this service will allow you to find the (i) 5' and 3' splice-sites scores (ii) number of H-bonds between U1 and the 5' splice-site, and (iii) the ΔG of U1/5' splice site pairing

Please choose species: Primates Rodents

Please enter the splice-site sequences:

5' Splice-Site: please enter/paste 9 nucleotides from position -3 through 6:
(-3 is in third position upstream of the 5'ss; in case you enter "N" (any nucleotide) to the sequence it will calculate only the ΔG)

Or Enter your own file multi-Fasta or multi-Line text file(ASCII file) such as notepad :

3' Splice-Site: please enter/paste 15 nucleotides from position -14 through 1
(position -14 is the 14th nucleotide upstream of the 3'ss)

Or Enter your own file (multi-Fasta or multi-Line text files):

The algorithm to calculate the scores of donor and acceptor sequences is based on Shapiro and Senapathy (1987 Sep), Nucleic Acids Res., v15, n17, pp7155-7174 [download PDF].

    The score expresses how similar the splice-sites fit the consensus sequences:
  • 5' splice-site : CAG/GTAAGT will give the score of 100.
  • 3' splice-site : TTTTTTTTTTTCAG/G ("/" indicate the intron/exon junction) will give score of 100.

The tables used to calculate the score of the splice-sites are based on Carmel et al. (2004) analysis of 45,552 splice-sites (not containing U12 introns).

The ΔG was calculated using OligoArrayAux 1.9 that was developed by Nick Markham & Michael Zuker at Rensselaer Polytechnic Institute for the purpose of replacing mfold in Jean-Marie Rouillard's OligoArray software.
To predict the ΔG of U1:5'splice-site annealing we concatenate their sequence strand into one RNA strand as follows:
"NN- 5'splice-site - NNNNN - reversed U1(UACUUACCUG) - NN". Since the software does not hybridize the "N" sequence (it is consider neutral), the resulting calculated free energy is that of the U1:5'splice-site hybrid. A more detailed description is found in Carmel et al. (2004).



UCSC 2 FASTA Format - conversion tool