Figure 5.

Variation in UTR lengths affects transcript and AS quantification. (A) AT1G04400 (CRY2; CRYPTOCHROME 2) has two different AS events (an Alt3΄ss in exon 2 and Alt3΄ss in exon 4). The difference between the shortest (ID6) and longest (P1) transcripts is 237 and 43 nt at the 5΄ UTR and 3΄ UTR, respectively. (B) Read alignment showing the relatively low level of Alt3΄ss splice junction reads. (C) Average TPMs of the 3 transcripts using Salmon and kallisto and the AtRTD2 and AtRTD2-padded; (D) AS ratios of the transcript with Alt3΄ss in exon 2 to FS (fully spliced) transcripts with HR RT-PCR, manual counting of splice junction reads in this region using the Tablet read alignment viewer, Salmon and kallisto with AtRTD2-padded and AtRTD2, Salmon and kallisto with uncorrected functions with AtRTD2, and Salmon with Araport11.