A General Definition and Nomenclature for Alternative Splicing Events

by: micha
August 12, 2008

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Peer-Reviewed Paper, View Original
Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most... » More
PLoS Comput Biol. 2008 Aug 8; 4(8):e1000147
Michael Sammeth, Sylvain Foissac, Roderic Guigó

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  1. Black DL (2003) Mechanisms of alternative pre-messenger RNA splicing.. Annu Rev Biochem 72: 291-336.
  2. Lopez AJ (1998) Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation.. Annu Rev Genet 32: 279-305.
  3. Smith CW, Valcarcel J (2000) Alternative pre-mRNA splicing: the logic of combinatorial control.. Trends Biochem Sci 25: 381-388.
  4. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC (2001) Initial sequencing and analysis of the human genome.. Nature 409: 860-921.
  5. Florea L (2006) Bioinformatics of alternative splicing and its regulation.. Brief Bioinform 7: 55-69.
  6. Xing Y, Lee C (2006) Alternative splicing and RNA selection pressure—evolutionary consequences for eukaryotic genomes.. Nat Rev Genet 7: 499-509.
  7. Zavolan M, van Nimwegen E (2006) The types and prevalence of alternative splice forms.. Curr Opin Struct Biol 16: 362-367.
  8. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays.. Science 302: 2141-2144.
  9. Kim H, Klein R, Majewski J, Ott J (2004) Estimating rates of alternative splicing in mammals and invertebrates.. Nat Genet 36: 915-916; author reply 916–917.
  10. Breithart RE, Andreadis A, Nadal-Ginard B (1987) Alternative splicing: a ubiquitous mechanism for the generation of multiple protein isoforms from single genes.. Annu Rev Biochem 56: 467-495.
  11. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.. Nature 447: 799-816.
  12. Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.. Nucleic Acids Res 35: D61-D65.
  13. Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O (2000) An alternative-exon database and its statistical analysis.. DNA Cell Biol 19: 739-756.
  14. Stamm S, Riethoven JJ, Le Texier V, Gopalakrishnan C, Kumanduri V (2006) ASD: a bioinformatics resource on alternative splicing.. Nucleic Acids Res 34: D46-D55.
  15. Le Texier V, Riethoven JJ, Kumanduri V, Gopalakrishnan C, Lopez F (2006) AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation.. BMC Bioinformatics 7: 169.
  16. Holste D, Huo G, Tung V, Burge CB (2006) HOLLYWOOD: a comparative relational database of alternative splicing.. Nucleic Acids Res 34: D56-D62.
  17. Zhou Y, Zhou C, Ye L, Dong J, Xu H (2003) Database and analyses of known alternatively spliced genes in plants.. Genomics 82: 584-595.
  18. Coward E, Haas SA, Vingron M (2002) SpliceNest: visualization of gene structure and alternative splicing based on EST clusters.. Trends Genet 18: 53-55.
  19. Huang YH, Chen YT, Lai JJ, Yang ST, Yang UC (2002) PALS db: Putative Alternative Splicing database.. Nucleic Acids Res 30: 186-190.
  20. Burset M, Seledtsov IA, Solovyev VV (2001) SpliceDB: database of canonical and non-canonical mammalian splice sites.. Nucleic Acids Res 29: 255-259.
  21. Ji H, Zhou Q, Wen F, Xia H, Lu X (2001) AsMamDB: an alternative splice database of mammals.. Nucleic Acids Res 29: 260-263.
  22. Modrek B, Resch A, Grasso C, Lee C (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes.. Nucleic Acids Res 29: 2850-2859.
  23. Huang HD, Horng JT, Lee CC, Liu BJ (2003) ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data.. Genome Biol 4: R29.
  24. Bhasi A, Pandey RV, Utharasamy SP, Senapathy P (2007) EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes.. Bioinformatics 23: 1815-1823.
  25. Kim N, Alekseyenko AV, Roy M, Lee C (2007) The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.. Nucleic Acids Res 35: D93-D98.
  26. Malko DB, Makeev VJ, Mironov AA, Gelfand MS (2006) Evolution of exon–intron structure and alternative splicing in fruit flies and malarial mosquito genomes.. Genome Res 16: 505-509.
  27. Collins L, Penny D (2006) Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Investigating the intron recognition mechanism in eukaryotes.. Mol Biol Evol 23: 901-910.
  28. Fox-Walsh KL, Dou Y, Lam BJ, Hung SP, Baldi PF (2005) The architecture of pre-mRNAs affects mechanisms of splice-site pairing.. Proc Natl Acad Sci U S A 102: 16176-16181.
  29. Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O (2005) Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes.. Gene 364: 53-62.
  30. Buratti E, Baralle M, Baralle FE (2006) Defective splicing, disease and therapy: searching for master checkpoints in exon definition.. Nucleic Acids Res 34: 3494-3510.
  31. Kornblihtt AR, de la Mata M, Fededa JP, Munoz MJ, Nogues G (2004) Multiple links between transcription and splicing.. RNA 10: 1489-1498.
