R3DSVS: RNA 3D Motif Sequence Variability Server

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.

Enter unit id(s)/loop id(s)
Choose output format
Choose count restriction

Choose extension (beyond the specified loop limits)
Select Source (choose from A,B,C,E,M,V,U. Can choose multiple sources and separate them with commas)

Choose data source

Examples

Example 1
Watson-Crick-Franklin 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
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 cordinates at this link

Example 4
Eukaryotic internal loop with intercalated nucleotide.
Visualize the 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