It's a bit over, is that ok? The subtle surplus from tandem alternative splicing

References

• Akerman M, Mandel-Gutfreund Y. Alternative splicing regulation at tandem 3′ splice sites. Nucleic Acids Res 2006, 34:23-31; PMID:16394021; http://dx.doi.org/10.1093/nar/gkj408
   PubMedGoogle Scholar
• Akerman M, Mandel-Gutfreund Y. Does distance matter? Variations in alternative 3′ splicing regulation. Nucleic Acids Res 2007, 35:5487-98; PMID:17704130; http://dx.doi.org/10.1093/nar/gkm603
   PubMedGoogle Scholar
• Bengtsson M, Stahlberg A, Rorsman P, Kubista M. Gene expression profiling in single cells from the pancreatic islets of langerhans reveals lognormal distribution of mrna levels. Genome Res 2005, 15:1388-92; PMID:16204192; http://dx.doi.org/10.1101/gr.3820805
   PubMed Web of Science ®Google Scholar
• Black DL. Mechanisms of alternative pre-messenger Rna splicing. Annu Rev Biochem 2003, 72:291-336; PMID:12626338; http://dx.doi.org/10.1146/annurev.biochem.72.121801.161720
   PubMed Web of Science ®Google Scholar
• Blaustein M, Pelisch F, Srebrow A. Signals, pathways and splicing regulation. Int J Biochem Cell Biol 2007, 39:2031-48; PMID:17507279; http://dx.doi.org/10.1016/j.biocel.2007.04.004
   PubMed Web of Science ®Google Scholar
• Bradley RK, Merkin J, Lambert NJ, Burge CB. Alternative splicing of Rna triplets is often regulated and accelerates proteome evolution. PLoS Biol 2012, 10:e1001229; PMID:22235189; http://dx.doi.org/10.1371/journal.pbio.1001229
   PubMedGoogle Scholar
• Buckingham M, Rigby PW. Gene regulatory networks and transcriptional mechanisms that control myogenesis. Dev Cell 2014, 28:225-38; PMID:24525185; http://dx.doi.org/10.1016/j.devcel.2013.12.020
   PubMed Web of Science ®Google Scholar
• Buratti E, Baralle FE. Influence of Rna secondary structure on the pre-mrna splicing process. Mol Cell Biol 2004, 24:10505-14; PMID:15572659; http://dx.doi.org/10.1128/MCB.24.24.10505-10514.2004
   PubMed Web of Science ®Google Scholar
• Busch A, Hertel KJ. Extensive regulation of nagnag alternative splicing: new tricks for the spliceosome?. Genome Biol 2012, 13:143; PMID:22356731; http://dx.doi.org/10.1186/gb3999
   PubMedGoogle Scholar
• Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, Hayashizaki Y, Zavolan M. A simple physical model predicts small exon length variations. PLoS Genet 2006, 2:e45; PMID:16683028; http://dx.doi.org/10.1371/journal.pgen.0020045
   PubMedGoogle Scholar
• Chisa JL, Burke DT. Mammalian mrna splice-isoform selection is tightly controlled. Genetics 2007, 175:1079-87; PMID:17179090; http://dx.doi.org/10.1534/genetics.106.066183
   PubMedGoogle Scholar
• Chua K, Reed R. The Rna splicing factor hslu7 is required for correct 3′ splice-site choice. Nature 1999, 402:207-10; PMID:10647016; http://dx.doi.org/10.1038/46086
   PubMed Web of Science ®Google Scholar
• Dou Y, Fox-Walsh KL, Baldi PF, Hertel KJ. Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site. RNA 2006, 12:2047-56; PMID:17053087; http://dx.doi.org/10.1261/rna.151106
   PubMed Web of Science ®Google Scholar
• Haber DA, Sohn RL, Buckler AJ, Pelletier J, Call KM, Housman DE. Alternative splicing and genomic structure of the wilms tumor gene Wt1. Proc Natl Acad Sci U S A 1991, 88:9618-22; PMID:1658787; http://dx.doi.org/10.1073/pnas.88.21.9618
   PubMed Web of Science ®Google Scholar
• Hammes A, Guo JK, Lutsch G, Leheste JR, Landrock D, Ziegler U, Gubler MC, Schedl A. Two splice variants of the wilms' tumor 1 gene have distinct functions during sex determination and nephron formation. Cell 2001, 106:319-29; PMID:11509181; http://dx.doi.org/10.1016/S0092-8674(01)00453-6
