R. Blanco, E. Parra, G. Guigo, and R. , down-stream) was used as input when possible; if not, the requested size of the constitutive splice site was used for the corresponding software NA: not available. The complete list of references for each bioinformatics resource is available in Supp Using geneid to identify genes, Curr Protoc Bioinformatics Chapter, vol.4, issue.3, 2007.

V. Brendel and J. Kleffe, Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA, Nucleic Acids Research, vol.26, issue.20, pp.4748-57, 1998.
DOI : 10.1093/nar/26.20.4748

S. Brunak, J. Engelbrecht, and S. Knudsen, Prediction of human mRNA donor and acceptor sites from the DNA sequence, Journal of Molecular Biology, vol.220, issue.1, pp.49-65, 1991.
DOI : 10.1016/0022-2836(91)90380-O

C. Burge and S. Karlin, Prediction of complete gene structures in human genomic DNA, Journal of Molecular Biology, vol.268, issue.1, pp.78-94, 1997.
DOI : 10.1006/jmbi.1997.0951

L. Cartegni, J. Wang, Z. Zhu, M. Zhang, and A. Krainer, ESEfinder: a web resource to identify exonic splicing enhancers, Nucleic Acids Research, vol.31, issue.13, pp.3568-71, 2003.
DOI : 10.1093/nar/gkg616

F. Desmet, D. Hamroun, M. Lalande, G. Collod-beroud, M. Claustres et al., Human Splicing Finder: an online bioinformatics tool to predict splicing signals, Nucleic Acids Research, vol.37, issue.9, p.67, 2009.
DOI : 10.1093/nar/gkp215

URL : https://hal.archives-ouvertes.fr/inserm-00396239

R. Dogan, L. Getoor, W. Wilbur, and S. Mount, SplicePort--An interactive splice-site analysis tool, Nucleic Acids Research, vol.35, issue.Web Server, pp.285-91, 2007.
DOI : 10.1093/nar/gkm407

G. Kol, G. Lev-maor, and G. Ast, Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation, Human Molecular Genetics, vol.14, issue.11, pp.1559-68, 2005.
DOI : 10.1093/hmg/ddi164

F. Pagani, E. Buratti, C. Stuani, and F. Baralle, Missense, Nonsense, and Neutral Mutations Define Juxtaposed Regulatory Elements of Splicing in Cystic Fibrosis Transmembrane Regulator Exon 9, Journal of Biological Chemistry, vol.278, issue.29, pp.26580-26588, 2003.
DOI : 10.1074/jbc.M212813200

F. Pagani, C. Stuani, M. Tzetis, E. Kanavakis, A. Efthymiadou et al., New type of disease causing mutations: the example of the composite exonic regulatory elements of splicing in CFTR exon 12, Human Molecular Genetics, vol.12, issue.10, pp.1111-1131, 2003.
DOI : 10.1093/hmg/ddg131

M. Raponi, J. Kralovicova, E. Copson, P. Divina, D. Eccles et al., Prediction of single-nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6, Human Mutation, vol.35, issue.4, pp.436-480, 2011.
DOI : 10.1002/humu.21458

URL : https://hal.archives-ouvertes.fr/hal-00620579

M. Reese, F. Eeckman, D. Kulp, and D. Haussler, Improved Splice Site Detection in Genie, Journal of Computational Biology, vol.4, issue.3, pp.311-334, 1997.
DOI : 10.1089/cmb.1997.4.311

S. Schwartz, E. Hall, and G. Ast, SROOGLE: webserver for integrative, user-friendly visualization of splicing signals, Nucleic Acids Research, vol.37, issue.Web Server, pp.189-92, 2009.
DOI : 10.1093/nar/gkp320

S. Schwartz, J. Silva, D. Burstein, T. Pupko, E. Eyras et al., Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes, Genome Research, vol.18, issue.1, pp.88-103, 2008.
DOI : 10.1101/gr.6818908

A. Woolfe, J. Mullikin, and L. Elnitski, Genomic features defining exonic variants that modulate splicing, Genome Biology, vol.11, issue.2, p.20, 2010.
DOI : 10.1186/gb-2010-11-2-r20

URL : http://doi.org/10.1186/gb-2010-11-2-r20

G. Yeo and C. Burge, Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals, Journal of Computational Biology, vol.11, issue.2-3, pp.377-94, 2004.
DOI : 10.1089/1066527041410418