Genome-wide identification of Ty1/Copia shGAG RNA 3′ ends and splicing-induced stop codon generation. (A,B) RNA 3′ end tags were clustered on a distance basis to generate distinct 3′ end clusters, shown here for ACTIN 2 (ACT2; A) and COPIA89 (B). Distinct coverage peaks resulting in two 3′ end clusters appear for shGAG (red asterisk) and GAG-POL (blue asterisk) mRNAs. (C) Density of introns and their most proximal RNA 3′ ends on a multiple sequence alignment of Ty1/Copia elements. (D,E) Relative densities of open reading frames (ORFs), introns, and stop codons found in the genomic sequence of full-length (D) and spliced (E) Ty1/Copia elements. (F) Scheme representing the three possible RNA isoforms produced by Ty1/Copia elements, illustrated here with EVD, as well as the resulting 3′ UTRs and stop codon distribution in red. (SD) splice donor; (SA) splice acceptor; (EJ) exon junction; (n) number of individual elements.
