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:

it is case insensitive
characters other than atgcun will be deleted
'u's will be changed to 't's
'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.

Exon	Intron
A/C A G	g t a a g t	consensus
		entry

For a 3' splice site, you must specify 12 nt in intronand 1 nt in exon.

Intron Exon
y y y y y . y y y y c . a g G consensus
entry

Intron	Exon
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