MOR-1V and MOR-1W) from GenBank annotations (http://www.ncbi.nlm.nih.gov/) to locate unidentified human orthologous exons. Annotated alternative mouse and human variants from altervative splice database (http://www.ebi.ac.uk/asd) and UCSC database (http://genome.ucsc.edu/) were also used in the analysis. BLAST (66) and BLAT (http://genome.ucsc.edu/) were used to confirm the synteny of aligned full-length sequences of the human and mouse OPRM1 genes. Detailed alignments of orthologous pairs of the human and mouse OPRM1 genomic and mRNA sequences were produced using OWEN (36). For the CDS, the alignment of the nucleotide sequences was guided by the amino acid sequence alignment (67). Multiple alignments of nucleotide sequences were constructed using the CLUSTALW program with default parameters (68) and edited to take into account results of pairwise comparisons, which was done using the OWEN program (36). In all cases, our alignments contained putative exons presented in GenBank. We masked sequences using RepeatMasker (http://humangen.med.ub.es/tools/RepeatMasker.html), because numerous low-complexity and repetitive regions in long intronic sequences obscured the pattern of orthology.
