Characterization and prediction of alternative splice sites

Gene

Volumn 366, Issue 2, 2006, Pages 219-227

  Wang, Magnus ^a   Marín, Antonio ^a  

^a UNIVERSITY OF SEVILLE   (Spain)

Author keywords

Alternative splicing; ASSP; GC content; Neural networks; Oligonucleotide frequency models; Splice site prediction

Indexed keywords

GUANINE NUCLEOTIDE; OLIGONUCLEOTIDE; PYRIMIDINE NUCLEOTIDE;

ALTERNATIVE RNA SPLICING; ARTICLE; ARTIFICIAL NEURAL NETWORK; BINDING SITE; CLASSIFICATION; CONTENT ANALYSIS; DONOR SITE; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RNA BINDING; SCORING SYSTEM;

ALTERNATIVE SPLICING; BINDING SITES; DATABASES, NUCLEIC ACID; HUMANS; NUCLEAR PROTEINS; RIBONUCLEOPROTEINS; RNA SPLICE SITES; SEQUENCE ANALYSIS, DNA;

EID: 32544456772     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2005.07.015     Document Type: Article

References (36)

1. G. Bernardi The human genome: organization and evolutionary history Annu. Rev. Genet. 29 1995 445 476
2. J. Bouck, X. Fu, A.M. Skalka, and R.A. Kratz Genetic selection for balanced retroviral splicing: novel regulation involving the second step can be mediated by transitions in the polypyrimidine tract Mol. Cell. Biol. 15 1995 2663 2671
3. C. Burge, and S. Karlin Prediction of complete gene structures in human genomic DNA J. Mol. Biol. 268 1997 78 94
4. L. Cartegni, S.L. Chew, and A.R. Krainer Listening to silence and understanding nonsense: exonic mutations that affect splicing Nat. Rev., Genet. 3 2002 285 298
5. S.L. Cawley, and L. Patcher HMM sampling and applications to gene finding and alternative splicing Bioinformatics 19 Suppl. 2 2003 ii36 ii41
6. F. Clark, and T.A. Thanaraj Catergorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human Hum. Mol. Genet. 11 2002 451 464
7. C.J. Coolidge, R.J. Seely, and J.G. Patton Functional analysis of the polypyrimidine tract in pre-mRNA splicing Nucleic Acids Res. 25 1997 888 896
8. E. Coward, S.A. Haas, and M. Vingron SpliceNest: visualization of gene structure and alternative splicing based on EST clusters Trends Genet. 18 2002 53 55
9. G. Dror, R. Sorek, and R. Shamir Accurate identification of alternatively spliced exons using support vector machine Bioinformatics 21 2004 897 901
10. I. Goncalves, L. Duret, and D. Mouchiroud Nature and structure of human genes that generate retropseudogenes Genome Res. 10 2000 672 678
11. B.R. Graveley Alternative splicing: increasing diversity in the proteomic world Trends Genet. 17 2001 100 107
12. R. Guigó, S. Knudsen, N. Drake, and T.F. Smith Prediction of gene structure J. Mol. Biol. 226 1992 141 157
13. 35 in AG-dependent pre m-RNA splicing Mol. Cell. Biol. 21 2001 7673 7681
14. J.M. Johnson Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays Science 302 2003 2141 2144
15. O.O. Konu, and M.D. Li Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents J. Mol. Evol. 54 2002 35 41
16. E.V. Kriventseva Increase of functional diversity by alternative splicing Trends Genet. 19 2003 124 128
17. D. Kulp, D. Haussler, M.G. Reese, and F.H. Eeckman A generalized hidden Markov model for the recognition of human genes in DNA D.J. States P. Agarwal T. Gaasterland L. Hunter R.F Smith Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology 1996 AAAI Press Menlo Park 134 142
18. A.J. Lopez Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation Annu. Rev. Genet. 32 1998 279 305
19. A.J. McCullough, and S.M. Berget An intronic splicing enhancer binds U1 snRNPs to enhance splicing and select 5′ splice sites Mol. Cell. Biol. 20 2000 9225 9235
20. L. Milanesi, and I.B. Rogozin Prediction of human gene structure M.J. Bishop Guide to Human Genome Computing 2nd ed. 1998 Academic Press London 215 259
21. L. Milanesi, D. D'Angelo, and I.B. Rogozin GeneBuilder: interactive in silico prediction of gene structure Bioinformatics 15 1999 612 621
22. A.A. Mironov, J.W. Fickett, and M.S. Gelfand Frequent alternative splicing of human genes Genome Res. 9 1999 1288 1293
23. B. Modrek, A. Resch, C. Grasso, and C. Lee Genome-wide analysis of alternative splicing using human expressed sequence tags Nucleic Acids Res. 29 2001 2850 2859
24. G. Pesole, G. Bernardi, and C. Saccone Isochore specificity of AUG initiator context of human genes FEBS Lett. 464 1999 60 62
25. L. Ponger, L. Duret, and D. Mouchiroud Determinants of CpG islands: expression in early embryo and isochore structure Genome Res. 11 2001 1854 1860
26. I.B. Rogozin, and L. Milanesi Analysis of donor splice sites in different eukaryotic organisms J. Mol. Evol. 45 1997 50 59
27. R.F. Rossigno, M. Weiner, and M.A. Garcia-Blanco A mutational analysis of the polypyrimidine tract of introns J. Biol. Chem. 268 1993 11222 11229
28. T.D. Schneider Information content of individual genetic sequences J. Theor. Biol. 189 1997 427 441
29. P. Senapathy, M.B. Shapiro, and N.L. Harris Splice junctions, branch point sites, and exons: sequence statsistics, identifications, and applications to Genome Project Methods Enzymol. 183 1990 252 278
30. R. Singh, J. Valcarcel, and M.R. Green Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins Science 268 1995 1173 1176
31. C.W. Smith, and J. Valcárcel Alternative pre-mRNA splicing: the logic of combinatorial control Trends Biochem Sci. 25 2000 381 388
32. R. Sorek, R. Shemesh, Y. Cohen, O. Basechess, G. Ast, and R. Shamir A non-EST-based method for exon-skipping prediction Genome Res. 14 2004 1617 1623
33. T.A. Thanaraj, and S. Stamm Prediction and statistical analysis of alternatively splices exons Prog. Mol. Subcell. Biol. 31 2003 1 31
34. A.E. Vinogradov Isochores and tissue-specifity Nucleic Acids Res. 31 2003 5212 5220
35. Wang, M., Marín, A., in preparation. Identification and analysis of splicing regulatory elements with Seqool, a sequence analysis tool.
36. 35 Nature 402 1999 832 835