Validation of Human Alternative Splice Forms Using the EASED Platform and Multiple Splice Site Discriminating Features

  • Ralf Bortfeldt
  • Alexander Herrmann
  • Heike Pospisil
  • Stefan Schuster
Part of the Modeling and Simulation in Science, Engineering and Technology book series (MSSET)


We have shown for a dataset of computationally predicted alternative splice sites how inherent information can be utilized to validate the predictions by applying statistics on different features typical for splice sites. As a promising splice site feature we investigated the frequencies of binding motifs in the context of exonic and intronic splice site flanks and between the alternative and reference splice sites. We show that both partitions of splice sites can statistically be separated not only by their distance to the splice signal consensus but also via frequencies of splice regulatory protein (SRp) binding motifs in the splice site environment.

Key words

Splicing alternative splicing SR proteins splicing enhancer 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Black, D.L.: Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem., 72, 291–336 (2003).CrossRefGoogle Scholar
  2. 2.
    Boguski, M.S., Lowe, T.M., Tolstoshev, C.M.: dbEST–database for ‘expressed sequence tags’. Nat. Genet., 4, 332–3 (1993).CrossRefGoogle Scholar
  3. 3.
    Bourgeois, C.F., Lejeune, F., Stevenin, J.: Broad specificity of SR (serine/arginine) proteins in the regulation of alternative splicing of pre-messenger RNA. Prog. Nucleic. Acid. Res. Mol. Biol., 78, 37–88 (2004).CrossRefGoogle Scholar
  4. 4.
    Cartegni, L., Chew, S.L., Krainer, A.R.: Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev. Genet., 3, 285–298 (2002).CrossRefGoogle Scholar
  5. 5.
    Cartegni, L., Wang, J., Zhu, Z., et al.: ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic. Acids. Res., 31, 3568–3571 (2003).CrossRefGoogle Scholar
  6. 6.
    Clark, F., Thanaraj, T.A.: Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human. Hum. Mol. Genet., 11, 451–464 (2002).CrossRefGoogle Scholar
  7. 7.
    D’Souza, I., Schellenberg, G.D.: Determinants of 4-repeat tau expression. Coordination between enhancing and inhibitory splicing sequences for exon 10 inclusion. J. Biol. Chem., 275, 17700–17709 (2000).CrossRefGoogle Scholar
  8. 8.
    Elrick, L.L., Humphrey, M.B., Cooper, T.A., Berget, S.M.: A short sequence within two purine-richenhancers determines 5splice site specificity. Mol. Cell. Biol., 18, 343–352 (1998).Google Scholar
  9. 9.
    Fairbrother, W.G., Yeh, R.F., Sharp, P.A., Burge, C.B.: Predictive identification of exonic splicing enhancers in human genes. Science, 297, 1007–1013 (2002).CrossRefGoogle Scholar
  10. 10.
    Galperin, M.Y.: The molecular biology database collection: 2005 update. Nucleic. Acids. Res., 33, D5–D24 (2005).CrossRefGoogle Scholar
  11. 11.
    Graveley, B.R.: Sorting out the complexity of SR protein functions. Rna, 6, 1197–1211 (2000).CrossRefGoogle Scholar
  12. 12.
    Graveley, B.R.: Alternative splicing: increasing diversity in the proteomic world. Trends. Genet., 17, 100–107 (2001).CrossRefGoogle Scholar
  13. 13.
    Hertel, K.J., Graveley, B.R.: RS domains contact the pre-mRNA throughout spliceosome assembly. Trends. Biochem. Sci., 30, 115–118 (2005).CrossRefGoogle Scholar
  14. 14.
    Hertel, K.J., Maniatis, T.: The function of multisite splicing enhancers. Mol. Cell., 1: 449– 455 (1998).CrossRefGoogle Scholar
