R. 1. Kan, Z. Garrett-engele, P. Johnson, J. Castle, and J. , Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles, Nucleic Acids Research, vol.33, issue.17, pp.5659-5666, 2005.
DOI : 10.1093/nar/gki834

L. Lareau, R. Green, R. Bhatnagar, and S. Brenner, The evolving roles of alternative splicing, Current Opinion in Structural Biology, vol.14, issue.3, pp.273-282, 2004.
DOI : 10.1016/j.sbi.2004.05.002

S. Stamm, Signals and their transduction pathways regulating alternative splicing: a new dimension of the human genome, Human Molecular Genetics, vol.11, issue.20, pp.2409-2416, 2002.
DOI : 10.1093/hmg/11.20.2409

L. Lareau, M. Inada, R. Green, J. Wengrod, and S. Brenner, Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements, Nature, vol.2, issue.7138, pp.926-929, 2007.
DOI : 10.1038/nature05676

J. Ni, L. Grate, J. Donohue, C. Preston, and N. Nobida, Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay, Genes & Development, vol.21, issue.6, pp.708-718, 2007.
DOI : 10.1101/gad.1525507

N. Mcglincy and C. Smith, Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?, Trends in Biochemical Sciences, vol.33, issue.8, pp.385-393, 2008.
DOI : 10.1016/j.tibs.2008.06.001

T. Nilsen and B. Graveley, Expansion of the eukaryotic proteome by alternative splicing, Nature, vol.114, issue.7280, pp.457-463, 2010.
DOI : 10.1038/nature08909

S. Grellscheid and C. Smith, An Apparent Pseudo-Exon Acts both as an Alternative Exon That Leads to Nonsense-Mediated Decay and as a Zero-Length Exon, Molecular and Cellular Biology, vol.26, issue.6, pp.2237-2246, 2006.
DOI : 10.1128/MCB.26.6.2237-2246.2006

D. Licatalosi and R. Darnell, RNA processing and its regulation: global insights into biological networks, Nature Reviews Genetics, vol.6, issue.1, pp.75-87, 2010.
DOI : 10.1038/nrg2673

Z. Wang and C. Burge, Splicing regulation: From a parts list of regulatory elements to an integrated splicing code, RNA, vol.14, issue.5, pp.802-813, 2008.
DOI : 10.1261/rna.876308

C. Smith and J. Valcarcel, Alternative pre-mRNA splicing: the logic of combinatorial control, Trends in Biochemical Sciences, vol.25, issue.8, pp.381-388, 2000.
DOI : 10.1016/S0968-0004(00)01604-2

R. Tacke, M. Tohyama, S. Ogawa, and J. Manley, Human Tra2 Proteins Are Sequence-Specific Activators of Pre-mRNA Splicing, Cell, vol.93, issue.1, pp.139-148, 1998.
DOI : 10.1016/S0092-8674(00)81153-8

B. Beil, G. Screaton, and S. Stamm, Molecular cloning of htra2-beta-1 and htra2-beta-2, two human homologs of tra-2 generated by alternative splicing, DNA Cell Biol, vol.16, pp.679-690, 1997.

B. Dauwalder, F. Amaya-manzanares, and W. Mattox, A human homologue of the Drosophila sex determination factor transformer-2 has conserved splicing regulatory functions., Proceedings of the National Academy of Sciences, vol.93, issue.17, pp.9004-9009, 1996.
DOI : 10.1073/pnas.93.17.9004

P. Shepard and K. Hertel, The SR protein family, Genome Biology, vol.10, issue.10, p.242, 2009.
DOI : 10.1186/gb-2009-10-10-242
URL : http://doi.org/10.1186/gb-2009-10-10-242

J. Belote and B. Baker, The dual functions of a sex determination gene in Drosophila melanogaster, Developmental Biology, vol.95, issue.2, pp.512-517, 1983.
DOI : 10.1016/0012-1606(83)90054-4

A. Clery, J. S. Benderska, N. Dominguez, C. Stamm, and S. , Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-beta1, Nat Struct Mol Biol, 2011.

K. Tsuda, T. Someya, K. Kuwasako, M. Takahashi, and F. He, Structural basis for the dual RNA-recognition modes of human Tra2-{beta} RRM, Nucleic Acids Res, 2011.

