Search Results RNA secondary structure prediction

  Search page

Introduce a yeast gene name (i.e. MRK1, MUD1) or a systematic name (i.e. YDR092W, YCL005W-A) in the search box to find a list of all introns belonging to that gene included in the database

Any string introduced in the serch box will return all the genes containing that substring in the gene name or the systematic name. For instance, if we introduce the substring HN in the search box, this will return the genes YDL125C (HNT1) and YDR305C (HNT2) as both contain that substring in the gene name.


  Information displayed on the results page
  • Optimal secondary structure prediction between the BS and the annotated 3'ss.The colors of the nucleotides represent the pair probability of a pairticular base-pairing. Values close to 1 mean that the base pairing between those two nucleotides is very likely to occur whereas values close to 0 mean that that base-pairing is very unlikely to occur.
    For unpaired nucleotides, the colors represent the probability of a nucleotide of not being in a base-pairing. Thus, values close to 0 reflect that the probability of that nucleotide of being not involved in a base-pairing is very small whereas values close to one reflect that the probability of a nucleotide of being free is very high.
  • Branch Site sequence: 9-mer predicted as BS.
  • U2snRNA-BS base pairing energy: free energy of the base-pairing between the U2snRNA and the BS in kcal/mol.
  • Bs- 3'ss real distance for the annotated 3'ss
  • Full sequence: Sequence of the intron studied plus the sequence of the upstream and the downstream exon in fasta format. See more details below.
  • Intron ID, sequence, energy and optimal structure(bracket notation) predicted for the annotated 3'ss.
Full sequence

The full sequence page contains the sequence of the intron analyzed (lower case) plus the sequence of the upstream and dowstream exons (upper case). The different features analyzed are highlighted in the sequence:

  • Exons: sequence in upper case and bold.
  • Intron: sequence in lower case, gold color.
  • Branch site sequence: highlighted in color red.
  • Annotated 3'ss: highlighted in dark blue.
  • Other 3'ss: highlighted in light blue.
3'ss summary

For each of the candidate 3'ss evaluated (intronic, annotated 3'ss, and exonic) the following infomation is displayed:

  • Sequence of the candidate 3'ss.
  • 3'ss accessibility.
  • Real distance between the BS and the exon/intron boundary.
  • Effective distance between the BS and the exon/intron boundary.
  • Energy of the optimal structure predicted for the current 3'ss in kcal/mol
UCSC custom tracks

A link to the UCSC genome browser displaying custom tracks for the introns analyzed is provided.
For each of the introns the information displayed is the following:

  • Branch site information: location of the predicted branch site sequence in the intron
  • AGs: all AGs present in the intron downstream of the branch site and in the downstream exon.
    The color of the AGs represent its accessibility. Darker greys represent higher accessibility values whereas lighter greys show lower accessibility values.

If the intron sequence is available for more than a species, a sequence-based multiple created with Prank+F is provided


  RNA secondary structure prediction
Pair probablity measure

In the secondary structure pictures, the colors of nucleotides represent pair probability values calculated using the program RNAfold, included in the Vienna Package. The pair probabilities were computed on the sequence between the BS and the 3'ss.

The pair probability values range from 0 to 1 and show the probability of a given nucleotide to be base-pairing with a given nucleotide from the sequence. The colors that appear in the RNA secondary structure plots shows two differ values:

  • On unpaired nucleotides, the color represents the probability of that nucleotide being unpaired.
  • On paired nucleotides, the color represents the probability of that nucleotide having that specific base-pairing.
Accessibility measure

Accessibility is 1- pair probability. Thus, it represents the probability of a given nucleotide of being unpaired. For each of the 3'ss analyzed, the average accessibility of the triplet is given. For more details on the measure go to the Documentation page.