Total RNA sequencing provides a relatively unbiased view of the transcriptional state of a population of cells. However, most total RNA-seq experiments must contend with a large number of reads that are not helpful for gene-expression analysis. Here we present capture sequencing experiments using Twist's new RNA Exome panel, which uses a novel design strategy to specifically target every protein-coding isoform in Gencode v41 Basic. We evaluate the performance of the RNA exome on degraded RNA, in differential expression applications, and in its ability to capture novel transcript variants. Overall, we provide evidence that the Twist Targeted Enrichment for Gene Expression solution is an effective way to efficiently profile gene expression and detect gene fusions.