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. 2021 Apr 27;10:e65537. doi: 10.7554/eLife.65537

Figure 3. Nanopore and Helicos DRS identify NLR genes regulated by alternative polyadenylation.

(A–B) Protein domain enrichment analysis for loci with increased proximal poly(A) site selection in 35S::FPA:YFP line, as detected using (A) Nanopore DRS or (B) Helicos DRS. (C) Nanopore DRS reveals the complexity of RNA processing at RPS6. Protein domain locations (shown in grey) represent collapsed InterPro annotations. The novel TIR domain was annotated using InterProScan (Mitchell et al., 2019). (D) Protein alignment of the predicted TIR domain from the novel gene downstream of RPS6, with the sequence of the TIR domains from RPS6 and RPS4. Helix and strand secondary structures (from UniProt: RPS4, Q9XGM3) are shown in blue and yellow, respectively. Residues are shaded according to the degree of conservation.

Figure 3.

Figure 3—figure supplement 1. Nanopore DRS informs reannotation of the complex NLR locus encompassing the AT5G46490 and AT5G46500 annotations.

Figure 3—figure supplement 1.

Gene track showing alternative polyadenylation at the AT5G46490 gene locus, as detected with Illumina RNA-Seq, nanoPARE, Helicos DRS, and Nanopore DRS.
Figure 3—figure supplement 2. Nanopore DRS informs reannotation of the complex NLR locus encompassing the AT5G46490 and AT5G46500 annotations.

Figure 3—figure supplement 2.

Protein alignment showing similarity between the AT5G46500 protein sequence (which forms the C-terminal portion of distally polyadenylation AT5G46490–AT5G46500 mRNAs) and other NLR protein sequences in the RPS6 cluster. LRR predictions, generated with LRRpredictor (Martin et al., 2020), are shown in orange.