Y. Mende, M. Jakubik, M. Riessland, F. Schoenen, and K. Rossbach, Deficiency of the splicing factor Sfrs10 results in early embryonic lethality in mice and has no impact on full-length SMN/Smn splicing, Human Molecular Genetics, vol.19, issue.11, pp.2154-2167, 2010.
DOI : 10.1093/hmg/ddq094

R. Daoud, D. Penha-berzaghi, M. Siedler, F. Hubener, M. Stamm et al., Activity-dependent regulation of alternative splicing patterns in the rat brain, European Journal of Neuroscience, vol.11, issue.2, pp.788-802, 1999.
DOI : 10.1046/j.1460-9568.1999.00486.x

O. Nayler, C. Cap, and S. Stamm, Human Transformer-2-beta Gene (SFRS10): Complete Nucleotide Sequence, Chromosomal Localization, and Generation of a Tissue-Specific Isoform, Genomics, vol.53, issue.2, pp.191-202, 1998.
DOI : 10.1006/geno.1998.5471

P. Stoilov, R. Daoud, O. Nayler, and S. Stamm, Human tra2-beta1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA, Human Molecular Genetics, vol.13, issue.5, pp.509-524, 2004.
DOI : 10.1093/hmg/ddh051

W. Mattox, M. Palmer, and B. Baker, Alternative splicing of the sex determination gene transformer-2 is sex-specific in the germ line but not in the soma., Genes & Development, vol.4, issue.5, pp.789-805, 1990.
DOI : 10.1101/gad.4.5.789

T. Hazelrigg and C. Tu, Sex-specific processing of the Drosophila exuperantia transcript is regulated in male germ cells by the tra-2 gene., Proceedings of the National Academy of Sciences, vol.91, issue.22, pp.10752-10756, 1994.
DOI : 10.1073/pnas.91.22.10752

S. Madigan, P. Edeen, J. Esnayra, and M. Mckeown, att, a target for regulation by tra2 in the testes of Drosophila melanogaster, encodes alternative RNAs and alternative proteins., Molecular and Cellular Biology, vol.16, issue.8, pp.4222-4230, 1996.
DOI : 10.1128/MCB.16.8.4222

D. Elliott, M. Millar, K. Oghene, A. Ross, and F. Kiesewetter, Expression of RBM in the nuclei of human germ cells is dependent on a critical region of the Y chromosome long arm, Proceedings of the National Academy of Sciences, vol.94, issue.8, pp.3848-3853, 1997.
DOI : 10.1073/pnas.94.8.3848

J. Venables, D. Elliott, O. Makarova, E. Makarov, and H. Cooke, RBMY, a probable human spermatogenesis factor, and other hnRNP G proteins interact with Tra2beta and affect splicing, Human Molecular Genetics, vol.9, issue.5, pp.685-694, 2000.
DOI : 10.1093/hmg/9.5.685

S. Grellscheid, C. Dalgliesh, A. Rozanska, D. Grellscheid, and C. Bourgeois, Molecular design of a splicing switch responsive to the RNA binding protein Tra2??, Nucleic Acids Research, vol.39, issue.18, pp.8092-104, 2011.
DOI : 10.1093/nar/gkr495

J. Venables, C. Bourgeois, C. Dalgliesh, L. Kister, and J. Stevenin, Up-regulation of the ubiquitous alternative splicing factor Tra2?? causes inclusion of a germ cell-specific exon, Human Molecular Genetics, vol.14, issue.16, pp.2289-2303, 2005.
DOI : 10.1093/hmg/ddi233
URL : https://hal.archives-ouvertes.fr/hal-00187820

D. Licatalosi, A. Mele, J. Fak, J. Ule, and M. Kayikci, HITS-CLIP yields genome-wide insights into brain alternative RNA processing, Nature, vol.8, issue.7221, pp.464-469, 2008.
DOI : 10.1038/nature07488

J. Sanford, X. Wang, M. Mort, N. Vanduyn, and D. Cooper, Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts, Genome Research, vol.19, issue.3, pp.381-394, 2009.
DOI : 10.1101/gr.082503.108

R. Waterston, K. Lindblad-toh, E. Birney, J. Rogers, and J. Abril, Initial sequencing and comparative analysis of the mouse genome, Nature, vol.420, pp.520-562, 2002.

Y. Xue, Y. Zhou, T. Wu, T. Zhu, and X. Ji, Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping, Molecular Cell, vol.36, issue.6, pp.996-1006, 2009.
DOI : 10.1016/j.molcel.2009.12.003

J. Mattick and I. Makunin, Non-coding RNA, Human Molecular Genetics, vol.15, issue.90001, pp.17-29, 2006.
DOI : 10.1093/hmg/ddl046

M. Hafner, M. Landthaler, L. Burger, M. Khorshid, and J. Hausser, Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP, Cell, vol.141, issue.1, pp.129-141, 2010.
DOI : 10.1016/j.cell.2010.03.009

R. Darnell, Developing Global Insight into RNA Regulation, Cold Spring Harbor Symposia on Quantitative Biology, vol.16, issue.0, pp.321-327, 2006.
DOI : 10.1073/pnas.95.22.13254

H. Keren, G. Lev-maor, and G. Ast, Alternative splicing and evolution: diversification, exon definition and function, Nature Reviews Genetics, vol.31, issue.5, pp.345-355, 2010.
DOI : 10.1038/nrg2776

S. Ruppert, T. Cole, M. Boshart, E. Schmid, and G. Schutz, Multiple mRNA isoforms of the transcription activator protein CREB: generation by alternative splicing and specific expression in primary spermatocytes, EMBO J, vol.11, pp.1503-1512, 1992.