   PubMed Web of Science ®Google Scholar
• Hiller M, Huse K, Szafranski K, Jahn N, Hampe J, Schreiber S, Backofen R, Platzer M. Widespread occurrence of alternative splicing at nagnag acceptors contributes to proteome plasticity. Nat Genet 2004, 36:1255-7; PMID:15516930; http://dx.doi.org/10.1038/ng1469
   PubMed Web of Science ®Google Scholar
• Hiller M, Platzer M. Widespread and subtle: alternative splicing at short-distance tandem sites. Trends Genet 2008, 24:246-55; PMID:18394746; http://dx.doi.org/10.1016/j.tig.2008.03.003
   PubMedGoogle Scholar
• Hiller M, Szafranski K, Sinha R, Huse K, Nikolajewa S, Rosenstiel P, Schreiber S, Backofen R, Platzer M. Assessing the fraction of short-distance tandem splice sites under purifying selection. RNA 2008, 14:616-29; PMID:18268022; http://dx.doi.org/10.1261/rna.883908
   PubMed Web of Science ®Google Scholar
• Islam S, Kjallquist U, Moliner A, Zajac P, Fan JB, Lonnerberg P, Linnarsson S. Characterization of the single-cell transcriptional landscape by highly multiplex Rna-Seq. Genome Res 2011, 21:1160-7; PMID:21543516; http://dx.doi.org/10.1101/gr.110882.110
   PubMed Web of Science ®Google Scholar
• Kim TD, Kim JS, Kim JH, Myung J, Chae HD, Woo KC, Jang SK, Koh DS, Kim KT. Rhythmic serotonin n-acetyltransferase mrna degradation is essential for the maintenance of its circadian oscillation. Mol Cell Biol 2005, 25:3232-46; PMID:15798208; http://dx.doi.org/10.1128/MCB.25.8.3232-3246.2005
   PubMedGoogle Scholar
• Klamt B, Koziell A, Poulat F, Wieacker P, Scambler P, Berta P, Gessler M. Frasier syndrome is caused by defective alternative splicing of Wt1 leading to an altered ratio of Wt1 +/-Kts splice isoforms. Hum Mol Genet 1998, 7:709-14; PMID:9499425; http://dx.doi.org/10.1093/hmg/7.4.709
   PubMed Web of Science ®Google Scholar
• Kozmik Z, Czerny T, Busslinger M. Alternatively spliced insertions in the paired domain restrict the dna sequence specificity of Pax6 and Pax8. EMBO J 1997, 16:6793-803.
   Google Scholar
• Kramer M, Huse K, Menzel U, Backhaus O, Rosenstiel P, Schreiber S, Hampe J, Platzer M. Constant splice-isoform ratios in human lymphoblastoid cells support the concept of a splico-stat. Genetics 2011, 187:761-70.
   Google Scholar
• Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. Unproductive splicing of sr genes associated with highly conserved and ultraconserved DNA elements. Nature 2007, 446:926-9; PMID:17361132; http://dx.doi.org/10.1038/nature05676
   PubMed Web of Science ®Google Scholar
• Manley JL, Krainer AR. A rational nomenclature for serine/arginine-rich protein splicing factors Sr proteins. Genes Dev 2010, 24:1073-4; PMID:20516191; http://dx.doi.org/10.1101/gad.1934910
   PubMed Web of Science ®Google Scholar
• Raj A, van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 2008, 135:216-26; PMID:18957198; http://dx.doi.org/10.1016/j.cell.2008.09.050
   PubMed Web of Science ®Google Scholar
• Reeb PD, Steibel JP. Evaluating Statistical Analysis Models for Rna Sequencing Experiments. Front Genet 2013, 4:178; PMID:24062766; http://dx.doi.org/10.3389/fgene.2013.00178
   PubMedGoogle Scholar
• Saltzman AL, Pan Q, Blencowe BJ. Regulation of alternative splicing by the core spliceosomal machinery. Genes Dev 2011, 25:373-84; PMID:21325135; http://dx.doi.org/10.1101/gad.2004811
   PubMed Web of Science ®Google Scholar
• Schindler S, Heiner M, Platzer M, Szafranski K. Comparison of methods for quantification of subtle splice variants. Electrophoresis 2009, 30:3674-81; PMID:19862747; http://dx.doi.org/10.1002/elps.200900292
