Identification, evolution and alternative splicing profile analysis of the splicing factor 30 (SPF30) in plant species

[1]  Bei Gao,et al.  Genome-wide identification and functional analysis of the splicing component SYF2/NTC31/p29 across different plant species , 2018, Planta.

[2]  Peer Bork,et al.  20 years of the SMART protein domain annotation resource , 2017, Nucleic Acids Res..

[3]  Ge-Fei Hao,et al.  Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings , 2017, The Plant journal : for cell and molecular biology.

[4]  M. Tress,et al.  Most Alternative Isoforms Are Not Functionally Important. , 2017, Trends in biochemical sciences.

[5]  B. Blencowe.  The Relationship between Alternative Splicing and Proteomic Complexity. , 2017, Trends in biochemical sciences.

[6]  James C. Schnable,et al.  Evolutionarily Conserved Alternative Splicing Across Monocots , 2017, Genetics.

[7]  Araxi O. Urrutia,et al.  Alternative splicing and the evolution of phenotypic novelty , 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.

[8]  Ariel Chernomoretz,et al.  The spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms , 2015, Proceedings of the National Academy of Sciences.

[9]  M. Tress,et al.  The Evolutionary Fate of Alternatively Spliced Homologous Exons after Gene Duplication , 2015, Genome biology and evolution.

[10]  W. Barbazuk,et al.  Genome-Wide Identification of Evolutionarily Conserved Alternative Splicing Events in Flowering Plants , 2015, Front. Bioeng. Biotechnol..

[11]  A. Gregory Matera,et al.  A day in the life of the spliceosome , 2014, Nature Reviews Molecular Cell Biology.

[12]  John W. S. Brown,et al.  Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses[OPEN] , 2013, Plant Cell.

[13]  M. Alló,et al.  Alternative splicing: a pivotal step between eukaryotic transcription and translation , 2013, Nature Reviews Molecular Cell Biology.

[14]  K. Adams,et al.  Features of evolutionarily conserved alternative splicing events between Brassica and Arabidopsis. , 2013, The New phytologist.

[15]  Yamile Marquez,et al.  Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis , 2012, Genome research.

[16]  D. Reinberg,et al.  Crystal Structure of TDRD3 and Methyl-Arginine Binding Characterization of TDRD3, SMN and SPF30 , 2012, PloS one.

[17]  Yamile Marquez,et al.  Challenges in Plant Alternative Splicing , 2012 .

[18]  D. Fessas,et al.  Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins , 2011, Nature Structural &Molecular Biology.

[19]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[20]  C. Will,et al.  Spliceosome structure and function. , 2011, Cold Spring Harbor perspectives in biology.

[21]  Sean R. Eddy,et al.  Hidden Markov model speed heuristic and iterative HMM search procedure , 2010, BMC Bioinformatics.

[22]  Xuehui Huang,et al.  Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. , 2010, Genome research.

[23]  G. Ast,et al.  Alternative splicing and evolution: diversification, exon definition and function , 2010, Nature Reviews Genetics.

[24]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[25]  S. Dheur,et al.  Splicing Factor Spf30 Assists Exosome-Mediated Gene Silencing in Fission Yeast , 2009, Molecular and Cellular Biology.

[26]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[27]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[28]  Larry S. Davis,et al.  Automatic online tuning for fast Gaussian summation , 2008, NIPS.

[29]  B. Frey,et al.  Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing , 2008, Nature Genetics.

[30]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[31]  Lili Wan,et al.  SMN Deficiency Causes Tissue-Specific Perturbations in the Repertoire of snRNAs and Widespread Defects in Splicing , 2008, Cell.

[32]  M. Jurica,et al.  Splicing Factor SPF30 Bridges an Interaction between the Prespliceosome Protein U2AF35 and Tri-small Nuclear Ribonucleoprotein Protein hPrp3* , 2008, Journal of Biological Chemistry.

[33]  Volker Brendel,et al.  Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes , 2008, BMC Plant Biology.

[34]  G. Ast,et al.  Alternative splicing: current perspectives , 2008, BioEssays : news and reviews in molecular, cellular and developmental biology.

[35]  Rotem Sorek,et al.  The birth of new exons: mechanisms and evolutionary consequences. , 2007, RNA.

[36]  A. Reddy.  Alternative splicing of pre-messenger RNAs in plants in the genomic era. , 2007, Annual review of plant biology.

[37]  Christopher J. Lee,et al.  Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. , 2007, RNA.

[38]  A. Barta,et al.  Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins , 2006, Nucleic acids research.

[39]  Christopher J. Lee,et al.  Alternative splicing and RNA selection pressure — evolutionary consequences for eukaryotic genomes , 2006, Nature Reviews Genetics.

[40]  Huanming Yang,et al.  Origin and evolution of new exons in rodents. , 2005, Genome research.

[41]  S. Richard,et al.  Tudor Domains Bind Symmetrical Dimethylated Arginines* , 2005, Journal of Biological Chemistry.

[42]  Doron Lancet,et al.  Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms , 2005, Nature Genetics.

[43]  Jonathan F Wendel,et al.  Polyploidy and Genome Evolution in Plants This Review Comes from a Themed Issue on Genome Studies and Molecular Genetics Edited , 2022 .

[44]  Jenn-Kang Hwang,et al.  Predicting subcellular localization of proteins for Gram‐negative bacteria by support vector machines based on n‐peptide compositions , 2004, Protein science : a publication of the Protein Society.

[45]  S. Brenner,et al.  Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[46]  A. Kornblihtt,et al.  Alternative splicing: multiple control mechanisms and involvement in human disease. , 2002, Trends in genetics : TIG.

[47]  A. Lamond,et al.  SPF30 Is an Essential Human Splicing Factor Required for Assembly of the U4/U5/U6 Tri-small Nuclear Ribonucleoprotein into the Spliceosome* , 2001, The Journal of Biological Chemistry.

[48]  G. Meister,et al.  SMNrp is an essential pre‐mRNA splicing factor required for the formation of the mature spliceosome , 2001, The EMBO journal.

[49]  R. Lührmann,et al.  Essential role for the tudor domain of SMN in spliceosomal U snRNP assembly: implications for spinal muscular atrophy. , 1999, Human molecular genetics.

[50]  C. Ponting,et al.  Characterization of a gene encoding survival motor neuron (SMN)-related protein, a constituent of the spliceosome complex. , 1998, Human molecular genetics.

[51]  Juri Rappsilber,et al.  Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex , 1998, Nature Genetics.

[52]  F. Corpet.  Multiple sequence alignment with hierarchical clustering. , 1988, Nucleic acids research.

[53]  Kathleen Marchal,et al.  PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences , 2002, Nucleic Acids Res..

[54]  G. Stier,et al.  SMN Tudor domain structure and its interaction with the Sm proteins , 2001, Nature Structural Biology.