Computational identification of the selenocysteine tRNA (tRNASec) in genomes
Fig 6
Duplication of tRNASec in hominids.
Pol III binding in human tRNASec1 (A) and tRNASec2 (B) by Chip-seq (tracks ERR039133 and ERR039141, see Materials and Methods). Conserved syntenic genes surrounding tRNASec1 (C) and tRNASec2 (D) in the genome of five hominids. tRNASec1 is flanked by the genes FOSB and RTN2, and tRNASec2 is located within an intron of PARVB. (E) Structural alignment of tRNASec1 in eleven primates (top) and tRNASec2, only found in hominids (bottom). Panels A and B were produced with the UCSC genome browser [60] on the human hg19 assembly. “100 Vert. Cons” track corresponds to sequence conservation across 100 vertebrates. Protein coding annotations in panels C and D were obtained with Selenoprofiles [24]. Sequences in panel E were obtained with Secmarker, aligned using Infernal (cmalign program) [31], and visualized with RALEE [61]. RALEE highlights the nucleotides that are paired according to the consensus secondary structure at the bottom of the alignment, and that also respect the standard pairing rules. The rightmost column in the alignment corresponds to the discriminator base.