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. 2017 Feb 20;7:43044. doi: 10.1038/srep43044

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Copyright © 2017, The Author(s)

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(A) Determination of promoter elements. TATA boxes (5′-TTWTAW), polyA BRE motifs upstream of the TATA box, and PPE motifs “A” at −10 were identified relative to the TSS (+1). The bottom panels show the conservation of each motif of umRNAs and lmRNAs. (B) Proportion of each nucleotide at TSS (+1) and two nt upstream and downstream of the TSS of umRNAs and lmRNAs. The pyrimidine-purine dinucleotide motif is shown at −1 and +1 positions. (C) Start codon usage of all ORFs (primary TSS-associated ORFs, umRNAs, and lmRNAs. (D) Conserved ribosome-binding site (RBS) motif (5′-GGTG) for umRNAs (n = 796) and lmRNAs (n = 117). For lmRNAs, the absence of an RBS was confirmed.