Identical sequence patterns in the ends of exons and introns of human protein-coding genes

Computational Biology and Chemistry

Volumn 36, Issue , 2012, Pages 55-61

  Tavares, Raphael ^a   Renaud, Gabriel ^a   Oliveira, Paulo Sergio Lopes ^b   Ferreira, Carlos G ^a   Dias Neto, Emmanuel ^c,d   Passetti, Fabio ^a  

^a INSTITUTO NACIONAL DE CÂNCER   (Brazil)

^b BRAZILIAN CENTER FOR RESEARCH IN ENERGY AND MATERIALS CNPEM   (Brazil)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

^d A C CAMARGO CANCER CENTER   (Brazil)

Author keywords

Bioinformatics; Genome; Sequence analysis; Transcriptomics

Indexed keywords

ACCEPTOR SITES; INTRONIC SEQUENCES; PRE-MRNA; PROTEIN-CODING GENES; SEQUENCE ANALYSIS; SEQUENCE IDENTITY; SEQUENCE PATTERNS; SPLICE SITE; TRANSCRIPTOMICS;

BIOINFORMATICS; CODES (SYMBOLS); GENES; NUCLEOTIDES; PROTEINS;

TRANSCRIPTION;

PROTEIN;

ARTICLE; EXON; GENETICS; HUMAN; INTRON; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; EXONS; HUMANS; INTRONS; PROTEINS;

EID: 84856318100     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2012.01.002     Document Type: Article

References (21)

1. M. Akerman, and Y. Mandel-Gutfreund Alternative splicing regulation at tandem 3′ splice sites Nucleic Acids Res. 34 2006 23 31 (Pubitemid 43160032)
2. D. Baralle, and M. Baralle Splicing in action: assessing disease causing sequence changes J. Med. Genet. 42 2005 737 748 (Pubitemid 41475248)
3. E. Bernard, and J. Michel Computation of direct and inverse mutations with the SEGM web server (Stochastic Evolution of Genetic Motifs): an application to splice sites of human genome introns Comput. Biol. Chem. 33 2009 245 252
4. R. Breathnach, and P. Chambon Organization and expression of eukaryotic split genes coding for proteins Annu. Rev. Biochem. 50 1981 349 393
5. M. Burset, I.A. Seledtsov, and V.V. Solovyev Analysis of canonical and non-canonical splice sites in mammalian genomes Nucleic Acids Res. 28 2000 4364 4375
6. G.E. Crooks, G. Hon, J. Chandonia, and S.E. Brenner WebLogo: a sequence logo generator Genome Res. 14 2004 1188 1190 (Pubitemid 38811555)
7. M. Hiller, K. Huse, K. Szafranski, N. Jahn, J. Hampe, S. Schreiber, R. Backofen, and M. Platzer Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity Nat. Genet. 36 2004 1255 1257 (Pubitemid 39577932)
8. M. Hiller, K. Huse, K. Szafranski, P. Rosenstiel, S. Schreiber, and R. Backofen Phylogenetically widespread alternative splicing at unusual GYNGYN donors Genome Biol. 7 2006 65 1-65.12
9. O.M. Korzinov, T.V. Astakhova, P.K. Vlasov, and M.A. Roytberg Statistical analysis of DNA sequences in the neighborhood of splice sites Mol. Biol. 42 2008 133 145 (Pubitemid 351399863)
10. M. Lund, and J. Kjems Defining a 5′ splice site by functional selection in the presence and absence of U1 snRNA 5′ end RNA 8 2002 166 179 (Pubitemid 34288904)
11. B. Modrek, and C. Lee A genomic view of alternative splicing Nat. Genet. 30 2002 13 19
12. S.M. Mount A catalogue of splice junction sequences Nucleic Acids Res. 10 1982 459 472 (Pubitemid 12151141)
13. S.M. Mount, C. Burks, G. Hertz, G.D. Stormo, O. White, and C. Fields Splicing signals in Drosophila: intron size, information content, and consensus sequences Nucleic Acids Res. 20 1992 4255 4262
14. R.A. Padgett, P.J. Grabowski, M.M. Konarska, S. Seiler, and P.A. Sharp Splicing of messenger RNA precursors Annu. Rev. Biochem. 55 1986 1119 1150 (Pubitemid 16070797)
15. W.G. Qiu, N. Schisler, and A. Stoltzfus The evolutionary gain of spliceosomal introns: sequence and phase preferences Mol. Biol. Evol. 21 2004 1252 1263 (Pubitemid 38823728)
16. S.W. Roy, and W. Gilbert The evolution of spliceosomal introns: patterns, puzzles and progress Nat. Rev. Genet. 7 2006 211 221 (Pubitemid 43361532)
17. F. Schmit, S. Cremer, and S. Gaubatz LIN54 is an essential core subunit of the DREAM/LINC complex that binds to the cdc2 promoter in a sequence-specific manner FEBS J. 276 2009 5703 5716
18. M.B. Shapiro, and P. Senapathy RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression Nucleic Acids Res. 15 1987 7155 7174
19. R. Sinha, S. Nikolajewa, K. Szafranski, M. Hiller, N. Jahn, K. Huse, M. Platzer, and R. Backofen Accurate prediction of NAGNAG alternative splicing Nucleic Acids Res. 37 2009 3569 3579
20. M.Q. Zhang Statistical features of human exons and their flanking regions Hum. Mol. Genet. 7 1998 919 932 (Pubitemid 28221257)
21. D. Zhuo, R. Madden, S.A. Elela, and B. Chabot Modern origin of numerous alternatively spliced human introns from tandem arrays Proc. Natl. Acad. Sci. U.S.A. 104 2007 882 886 (Pubitemid 46154705)