HOT-SKIP systematically examines all possible substitutions in each exonic position that are most likely to skip the submitted exonic sequence. It calculates the total number of ESSs, ESEs and their ratio. Specifically, it computes the number of RESCUE-ESEs (Fairbrother 2004; Fairbrother 2002), FAS-ESSs (Wang 2004), PESEs/PESSs (Zhang 2004), neighbourhood inference (Stadler 2006) and EIE/IIEs (Zhang 2008) for each segment.

The input is an exonic sequences (strictly in UPPERCASE) flanked by at least 6-bp and 4-bp intronic sequence (strictly in lowercase) at 5' and 3' end of the exon, respectively in FASTA format up to a total length of 4000 bp. The output is a larger table listing predicted splicing regulatory sequences for all possible point mutations (the most common type of DNA alteration leading to genetic disease) at each exon position. The table is sortable by clicking on the column name (be patient due delays in some browsers). A summary sentence above the table confirms mutations that result in the highest ESS/ESE score, in other words, mutations that are most likely to skip this exon. These substitutions are likely to represent 'hot-spots' for exon skipping and are highlighted in the input sequence. Note: HOT-SKIP considers all possible exonic substitutions, except for changes in the first and the last three positions of the exon, ie. splice site consensus signals.

Contact and Feedback

Dr I Vorechovsky <>
Dr P Divina <>


Raponi, M., Kralovicova, J., Copson, E., Divina, P., Eccles, D., Johnson, P., Baralle, D., Vorechovsky, I. (2011) Prediction of single-nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6. Hum Mutat., 32, 436-444. [Pubmed] [Fulltext]

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