(a) Pie chart of exon usage changes in MeCP2-knockdown neurons examined by RNA-Seq and DEXSeq package. (b) Real-time PCR analysis of alternative splicing changes in MeCP2-knockdown neurons. Eight exons were chosen based on DEXSeq analysis. Exon-specific primers were designed to determine the expression level of selected exons, and gene-specific primers were used as internal control (**P < 0.01; ***P < 0.001). (c) Eight modes of alternative splicing events examined using ASD software. Black boxes representing constitutive exons while white boxes representing alternative spliced exons/regions. Solid lines representing exon inclusion while dotted lines representing exon exclusion. (d) Summay of alternative splicing analysis and changed alternative splicing events by ASD software in mouse Mecp2-knockdown neurons. (e) Summay of alternative splicing analysis and changed alternative splicing events by ASD software in Mecp2-null rat hippocampus.