Fig. 3: AU-rich elements (AREs) are potent splicing regulators in the PTRE-seq library.

A The nucleotide sequence of the PTRE-seq ARE element and a cartoon illustrating its impact on splice site selection. B Observed splicing fractions of ARE-containing (n = 371) and non-ARE-containing (n = 271) PTRE-seq transcripts. C Relationship between the number of intronic AREs and observed splicing fraction for blank (n = 51) and spacer (n = 27) splice acceptors. D Example read coverage tracts illustrating ability of 5’ AREs to block usage of adjacent P donors. E Comparison of donor usage in reporters with (n = 7) and without (n = 16) AREs 5’ to a 2^nd position P donor. F Splice acceptor usage based on location of the 3’-most ARE module. Box plots represent the distribution of observed splicing fractions observed at each potential acceptor site (1^st, 2^nd, 3^rd, or 4^th module sites, or spacer site) for different combinations of regulatory elements denoted along the bottom. G Example read coverage tracts illustrating ability of 3’ AREs to block usage of a strong upstream splice acceptor. H Comparison of acceptor usage in reporters without (n = 60) or with (n = 8) an ARE in the 4^th regulatory module. For (B, C, E, F, H), splicing fraction was computed as the median of 10 internal barcodes measured across two biological replicates (20 total measurements). For (C, E, F, H), only acceptors spliced at fractions above 1% are included. Box plots span the 25^th and 75^th percentile and the centers indicate the median. Whiskers indicate the furthest datum 1.5x outside the interquartile range. ✶ symbol represents all regulatory elements, ∀ symbol represents all regulatory elements except ARE.