A huge number of noncoding RNAs are transcribed from the genomes of higher eukaryotes, many of which are species-specific and localize in the nucleus with unknown function. 4.5SH RNA is a highly abundant, small rodent-specific noncoding RNA that localizes to nuclear speckles enriched in pre-mRNA splicing regulators. Here we show that mutant mice lacking the expression of 4.5SH RNA are embryonic lethal, suggesting that 4.5SH is an essential species-specific gene in mice. RNA-sequencing analyses revealed that 4.5SH RNA protects transcriptome from abnormal exonizations of the antisense insertions of retrotransposon SINE B1 (asB1), which would otherwise introduce deleterious premature stop codons or frameshift mutations. Mechanistically, 4.5SH RNA base-pairs with complementary asB1-containing exons and recruits effector proteins via its 5' stem loop. The modular organization of 4.5SH RNA enables us to engineer a programmable splicing regulator to induce the skipping of target exon of interest.