   PubMed Web of Science ®Google Scholar
• Schindler S, Szafranski K, Hiller M, Ali GS, Palusa SG, Backofen R, Platzer M, Reddy AS. Alternative splicing at nagnag acceptors in arabidopsis thaliana sr and sr-related protein-coding genes. BMC Genomics 2008, 9:159; PMID:18402682; http://dx.doi.org/10.1186/1471-2164-9-159
   PubMedGoogle Scholar
• Sinha R, Lenser T, Jahn N, Gausmann U, Friedel S, Szafranski K, Huse K, Rosenstiel P, Hampe J, Schuster S, Hiller M, Backofen R, Platzer M. Tassdb2 - a comprehensive database of subtle alternative splicing events. BMC Bioinformatics 2010, 11:216; PMID:20429909; http://dx.doi.org/10.1186/1471-2105-11-216
   PubMedGoogle Scholar
• Sinha R, Nikolajewa S, Szafranski K, Hiller M, Jahn N, Huse K, Platzer M, Backofen R. Accurate prediction of nagnag alternative splicing. Nucleic Acids Res 2009, 37:3569-79; PMID:19359358; http://dx.doi.org/10.1093/nar/gkp220
   PubMedGoogle Scholar
• Stamm S, Ben-Ari S, Rafalska I, Tang Y, Zhang Z, Toiber D, Thanaraj TA, Soreq H. Function of alternative splicing. Gene 2005, 344:1-20; PMID:15656968; http://dx.doi.org/10.1016/j.gene.2004.10.022
   PubMed Web of Science ®Google Scholar
• Szafranski K, Fritsch C, Schumann F, Siebel L, Sinha R, Hampe J, Hiller M, Englert C, Huse K, Platzer M. Physiological state co-regulates thousands of mammalian mrna splicing events at tandem splice sites and alternative exons. Nucleic Acids Res 2014, 42:8895-904; PMID:25030907; http://dx.doi.org/10.1093/nar/gku532
   PubMedGoogle Scholar
• Szafranski K, Schindler S, Taudien S, Hiller M, Huse K, Jahn N, Schreiber S, Backofen R, Platzer M. Violating the splicing rules: Tg dinucleotides function as alternative 3′ splice sites in U2-dependent introns. Genome Biol 2007, 8:R154; PMID:17672918; http://dx.doi.org/10.1186/gb-2007-8-8-r154
   PubMedGoogle Scholar
• Tadokoro K, Yamazaki-Inoue M, Tachibana M, Fujishiro M, Nagao K, Toyoda M, Ozaki M, Ono M, Miki N, Miyashita T, Yamada M. Frequent occurrence of protein isoforms with or without a single amino acid residue by subtle alternative splicing: The case of gln in drpla affects subcellular localization of the products. J Hum Genet 2005, 50:382-94; PMID:16091834; http://dx.doi.org/10.1007/s10038-005-0261-9
   PubMedGoogle Scholar
• Tsai KW, Chan WC, Hsu CN, Lin WC. Sequence features involved in the mechanism of 3′ splice junction wobbling. BMC Mol Biol 2010, 11:34; PMID:20459675; http://dx.doi.org/10.1186/1471-2199-11-34
   PubMedGoogle Scholar
• Tsai KW, Lin WC. Quantitative analysis of wobble splicing indicates that it is not tissue specific. Genomics 2006, 88:855-64; PMID:16920330; http://dx.doi.org/10.1016/j.ygeno.2006.07.004
   PubMedGoogle Scholar
• Vogan KJ, Underhill DA, Gros P. An alternative splicing event in the Pax-3 paired domain identifies the linker region as a key determinant of paired domain DNA-binding activity. Mol Cell Biol 1996, 16:6677-86.
   Google Scholar
• Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-6; PMID:18978772; http://dx.doi.org/10.1038/nature07509
   PubMed Web of Science ®Google Scholar
• Will CL, Luhrmann R. Spliceosome structure and function. Cold Spring Harb Perspect Biol 2011, 3: a003707; PMID:21441581; http://dx.doi.org/10.1101/cshperspect.a003707.
   PubMed Web of Science ®Google Scholar
• Yan M, Wang LC, Hymowitz SG, Schilbach S, Lee J, Goddard A, de Vos AM, Gao WQ, Dixit VM. Two-amino acid molecular switch in an epithelial morphogen that regulates binding to two distinct receptors. Science 2000, 290:523-7; PMID:11039935; http://dx.doi.org/10.1126/science.290.5491.523
   PubMed Web of Science ®Google Scholar