L. Zhang, M. Zeng, P. Chen, H. Sun, and D. Tao, Identification of messenger RNA substrates for mouse T-STAR, Biochemistry (Moscow), vol.74, issue.11, pp.1270-1277, 2009.
DOI : 10.1134/S0006297909110145

D. Ray, H. Kazan, E. Chan, P. Castillo, L. Chaudhry et al., Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins, Nature Biotechnology, vol.18, issue.7, pp.667-670, 2009.
DOI : 10.1126/science.1136800

R. Sorek, R. Shamir, and G. Ast, How prevalent is functional alternative splicing in the human genome?, Trends in Genetics, vol.20, issue.2, pp.68-71, 2004.
DOI : 10.1016/j.tig.2003.12.004

G. Yeo, E. Van-nostrand, D. Holste, T. Poggio, and C. Burge, Identification and analysis of alternative splicing events conserved in human and mouse, Proceedings of the National Academy of Sciences, vol.102, issue.8, pp.2850-2855, 2005.
DOI : 10.1073/pnas.0409742102

R. Richardson, O. Alekseev, G. Grossman, E. Widgren, and R. Thresher, Nuclear Autoantigenic Sperm Protein (NASP), a Linker Histone Chaperone That Is Required for Cell Proliferation, Journal of Biological Chemistry, vol.281, issue.30, pp.21526-21534, 2006.
DOI : 10.1074/jbc.M603816200

J. Coles, M. Hallegger, and C. Smith, A nonsense exon in the Tpm1 gene is silenced by hnRNP H and F, RNA, vol.15, issue.1, pp.33-43, 2009.
DOI : 10.1261/rna.1225209

X. Zhang and L. Chasin, Computational definition of sequence motifs governing constitutive exon splicing, Genes & Development, vol.18, issue.11, pp.1241-1250, 2004.
DOI : 10.1101/gad.1195304

X. Zhang, T. Kangsamaksin, M. Chao, J. Banerjee, and L. Chasin, Exon Inclusion Is Dependent on Predictable Exonic Splicing Enhancers, Molecular and Cellular Biology, vol.25, issue.16, pp.7323-7332, 2005.
DOI : 10.1128/MCB.25.16.7323-7332.2005
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1190244

F. Tronche, C. Kellendonk, O. Kretz, P. Gass, and K. Anlag, Disruption of the glucocorticoid receptor gene in the nervous system results in reduced anxiety, Nature Genetics, vol.23, issue.1, pp.99-103, 1999.
DOI : 10.1038/12703

O. Alekseev, R. Richardson, O. Rand, and M. , Linker Histones Stimulate HSPA2 ATPase Activity Through NASP Binding and Inhibit CDC2/Cyclin B1 Complex Formation During Meiosis in the Mouse1, Biology of Reproduction, vol.81, issue.4, pp.739-748, 2009.
DOI : 10.1095/biolreprod.109.076497

J. Welch, O. Rand, and M. , Characterization of a Sperm-specific Nuclear Autoantigenic Protein. II. Expression and Localization in the Testis1, Biology of Reproduction, vol.43, issue.4, pp.569-578, 1990.
DOI : 10.1095/biolreprod43.4.569

A. Osakabe, H. Tachiwana, T. Matsunaga, T. Shiga, and R. Nozawa, Nucleosome Formation Activity of Human Somatic Nuclear Autoantigenic Sperm Protein (sNASP), Journal of Biological Chemistry, vol.285, issue.16, pp.11913-11921, 2010.
DOI : 10.1074/jbc.M109.083238

M. Mcguffin, D. Chandler, D. Somaiya, B. Dauwalder, and W. Mattox, Autoregulation of transformer-2 alternative splicing is necessary for normal male fertility in Drosophila, Genetics, vol.149, pp.1477-1486, 1998.

