Multiple sequence alignment results of tetrahymena thermophila group I intron with other group IC1 introns (containing sequence level manually annotated secondary structures)

We fetched a multiple sequence alignment of the IC1 sub-family of group I introns from the Comparative RNA Web (CRW) Site. The precise exon-intron boundaries were determined using annotations from GISSD database. The intron sequences were extended with flanking exons (50nt each side) retrieved via the GenBank identifiers to build a 310 group IC1 intron sequences database. The intron regions following the 3’ end of the P1 stem were removed as irrelevant for further processing. Each individual sequence was then annotated with all possible candidate P0 and P0’ stems based on

nucleotide complementarity. We manually selected best P0 and P0' secondary structure candidates and realigned sequences based on their P1, P0, and P0' stems.

The consensus Tet-S2b secondary structure representing the pseudoknot was mapped to individual sequences to assess the structure conservation.

crw50_aligned_mapped.sto :

The raw alignment file with sequence level secondary structures annotation. The plus signs represent inconsistent (i.e. lost) base pairs - here we can see that P1 + P0 + P0' are present in almost all the sequences.

IC1 sequence type annotation by accession number.xlsx:

The file which annotate sequence types (rRNA or not with detailed sequence names). All 310 sequence in

our sequence alignment dataset are rRNAs.

 tet_align.pdf :

Visualization of the full sequence alignment. The alignment was trimmed on the Tetrahymena sequence positions (i.e., with columns of Tetrahymena gaps removed) based on crw50_aligned_mapped.sto for better visuliazation.