  32. Listerman I, Sapra AK, Neugebauer KM (2006) Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells.. Nat Struct Mol Biol 13: 815-822.
  33. Mironov AA, Fickett JW, Gelfand MS (1999) Frequent alternative splicing of human genes.. Genome Res 9: 1288-1293.
  34. Eyras E, Reymond A, Castelo R, Bye JM, Camara F (2005) Gene finding in the chicken genome.. BMC Bioinformatics 6: 131.
  35. Heber S, Alekseyev M, Sze SH, Tang H, Pevzner PA (2002) Splicing graphs and EST assembly problem.. Bioinformatics 18: S181-S188.
  36. Sperisen P, Iseli C, Pagni M, Stevenson BJ, Bucher P (2004) trome, trEST and trGEN: databases of predicted protein sequences.. Nucleic Acids Res 32: D509-D511.
  37. Sugnet CW, Kent WJ, Ares M, Haussler D (2004) Transcriptome and genome conservation of alternative splicing events in humans and mice.. Pac Symp Biocomput: 66-77.
  38. Bollina D, Lee BT, Tan TW, Ranganathan S (2006) ASGS: an alternative splicing graph web service.. Nucleic Acids Res 34: W444-W447.
  39. Gupta S, Zink D, Korn B, Vingron M, Haas SA (2004) Genome wide identification and classification of alternative splicing based on EST data.. Bioinformatics 20: 2579-2585.
  40. Kim N, Shin S, Lee S (2005) ECgene: genome-based EST clustering and gene modeling for alternative splicing.. Genome Res 15: 566-576.
  41. Lee BT, Tan TW, Ranganathan S (2004) DEDB: a database of Drosophila melanogaster exons in splicing graph form.. BMC Bioinformatics 5: 189.
  42. Foissac S, Sammeth M (2007) ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets.. Nucleic Acids Res 35: W297-W299.
  43. Kondrashov FA, Koonin EV (2003) Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences.. Trends Genet 19: 115-119.
  44. Yandell M, Mungall CJ, Smith C, Prochnik S, Kaminker J (2006) Large-scale trends in the evolution of gene structures within 11 animal genomes.. PLoS Comput Biol 2: e15doi:10.1371/journal.pcbi.0020015.
  45. Swinburne IA, Meyer CA, Liu XS, Silver PA, Brodsky AS (2006) Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription.. Genome Res 16: 912-921.
  46. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2008) GenBank.. Nucleic Acids Res 36: D25-D30.
  47. Boguski MS, Lowe TM, Tolstoshev CM (1993) dbEST—database for “expressed sequence tags”.. Nat Genet 4: 332-333.
  48. Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M (2007) Ensembl 2007.. Nucleic Acids Res 35: D610-D617.
  49. Harrow J, Denoeud F (2006) GENCODE: Producing a reference annotation for ENCODE.. Genome Biol 7: S4.1-S4.9.
  50. Akerman M, Mandel-Gutfreund Y (2006) Alternative splicing regulation at tandem 3′ splice sites.. Nucleic Acids Res 34: 23-31.
  51. Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P (2006) A simple physical model predicts small exon length variations.. PLoS Genet 2: e45doi:10.1371/journal.pgen.0020045.
  52. Hiller M, Huse K, Szafranski K, Jahn N, Hampe J (2004) Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity.. Nat Genet 36: 1255-1257.
  53. Senapathy P (1988) Possible evolution of splice-junction signals in eukaryotic genes from stop codons.. Proc Natl Acad Sci U S A 85: 1129-1133.
  54. Kaessmann H, Zollner S, Nekrutenko A, Li WH (2002) Signatures of domain shuffling in the human genome.. Genome Res 12: 1642-1650.
  55. Kim E, Magen A, Ast G (2007) Different levels of alternative splicing among eukaryotes.. Nucleic Acids Res 35: 125-131.
  56. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.. Nat Genet 25: 25-29.
  57. Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J (2007) What is a gene, post-ENCODE? History and updated definition.. Genome Res 17: 669-681.
  58. Pearson H (2006) Genetics: what is a gene?. Nature 441: 398-401.
  59. Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A (2006) Transcription-mediated gene fusion in the human genome.. Genome Res 16: 30-36.
  60. Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R (2006) Tandem chimerism as a means to increase protein complexity in the human genome.. Genome Res 16: 37-44.
  61. Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R (2006) Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions.. Genome Res 17: 746-759.
  62. Takeda J, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.. Nucleic Acids Res 34: 3917-3928.
  63. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.. Nature 447: 799-816.
  64. (1994) FlyBase—the Drosophila database.. Nucleic Acids Res 22: 3456-3458.
  65. Stein L, Sternberg P, Durbin R, Thierry-Mieg J, Spieth J (2001) WormBase: network access to the genome and biology of Caenorhabditis elegans.. Nucleic Acids Res 29: 82-86.
  66. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator.. Genome Res 14: 1188-1190.
  67. Hedges SB (2002) The origin and evolution of model organisms.. Nat Rev Genet 3: 838-849.