The RNA 3D Motif Sequence Variability Server (R3DSVS) maps the given nucleotides to columns of a multiple sequence alignment and returns sequence variants in a variety of formats. This makes it possible to see how the sequence of a 3D motif varies across many species, including ones for which we do not have a 3D structure. R3DSVS can be used to study the sequence variability of individual nucleotides, base paired nucleotides, or small motifs.
This site is under construction as of September 2024, but seems to be working well.
Example 1
Watson-Crick basepair from the spliceosome. Only the unique sequences will be shown. They are usually U*A but sometimes U*U.
Visualize the coordinates at this link
Example 2
Watson-Crick basepair making A-minor interaction. E. coli has GC basepair, other bacteria have AU or UA or CG.
Visualize the coordinates at this link
Example 3
Hairpin loop from Helix 95 of archaeal LSU in fasta format.
Visualize the coordinates at this link
Example 4
Eukaryotic internal loop with intercalated nucleotide that is nearly always A.
Visualize the loop coordinates at this link
In addition to R3D SVS, several other APIs are available, where one can input unit ids or loop ids or chain ids and get back useful information. RNA APIs