Examples of novel mammalian conventional mirtrons annotated in this study. (A) Human TRIM28 contains a mirtron (hsa-mir-6807) that is selectively conserved among primates. The dominant 5p and 3p reads form a typical miRNA/star duplex with 3′ overhang on the Dicer-cleaved end, and mature species were recovered from independent Ago-IP data sets. (B) Murine Baiap3 contains a mirtron (mmu-mir-3547) with relatively high expression. The orthologous intron was annotated as the canonical miRNA Mir3547 in rat; our observations indicate this as a conserved rodent mirtron. The red box and arrow highlight a terminal loop nucleotide that has diverged between the mouse and rat orthologs. Note that the 3p species of Trim28 and Baiap3 mirtrons accumulate high levels of untemplated uridine, with a lower level of untemplated adenine (yellow highlight). (C) An intron in mouse Mllt6 generates small RNAs that are reminiscent of a 3′-tailed layout. However, the 3′ end of its dominant 3p species end in CAG and are strongly uridylated, and the CAG is conserved across mammals. These features suggest it to be a conventional mirtron (mmu-mir-6927) in an alternatively spliced intron.
