Species-specific splicing differences are primarily governed by changes in cis-acting sequences

We assessed whether human transcripts expressed in an aneuploid mouse that carries human chromosome 21 (HsChr21) are spliced in a human-specific or mouse-specific fashion. In almost all cases, human-specific alternative splicing is maintained in the mouse nucleus. Species-specific splicing therefore appears to be primarily directed by cis-acting elements, rather than changes in the levels or activities of trans-acting factors. Approximately 485 million Illumina 50-nt sequence reads were generated for brain and liver tissues from normal human, Tc0 (wildtype) mouse and Tc1 mouse strains. Sequence reads were mapped to splice junctions and %in levels were estimated.