TY - JOUR AU - Campbell, M. A. AU - Haas, B. J. AU - Hamilton, J. P. AU - Mount, S. M. AU - Buell, C. R. PY - 2006 DA - 2006// TI - Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis JO - BMC Genomics VL - 7 UR - https://doi.org/10.1186/1471-2164-7-327 DO - 10.1186/1471-2164-7-327 ID - Campbell2006 ER - TY - JOUR AU - Kim, E. AU - Magen, A. AU - Ast, G. PY - 2007 DA - 2007// TI - Different levels of alternative splicing among eukaryotes JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl924 DO - 10.1093/nar/gkl924 ID - Kim2007 ER - TY - JOUR AU - Wang, B. B. AU - Brendel, V. PY - 2006 DA - 2006// TI - Genomewide comparative analysis of alternative splicing in plants JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0602039103 DO - 10.1073/pnas.0602039103 ID - Wang2006 ER - TY - JOUR AU - Modrek, B. AU - Lee, C. PY - 2002 DA - 2002// TI - A genomic view of alternative splicing JO - Nat Genet VL - 30 UR - https://doi.org/10.1038/ng0102-13 DO - 10.1038/ng0102-13 ID - Modrek2002 ER - TY - JOUR AU - Reddy, A. S. PY - 2007 DA - 2007// TI - Alternative splicing of pre-messenger RNAs in plants in the genomic era JO - Annu Rev Plant Biol VL - 58 UR - https://doi.org/10.1146/annurev.arplant.58.032806.103754 DO - 10.1146/annurev.arplant.58.032806.103754 ID - Reddy2007 ER - TY - JOUR AU - Lewis, B. P. AU - Green, R. E. AU - Brenner, S. E. PY - 2003 DA - 2003// TI - Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.0136770100 DO - 10.1073/pnas.0136770100 ID - Lewis2003 ER - TY - JOUR AU - Birzele, F. AU - Csaba, G. AU - Zimmer, R. PY - 2008 DA - 2008// TI - Alternative splicing and protein structure evolution JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm1054 DO - 10.1093/nar/gkm1054 ID - Birzele2008 ER - TY - JOUR AU - Tress, M. L. AU - Martelli, P. L. AU - Frankish, A. AU - Reeves, G. A. AU - Wesselink, J. J. AU - Yeats, C. AU - Olason, P. L. AU - Albrecht, M. AU - Hegyi, H. AU - Giorgetti, A. PY - 2007 DA - 2007// TI - The implications of alternative splicing in the ENCODE protein complement JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0700800104 DO - 10.1073/pnas.0700800104 ID - Tress2007 ER - TY - JOUR AU - Yura, K. AU - Shionyu, M. AU - Hagino, K. AU - Hijikata, A. AU - Hirashima, Y. AU - Nakahara, T. AU - Eguchi, T. AU - Shinoda, K. AU - Yamaguchi, A. AU - Takahashi, K. PY - 2006 DA - 2006// TI - Alternative splicing in human transcriptome: functional and structural influence on proteins JO - Gene VL - 380 UR - https://doi.org/10.1016/j.gene.2006.05.015 DO - 10.1016/j.gene.2006.05.015 ID - Yura2006 ER - TY - JOUR AU - Iida, K. AU - Go, M. PY - 2006 DA - 2006// TI - Survey of conserved alternative splicing events of mRNAs encoding SR proteins in land plants JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msj118 DO - 10.1093/molbev/msj118 ID - Iida2006 ER - TY - JOUR AU - Kalyna, M. AU - Lopato, S. AU - Voronin, V. AU - Barta, A. PY - 2006 DA - 2006// TI - Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl570 DO - 10.1093/nar/gkl570 ID - Kalyna2006 ER - TY - JOUR AU - Li, J. AU - Li, X. AU - Guo, L. AU - Lu, F. AU - Feng, X. AU - He, K. AU - Wei, L. AU - Chen, Z. AU - Qu, L. J. AU - Gu, H. PY - 2006 DA - 2006// TI - A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice JO - J Exp Bot VL - 57 UR - https://doi.org/10.1093/jxb/erj094 DO - 10.1093/jxb/erj094 ID - Li2006 ER - TY - JOUR AU - Valenzuela, A. AU - Talavera, D. AU - Orozco, M. AU - de la Cruz, X. PY - 2004 DA - 2004// TI - Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species JO - J Mol Biol VL - 335 UR - https://doi.org/10.1016/j.jmb.2003.10.061 DO - 10.1016/j.jmb.2003.10.061 ID - Valenzuela2004 ER - TY - JOUR AU - Baek, J. M. AU - Han, P. AU - Iandolino, A. AU - Cook, D. R. PY - 2008 DA - 2008// TI - Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice JO - Plant Mol Biol VL - 67 UR - https://doi.org/10.1007/s11103-008-9334-4 DO - 10.1007/s11103-008-9334-4 ID - Baek2008 ER - TY - JOUR AU - Irimia, M. AU - Rukov, J. L. AU - Penny, D. AU - Roy, S. W. PY - 2007 DA - 2007// TI - Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-188 DO - 10.1186/1471-2148-7-188 ID - Irimia2007 ER - TY - JOUR AU - Liu, S. AU - Altman, R. B. PY - 2003 DA - 2003// TI - Large scale study of protein domain distribution in the context of alternative splicing JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg668 DO - 10.1093/nar/gkg668 ID - Liu2003 ER - TY - JOUR AU - Kriventseva, E. V. AU - Koch, I. AU - Apweiler, R. AU - Vingron, M. AU - Bork, P. AU - Gelfand, M. S. AU - Sunyaev, S. PY - 2003 DA - 2003// TI - Increase of functional diversity by alternative splicing JO - Trends Genet VL - 19 UR - https://doi.org/10.1016/S0168-9525(03)00023-4 DO - 10.1016/S0168-9525(03)00023-4 ID - Kriventseva2003 ER - TY - JOUR AU - Taneri, B. AU - Snyder, B. AU - Novoradovsky, A. AU - Gaasterland, T. PY - 2004 DA - 2004// TI - Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-10-r75 DO - 10.1186/gb-2004-5-10-r75 ID - Taneri2004 ER - TY - JOUR AU - Resch, A. AU - Xing, Y. AU - Modrek, B. AU - Gorlick, M. AU - Riley, R. AU - Lee, C. PY - 2004 DA - 2004// TI - Assessing the impact of alternative splicing on domain interactions in the human proteome JO - J Proteome Res VL - 3 UR - https://doi.org/10.1021/pr034064v DO - 10.1021/pr034064v ID - Resch2004 ER - TY - JOUR AU - Kim, E. AU - Goren, A. AU - Ast, G. PY - 2008 DA - 2008// TI - Alternative splicing: current perspectives JO - Bioessays VL - 30 UR - https://doi.org/10.1002/bies.20692 DO - 10.1002/bies.20692 ID - Kim2008 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. AU - Davis, A. P. AU - Dolinski, K. AU - Dwight, S. S. AU - Eppig, J. T. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology. The Gene Ontology Consortium JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR AU - Su, Z. AU - Wang, J. AU - Yu, J. AU - Huang, X. AU - Gu, X. PY - 2006 DA - 2006// TI - Evolution of alternative splicing after gene duplication JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.4197006 DO - 10.1101/gr.4197006 ID - Su2006 ER - TY - JOUR AU - Nurtdinov, R. N. AU - Artamonova, I. I. AU - Mironov, A. A. AU - Gelfand, M. S. PY - 2003 DA - 2003// TI - Low conservation of alternative splicing patterns in the human and mouse genomes JO - Hum Mol Genet VL - 12 UR - https://doi.org/10.1093/hmg/ddg137 DO - 10.1093/hmg/ddg137 ID - Nurtdinov2003 ER - TY - JOUR AU - Berget, S. M. PY - 1995 DA - 1995// TI - Exon recognition in vertebrate splicing JO - J Biol Chem VL - 270 UR - https://doi.org/10.1074/jbc.270.6.2411 DO - 10.1074/jbc.270.6.2411 ID - Berget1995 ER - TY - JOUR AU - Barbazuk, W. B. AU - Fu, Y. AU - McGinnis, K. M. PY - 2008 DA - 2008// TI - Genome-wide analyses ofalternative splicing in plants: Opportunities and challenges JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.053678.106 DO - 10.1101/gr.053678.106 ID - Barbazuk2008 ER - TY - JOUR AU - O'Toole, N. AU - Hattori, M. AU - Andres, C. AU - Iida, K. AU - Lurin, C. AU - Schmitz-Linneweber, C. AU - Sugita, M. AU - Small, I. PY - 2008 DA - 2008// TI - On the expansion of the pentatricopeptide repeat gene family in plants JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msn057 DO - 10.1093/molbev/msn057 ID - O'Toole2008 ER - TY - JOUR AU - Paquette, S. AU - Moller, B. L. AU - Bak, S. PY - 2003 DA - 2003// TI - On the origin of family 1 plant glycosyltransferases JO - Phytochemistry VL - 62 UR - https://doi.org/10.1016/S0031-9422(02)00558-7 DO - 10.1016/S0031-9422(02)00558-7 ID - Paquette2003 ER - TY - JOUR AU - Paquette, S. M. AU - Bak, S. AU - Feyereisen, R. PY - 2000 DA - 2000// TI - Intron-exon organization and phylogeny in a large superfamily, the paralogous cytochrome P450 genes of Arabidopsis thaliana JO - DNA Cell Biol VL - 19 UR - https://doi.org/10.1089/10445490050021221 DO - 10.1089/10445490050021221 ID - Paquette2000 ER - TY - JOUR AU - Hughes, A. L. AU - Friedman, R. PY - 2008 DA - 2008// TI - Alternative splicing, gene duplication and connectivity in the genetic interaction network of the nematode worm Caenorhabditis elegans JO - Genetica VL - 134 UR - https://doi.org/10.1007/s10709-007-9223-9 DO - 10.1007/s10709-007-9223-9 ID - Hughes2008 ER - TY - JOUR AU - Kopelman, N. M. AU - Lancet, D. AU - Yanai, I. PY - 2005 DA - 2005// TI - Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms JO - Nat Genet VL - 37 UR - https://doi.org/10.1038/ng1575 DO - 10.1038/ng1575 ID - Kopelman2005 ER - TY - JOUR AU - Lin, H. AU - Ouyang, S. AU - Egan, A. AU - Nobuta, K. AU - Haas, B. J. AU - Zhu, W. AU - Gu, X. AU - Silva, J. C. AU - Meyers, B. C. AU - Buell, C. R. PY - 2008 DA - 2008// TI - Characterization of paralogous protein families in rice JO - BMC Plant Biol VL - 8 UR - https://doi.org/10.1186/1471-2229-8-18 DO - 10.1186/1471-2229-8-18 ID - Lin2008 ER - TY - JOUR AU - Schindler, S. AU - Szafranski, K. AU - Hiller, M. AU - Ali, G. S. AU - Palusa, S. G. AU - Backofen, R. AU - Platzer, M. AU - Reddy, A. S. PY - 2008 DA - 2008// TI - Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes JO - BMC Genomics VL - 9 UR - https://doi.org/10.1186/1471-2164-9-159 DO - 10.1186/1471-2164-9-159 ID - Schindler2008 ER - TY - JOUR AU - Artamonova, I. I. AU - Gelfand, M. S. PY - 2007 DA - 2007// TI - Comparative genomics and evolution of alternative splicing: the pessimists' science JO - Chem Rev VL - 107 UR - https://doi.org/10.1021/cr068304c DO - 10.1021/cr068304c ID - Artamonova2007 ER - TY - JOUR AU - De Kee, D. W. AU - Gopalan, V. AU - Stoltzfus, A. PY - 2007 DA - 2007// TI - A sequence-based model accounts largely for the relationship of intron positions to protein structural features JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm151 DO - 10.1093/molbev/msm151 ID - De Kee2007 ER - TY - JOUR AU - Wang, P. AU - Yan, B. AU - Guo, J. T. AU - Hicks, C. AU - Xu, Y. PY - 2005 DA - 2005// TI - Structural genomics analysis of alternative splicing and application to isoform structure modeling JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0506770102 DO - 10.1073/pnas.0506770102 ID - Wang2005 ER - TY - JOUR AU - Irimia, M. AU - Rukov, J. L. AU - Penny, D. AU - Garcia-Fernandez, J. AU - Vinther, J. AU - Roy, S. W. PY - 2008 DA - 2008// TI - Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msm262 DO - 10.1093/molbev/msm262 ID - Irimia2008 ER - TY - JOUR AU - Andrade, M. A. AU - Perez-Iratxeta, C. AU - Ponting, C. P. PY - 2001 DA - 2001// TI - Protein repeats: structures, functions, and evolution JO - J Struct Biol VL - 134 UR - https://doi.org/10.1006/jsbi.2001.4392 DO - 10.1006/jsbi.2001.4392 ID - Andrade2001 ER - TY - JOUR AU - Kondrashov, F. A. AU - Koonin, E. V. PY - 2001 DA - 2001// TI - Origin of alternative splicing by tandem exon duplication JO - Hum Mol Genet VL - 10 UR - https://doi.org/10.1093/hmg/10.23.2661 DO - 10.1093/hmg/10.23.2661 ID - Kondrashov2001 ER - TY - JOUR AU - McGuire, A. M. AU - Pearson, M. D. AU - Neafsey, D. E. AU - Galagan, J. E. PY - 2008 DA - 2008// TI - Cross-kingdom patterns of alternative splicing and splice recognition JO - Genome Biol VL - 9 UR - https://doi.org/10.1186/gb-2008-9-3-r50 DO - 10.1186/gb-2008-9-3-r50 ID - McGuire2008 ER - TY - JOUR AU - McGlincy, N. J. AU - Smith, C. W. PY - 2008 DA - 2008// TI - Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense? JO - Trends Biochem Sci VL - 33 UR - https://doi.org/10.1016/j.tibs.2008.06.001 DO - 10.1016/j.tibs.2008.06.001 ID - McGlincy2008 ER - TY - STD TI - Dong Q, Schlueter SD, Brendel V: PlantGDB, plant genome database and analysis tools. Nucleic Acids Res. 2004, D354-359. 