Predict Exon Skipping Variants
Input Instructions:Please upload a file with one variant per row. 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 and 6 nucleotides of the downstream intron (i.e. GGT…CAG|gtaagt).
VARIANT_PSIis the alternative exon sequence including variants.
WILDTYPE_PSIis the percent spliced in (PSI) fraction for the wildtype sequence--i.e. the percentage of alternative exon inclusion. This should be between 0-100.
Variants are not limited to SNPs. Variants can be included anywhere in the alternative exon, as well as in the splice donor. As of now, we do not support intronic variants (other than in the alternative exon's splice donor), but we hope to in the future. For now, we recommend scoring intronic variants with SPANR.
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 (SMN2):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.
variant_1 GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATTAAGGAgtaagt GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCAATTAAGGAgtaagt 21 variant_2 GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATTAAGGAgtaagt GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTGAATTAAGGAgtaagt 21 variant_3 GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATTAAGGAgtaagt GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAACTTAAGGAgtaagt 21 variant_4 GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATTAAGGAgtaagt GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATGAAGGAgtaagt 21