M. Gabut, S. Chaudhry, and B. Blencowe, SnapShot: The Splicing Regulatory Machinery, Cell, vol.133, issue.1, pp.192-191, 2008.
DOI : 10.1016/j.cell.2008.03.010

Y. Hofmann, C. Lorson, S. Stamm, E. Androphy, and B. Wirth, Htra2-beta 1 stimulates an exonic splicing enhancer and can restore full-length SMN expression to survival motor neuron 2 (SMN2), Proceedings of the National Academy of Sciences, vol.97, issue.17, pp.9618-9623, 2000.
DOI : 10.1073/pnas.160181697

Z. Jiang, H. Tang, N. Havlioglu, X. Zhang, and S. Stamm, Mutations in Tau Gene Exon 10 Associated with FTDP-17 Alter the Activity of an Exonic Splicing Enhancer to Interact with Tra2??, Journal of Biological Chemistry, vol.278, issue.21, pp.18997-19007, 2003.
DOI : 10.1074/jbc.M301800200

S. Stamm, D. Casper, V. Hanson, and D. Helfman, Regulation of the neuron-specific exon of clathrin light chain B, Molecular Brain Research, vol.64, issue.1, pp.108-118, 1999.
DOI : 10.1016/S0169-328X(98)00313-1

T. Yamada, I. Goto, and Y. Sakaki, Neuron-Specific Splicing of the Alzheimer Amyloid Precursor Protein Gene in a Mini-gene System, Biochemical and Biophysical Research Communications, vol.195, issue.1, pp.442-448, 1993.
DOI : 10.1006/bbrc.1993.2063

A. Disset, C. Bourgeois, N. Benmalek, M. Claustres, and J. Stevenin, An exon skipping-associated nonsense mutation in the dystrophin gene uncovers a complex interplay between multiple antagonistic splicing elements, Human Molecular Genetics, vol.15, issue.6, pp.999-1013, 2006.
DOI : 10.1093/hmg/ddl015
URL : https://hal.archives-ouvertes.fr/hal-00069368

P. Young, C. Didonato, D. Hu, R. Kothary, and E. Androphy, SRp30c-dependent stimulation of survival motor neuron (SMN) exon 7 inclusion is facilitated by a direct interaction with hTra2beta1, Human Molecular Genetics, vol.11, issue.5, pp.577-587, 2002.
DOI : 10.1093/hmg/11.5.577

L. Cartegni and A. Krainer, Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1, Nature Genetics, vol.30, issue.4, pp.377-384, 2002.
DOI : 10.1038/ng854

T. Kashima and J. Manley, A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy, Nature Genetics, vol.34, issue.4, pp.460-463, 2003.
DOI : 10.1038/ng1207

D. Elliott and S. Grellscheid, Alternative RNA splicing regulation in the testis, Reproduction, vol.132, issue.6, pp.811-819, 2006.
DOI : 10.1530/REP-06-0147

J. Venables, R. Klinck, C. Koh, J. Gervais-bird, and A. Bramard, Cancer-associated regulation of alternative splicing, Nature Structural & Molecular Biology, vol.17, issue.6, pp.670-676, 2009.
DOI : 10.1186/gb-2007-8-2-r19

Z. Wang, M. Kayikci, M. Briese, K. Zarnack, and N. Luscombe, iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions, PLoS Biology, vol.4, issue.10, 2010.
DOI : 10.1371/journal.pbio.1000530.s015

Y. Hofmann and B. Wirth, hnRNP-G promotes exon 7 inclusion of survival motor neuron (SMN) via direct interaction with Htra2-beta1, Human Molecular Genetics, vol.11, issue.17, pp.2037-2049, 2002.
DOI : 10.1093/hmg/11.17.2037

K. Sergeant, C. Bourgeois, C. Dalgliesh, J. Venables, and J. Stevenin, Alternative RNA splicing complexes containing the scaffold attachment factor SAFB2, Journal of Cell Science, vol.120, issue.2, pp.309-319, 2007.
DOI : 10.1242/jcs.03344
URL : https://hal.archives-ouvertes.fr/hal-00166256

B. Langmead, C. Trapnell, M. Pop, and S. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology, vol.10, issue.3, p.25, 2009.
DOI : 10.1186/gb-2009-10-3-r25

J. Mignone, V. Kukekov, A. Chiang, D. Steindler, and G. Enikolopov, Neural stem and progenitor cells in nestin-GFP transgenic mice, The Journal of Comparative Neurology, vol.50, issue.3, pp.311-324, 2004.
DOI : 10.1002/cne.10964

C. Bourgeois, M. Popielarz, G. Hildwein, and J. Stevenin, Identification of a Bidirectional Splicing Enhancer: Differential Involvement of SR Proteins in 5??? or 3??? Splice Site Activation, Molecular and Cellular Biology, vol.19, issue.11, pp.7347-7356, 1999.
DOI : 10.1128/MCB.19.11.7347

P. Fujita, B. Rhead, A. Zweig, A. Hinrichs, and D. Karolchik, The UCSC Genome Browser database: update 2011, Nucleic Acids Research, vol.39, issue.Database, pp.876-882, 2011.
DOI : 10.1093/nar/gkq963