10.1093/nar/gkh046. 32 Database ID - ref41 ER - TY - STD TI - DFCI Gene Indices Software Tools. [http://compbio.dfci.harvard.edu/tgi/software/] UR - http://compbio.dfci.harvard.edu/tgi/software/ ID - ref42 ER - TY - STD TI - Maize sequence ftp site. [http://ftp.maizesequence.org/] UR - http://ftp.maizesequence.org/ ID - ref43 ER - TY - STD TI - JGI Populus trichocarpa v1.1 Download page. [http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.download.ftp.html] UR - http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.download.ftp.html ID - ref44 ER - TY - STD TI - NCBI ftp site. [ftp://ftp.ncbi.nih.gov/blast/db/FASTA/] UR - ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ ID - ref45 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Brendel, V. AU - Xing, L. AU - Zhu, W. PY - 2004 DA - 2004// TI - Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth058 DO - 10.1093/bioinformatics/bth058 ID - Brendel2004 ER - TY - JOUR AU - Kan, Z. AU - States, D. AU - Gish, W. PY - 2002 DA - 2002// TI - Selecting for functional alternative splices in ESTs JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.764102 DO - 10.1101/gr.764102 ID - Kan2002 ER - TY - JOUR AU - Hori, K. AU - Watanabe, Y. PY - 2007 DA - 2007// TI - Context analysis of termination codons in mRNA that are recognized by plant NMD JO - Plant Cell Physiol VL - 48 UR - https://doi.org/10.1093/pcp/pcm075 DO - 10.1093/pcp/pcm075 ID - Hori2007 ER - TY - JOUR AU - Remm, M. AU - Storm, C. E. AU - Sonnhammer, E. L. PY - 2001 DA - 2001// TI - Automatic clustering of orthologs and in-paralogs from pairwise species comparisons JO - J Mol Biol VL - 314 UR - https://doi.org/10.1006/jmbi.2000.5197 DO - 10.1006/jmbi.2000.5197 ID - Remm2001 ER - TY - JOUR AU - Needleman, S. B. AU - Wunsch, C. D. PY - 1970 DA - 1970// TI - A general method applicable to the search for similarities in the amino acid sequence of two proteins JO - J Mol Biol VL - 48 UR - https://doi.org/10.1016/0022-2836(70)90057-4 DO - 10.1016/0022-2836(70)90057-4 ID - Needleman1970 ER - TY - JOUR AU - Rice, P. AU - Longden, I. AU - Bleasby, A. PY - 2000 DA - 2000// TI - EMBOSS: the European Molecular Biology Open Software Suite JO - Trends Genet VL - 16 UR - https://doi.org/10.1016/S0168-9525(00)02024-2 DO - 10.1016/S0168-9525(00)02024-2 ID - Rice2000 ER - TY - JOUR AU - Xing, Y. AU - Resch, A. AU - Lee, C. PY - 2004 DA - 2004// TI - The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1304504 DO - 10.1101/gr.1304504 ID - Xing2004 ER - TY - JOUR AU - Tress, M. L. AU - Wesselink, J. J. AU - Frankish, A. AU - Lopez, G. AU - Goldman, N. AU - Loytynoja, A. AU - Massingham, T. AU - Pardi, F. AU - Whelan, S. AU - Harrow, J. PY - 2008 DA - 2008// TI - Determination and validation of principal gene products JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btm547 DO - 10.1093/bioinformatics/btm547 ID - Tress2008 ER - TY - JOUR AU - Zdobnov, E. M. AU - Apweiler, R. PY - 2001 DA - 2001// TI - InterProScan – an integration platform for the signature-recognition methods in InterPro JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.9.847 DO - 10.1093/bioinformatics/17.9.847 ID - Zdobnov2001 ER - TY - STD TI - Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R: Pfam: clans, web tools and services. Nucleic Acids Res. 2006, D247-251. 10.1093/nar/gkj149. 34 Database ID - ref56 ER - TY - JOUR AU - Holm, S. PY - 1979 DA - 1979// TI - A simple sequentially rejective multiple test procedure JO - Scandinavian Journal of Statistics VL - 6 ID - Holm1979 ER -