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Human Splicing Finder
Version 2.4.1

With the completion of the Human Genome Project our vision of human genetic diseases has changed. Thousands of mutations are identified in diagnostic and research laboratories yearly. The knowledge of these mutations associated with clinical and biological data is essential for clinicians, geneticists and researchers.

In order to better understand intronic and exonic mutations leading to splicing defects, we decided to create the Human Splicing Finder website. This tool is aimed to help study of the pre-mRNA splicing [more about splicing background].

To calculate the consensus values of potential splice sites and search for branch points, new algorithms were developed. Furthermore, we have integrated all available matrices to identify exonic and intronic motifs, as well as new matrices to identify hnRNP A1, Tra2-β and 9G8.

We hope that this tool will be useful for your research. In order to improve it, please send us comments and new matrices to identify specific sequences involved in splicing.

In referring to work done using Human Splicing Finder, please cite: FO Desmet, Hamroun D, Lalande M, Collod-Beroud G, Claustres M, Beroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acid Research, 2009, April

To get more information about how splicing software work, please read, please also read: FO Desmet, D Hamroun, G Collod-Beroud, C Beroud: Bioinformatics identification of splice site signals and prediction of mutation effects. Global Research Network, Res. Adv. in Nucleic Acid Research. Editor: RM Mohan, Kerala

Select an analysis type

Ensembl database release: 54 (May 2009)
Automatically select the longest transcript: Yes No
Search for SNPs related to the analyzed sequence: Yes No
Use specific matrices for +3 position: Yes No
Display ESE/ESS: All Do not display ESE/ESS located at splice junctions
Number of nucleotides surrounding the exon
Both 5' and 3' introns (max: 1000):
5' intron (max: 1000):
3' intron (max: 1000):

Choose a sequence by


You can select all or a subset of matrices (Show/Hide) and set their thresholds to display Splicing Elements.


Detailed help (Show/Hide)