With more than 1 million insertions in the human genome, Alu elements have and continue to shape primate genome architecture. One mechanism by which Alu elements contribute to genome evolution is through the formation of novel exons in mRNA transcripts. Such Alu exonization may represent an evolutionary strategy by which host genomes can modulate protein expression and protein behavior. Recent advances in long-read sequencing technology support more comprehensive detection and quantification of TEs. We have developed ESPRESSO-TEA (Error Statistics Promoted Evaluator of Splice Site Options – Transposable Element Analysis), a computational pipeline to profile locus-specific TE expression from long-read RNA-seq. ESPRESSO-TEA characterizes TE-derived exons within full-length transcripts, thereby capturing the complex, spliced structures of different TE-containing transcript isoforms. Using this platform, we characterize the transcriptional landscape of Alu exons across 30 human tissues. We highlight mechanisms by which Alus may drive tissue-specific and species-specific differences in gene expression and protein production. We expect our research will shed light on evolutionary and functional innovations that distinguish human and non-human primates.