Freiburg RNA Tools
NIPU - Splicing of regular motifs
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NIPU

NIPU - Splicing of regular motifs

This server allows to display splicing regulatory motifs and single-stranded regions.

For splicing regulatory motifs, we use the NI scores (see Stadler et al. (2006)). A hexamer with a positive NI score is considered to have ESE function, a hexamer with a negative NI score is considered to have ESS function. Strong ESEs have a score > 0.8, strong ESS a score < -0.8. Hexamers with a score between -0.8 and 0.8 are considered to be splicing-neutral, since their splicing effect is predicted to be weak.

For single-stranded regions, we compute the probability that a hexamer is completely unpaired (denoted as the PU value). PU values range between 0 (hexamer is completely base-paired) and 1 (hexamer is completely unpaired). The PU value for one hexamer is determined as the average of all local folding windows that comprise a context up- and downstream of 11 to 30 nt. PU value computations are based on RNAfold from the Vienna RNA package.
NOTE: For analyzing an entire exon, you have to input the exon sequence as well as 30 nt from its upstream and downstream intron flank.

Note: the NIPU tool is not maintained anymore.

For articles describing the tool refer to the reference section below. Please cite us when using our tools.
For more information check the help page.

Try NIPU with this example: human CFTR exon 12 (input|result) ?

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When using NIPU please cite :

Results are computed with NIPU version 1.0.1 using Vienna RNA package v2.1.8