NIPU web server

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

For splicing regulatory motifs, we use the NI scores (1). 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.
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. For example, input
aatgtaatttaatttccattttctttttagAGCAGTATACAAAGATGCTGATTTGTATTTATTAGACTCTCCTTTTGGATACCTAGATGTTTTAACAGAAAAAGAAATATTTGAAAGgtatgttctttgaataccttacttataatg
(upper case letters are exonic, lower case letters intronic) to analyze human CFTR exon 12.
The procedure to compute PU values is illustrated in this figure.

---

Compute NI and PU values.
NOTE: computation may take some minutes depending on the input sequence length (two sequences each 160 nt long takes about 2 minutes).

You have to enter one or two RNA sequences (plain sequences, no header).

1. RNA sequence
2. RNA sequence (optional)

---

PU value computations are based on RNAfold from the Vienna RNA package.
(1) Stadler, M.B., Shomron, N., Yeo, G.W., Schneider, A., Xiao, X. and Burge, C.B. (2006) Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS Genet, 2, e191.