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rRNA secondary structure models

This section includes secondary structure models SSU (small subunit) ribosomal RNA molecules. LSU (large subunit) ribosomal RNA models and additional SSU models will be added in the future.

The sequences are ordered according to the first 3 levels of the NCBI taxonomy. The first level corresponds to the superkingdom but subsequent levels are not neccessarily kingdom and phylum.

The Prokaryotic SSU rRNA model is in accordance with Van de Peer et al. (2000)
The Eukaryotic SSU rRNA model is in accordance with Wuyts et al. (2000)

SSU rRNA secondary structure models
NCBI taxonomy species name acc no.
Archaea Crenarchaeota Sulfolobales Sulfolobus acidocaldarius D14876
Euryarchaeota Methanococcales Methanococcus jannaschii U67517
Eukaryota Alveolata Apicomplexa Plasmodium vivax U03079
Ciliophora Tetrahymena canadensis M26359
Dinophyceae Gymnodinium breve AF172714
Fungi Ascomycota Saccharomyces cerevisiae V01335
Basidiomycota Coprinus cinereus M92991
Metazoa Arthropoda Daphnia pulex AF014011
Loricera foveata AF012503
Platyhelminthes Calicophoron calicophorum L06566
Rhodophyta Florideophyceae Palmaria palmata X53500
stramenopiles Bacillariophyta Bacillaria paxillifer M87325
Viridiplantae Chlorophyta Chlamydomonas reinhardtii M32703
Embryophyta Zea mays K02202


  • Van de Peer, Y.; De Rijk, P.; Wuyts, J.; Winkelmans, T.; De Wachter, R. (2000)
    "The European small subunit ribosomal RNA database"
    Nucleic Acids Res., 28, 175-176
  • Wuyts, J.; De Rijk, P.; Van de Peer, Y.; Pison, G.; Rousseeuw, P.; De Wachter, R. (2000)
    "Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA"
    Nucleic Acids Res., 28, 4698-4708