Koetschan et al. (2010) NAR 38:D275-9
Selig et al. (2008) NAR 36:D377-380.
Schultz et al. (2006) NAR 34:W704-7.
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ITS2 3D structure
(Keller et al. 2010)

Chlorophyta hypertree

(Buchheim et al. 2011)
Fig1, Fig2, Fig3, Fig4

ITS2 Motif Scan

This sequence based tool uses HMMer (Eddy 1998) to annotate eukaryote sequence motifs with Hidden Markov Models (HMMs). It returns three major ITS2 motifs for plants and fungi (unfortunately there are no data for animals). In plants we found the U-U mismatch (helix II, left), the U-U mismatch (helix II, right) additionally with AAA between helix II and III, as well as the UGGU motif 5' side to the apex of helix III. In fungi we also found three motifs (helix II left and helix II right) as well as one motif 5' side to the apex of helix III (however not as explicit as the UGGU in plants). Also the U-U mismatch in helix II is not as conserved as in plants. We identified all sequence motifs using MEME (Timothy et al. 1994).

  • Choose a Model:    
  • maximum E-values:
  • Input your sequences in FASTA-format
  • Multiple sequences are allowed
    E-value calculation is dependant of the amount of analyzed sequences (comparably to the size of a database). If you an alyze multiple sequence it may help to increase the maximum E-value.
  • Names will be truncated to 50 characters (must be unique)
  • Example test sequences: Plants, Fungi
Fig. 1: The three major ITS2 motifs for plants (U-U, AAA, UGGU). Scheme was drawn with Locomotif.

Motif U-U mismatch (helix II, right) with AAA (between helix II and III) Motif U-U mismatch (helix II, left) Motif UGGU (helix III, 5' side) Motifs of dahlia

ITS2 motif search
View Motif U-U mismatch (helix II, left) View Motif U-U mismatch (helix II, right) with AAA View Motif UGGU (helix III, 5' side)

If you use this tool, please refer to the ITS2-Database and remember to cite HMMer and MEME:

  • Eddy, S., 1998. Profile hidden Markov models. Bioinformatics 14, 755-763.
  • Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.

If you use the database please cite.