  15. 15.
    Hiller, M., Huse, K., Szafranski, K., et al.: Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. Nat. Genet., 36, 1255–1257 (2004).CrossRefGoogle Scholar
  16. 16.
    Humphrey, M.B., Bryan, J., Cooper, T.A., Berget, S.M.: A 32-nucleotide exon-splicing enhancer regulates usage of competing 5splice sites in a differential internal exon. Mol. Cell. Biol., 15, 3979–3988 (1995).Google Scholar
  17. 17.
    Konig, H., Ponta, H., Herrlich, P.: Coupling of signal transduction to alternative pre-mRNA splicing by a composite splice regulator. Embo. J., 17, 2904–2913 (1998).CrossRefGoogle Scholar
  18. 18.
    Lander, E.S., et al.: Initial sequencing and analysis of the human genome. Nature, 409, 860–921 (2001).CrossRefGoogle Scholar
  19. 19.
    Liu, H.X., Zhang, M., Krainer, A.R.: Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev., 12, 1998–2012 (1998).CrossRefGoogle Scholar
  20. 20.
    Lou, H., Neugebauer, K.M., Gagel, R.F., Berget, S.M.: Regulation of alternative polyadenylation by U1 snRNPs and SRp20. Mol. Cell. Biol., 18, 4977–4985 (1998).Google Scholar
  21. 21.
    Maniatis, T., Tasic, B.: Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature, 418, 236–243 (2002).CrossRefGoogle Scholar
  22. 22.
    Modrek, B., Resch, A., Grasso, C., Lee, C.: Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic. Acids Res., 29, 2850–2859 (2001).CrossRefGoogle Scholar
  23. 23.
    Pospisil, H., Herrmann, A., Bortfeldt, R.H., Reich, J.G. EASED: Extended Alternatively Spliced EST Database. Nucleic. Acids Res., 32, D70–D74 (2004).CrossRefGoogle Scholar
  24. 24.
    Ramchatesingh, J., Zahler, A.M., Neugebauer, K.M., et al.: A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer. Mol. Cell. Biol., 15, 4898–4907 (1995).Google Scholar
  25. 25.
    Shen, H., Green, M.R.: A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly. Mol. Cell., 16, 363–373 (2004).CrossRefGoogle Scholar
  26. 26.
    Smith, C.W., Valcarcel, J.: Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci., 25, 381–388 (2000).CrossRefGoogle Scholar
  27. 27.
    Tacke, R., Chen, Y., Manley, J.L.: Sequence-specific RNA binding by an SR protein requires RS domain phosphorylation: creation of an SRp40-specific splicing enhancer. Proc. Natl. Acad. Sci. USA, 94, 1148–1153 (1997).CrossRefGoogle Scholar
  28. 28.
    Tacke, R., Manley, J.L.: The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. Embo. J., 14, 3540–3551 (1995).Google Scholar
  29. 29.
    Venables, J.P.: Aberrant and alternative splicing in cancer. Cancer Res., 64, 7647–7654 (2004).CrossRefGoogle Scholar
  30. 30.
    Yeo, G., Burge, C.B.: Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals. RECOMB‘03 April 10–13 Berlin, Germany (2003).Google Scholar
  31. 31.
    Zhang, M.Q.: Statistical features of human exons and their flanking regions. Hum. Mol. Genet., 7, 919–932 (1998).CrossRefGoogle Scholar

Copyright information

© springer 2007

Authors and Affiliations

  • Ralf Bortfeldt
    • 1
    • 2
  • Alexander Herrmann
    • 2
  • Heike Pospisil
    • 3
  • Stefan Schuster
    • 1
  1. 1.Dept. of BioinformaticsFriedrich-Schiller University JenaD-07743 JenaGermany
  2. 2.Dept. of BioinformaticsMax-Delbrck Center for Molecular MedicineD-13092 BerlinGermany
  3. 3.Center for BioinformaticsUniversity of HamburgD-20146 HamburgGermany

Personalised recommendations