Extended Data Figure 3: Analysis of LAVA element insertion in genes and early termination of transcription.

a, The histogram shows the results of permutation analyses. We find a significant association between LAVA elements and genes. Moreover, insertions are significantly enriched in introns and depleted in exons, most probably as a result of selection against insertions in exons. b, Schematic representation of the mechanism through which LAVA intronic insertions in antisense orientation might cause early termination of transcription. The truncated transcript is indicated on the diagram as A and normal transcript indicated on the diagram as B (pA = polyadenylation site). c, We calculated the distance to the nearest exon for each intronic LAVA and compared this to what would be expected for random insertions (that is, background). We found fewer insertions than expected by chance within 1 kb of the nearest exon. d, Identification of pmiRGlo_LA_F polyadenylation sites by 3′ RACE. Alignment of thirteen 3′ RACE PCR clone sequences and the pmiRGlo_LA_F sequence. LAVA_F 3′ TSD is highlighted by dark green background; the major antisense LAVA_F polyadenylation signal (MAPS) is highlighted by red background. The termination sites are marked with arrows on the LAVA_F sequence. Poly(A) tails of the identified transcripts are in red text.