Predict Alt. 5' Splicing Variants
Input Instructions:For each variant, you need to include the following with tab deliminaters:
VARIANT_NAME WILDTYPE_SEQ VARIANT_SEQ WILDTYPE_PSI
VARIANT_NAMEis a user chosen id for the event.
WILDTYPE_SEQis the sequence of the whole wildtype alternative exon. Please include both splice donors and all the sequence between them (i.e. CAG|GTAAGT…GAG|gtaagt)
VARIANT_PSIis the alternative exon sequence including variants. Variants can be included in the splice donors as well as between them.
WILDTYPE_PSIis the percent spliced in (PSI) fraction for the wildtype sequence--i.e. the percentage of splicing at the downstream splice donor. It should be between 0-100.
As of now we do not support variants that are exonic or intronic to both the splice donors, but we hope to in the future. However, in our paper, we find that variants between alternative splice donors are much more likely to alter splicing than those upstream or downstream of both splice donors.
Output File:The output file will download automatically. It will contain the predicted PSI for the variant sequence as well as the change in PSI (delta PSI) in tab deliminated format.
Example (CDC45):Below is an example file. To get the output for this example file, just press submit. To score your own variants, upload your own file, and then press submit.
var_1 GAGGTGGTCCAGAGCCAGgtgacg GAGGTGGTCCTGAGCCAGgtgacg 87 var_2 GAGGTGGTCCAGAGCCAGgtgacg GAGGTGGTCCATAGCCAGgtgacg 87 var_3 GAGGTGGTCCAGAGCCAGgtgacg GAGGTGGTCCAGTGCCAGgtgacg 87 var_4 GAGGTGGTCCAGAGCCAGgtgacg GAGGTGGTCCAGAAGCCAGgtgacg 87