R3DSVS: RNA 3D Motif Sequence Variability Server

The RNA 3D Motif Sequence Variability Server 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. R3D SVS can be used to study the sequence variability of individual nucleotides, base paired nucleotides, or small motifs.

This site is under construction as of November 2023

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

Several APIs are available, where one can input unit ids or loop ids or chain ids and get back useful information.RNA APIs

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 coordinate 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