Splice Site Score Calculation


The score expresses how similar the splice sites fits the consensus sequence. A 100% match to the mammalian 3' splice site tt ttccc tccag|G would have a score of 14.2. A perfect 5' splice site AAG|gtaag t would have a score of 12.6. The mean score of the 3' splice site in constitutive exons is 7.9 and 8.1 for constitutive 5'splice sites (The original parameters were kindly provided by Dr. Michael Zhang, CSHL; Statistical data were calculated by Dr. Tetsushi Yada using the sequence compilation for the GENIE program).

Input sequence (either the 5'splice site or the 3' splice site):

Note that:
  1. it is case insensitive
  2. characters other than atgcun will be deleted
  3. 'u's will be changed to 't's
  4. 'n's are treated as positions without any contribution
For a 5' splice site, you must specify 3 nt in exon and 6 nt in intron.
ExonIntron
A/C A Gg t a a g t consensus
entry

For a 3' splice site, you must specify 12 nt in intronand 1 nt in exon.
IntronExon
y y y y y . y y y y c . a g G consensus
entry


Last update: January 30, 1998
nakai@imcb.osaka-u.ac.jp