Searching journal content for articles similar to Sorek et al. 12 (7): 1060.

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  1. LETTER: Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse
    • Rotem Sorek and
    • Gil Ast
    Genome Res. July 2003 13: 1631-1637; doi:10.1101/gr.1208803
    ...Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse Rotem Sorek 1 , 2 and Gil Ast 1 , 3 1 Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel 2...
  2. LETTER: Origin and evolution of new exons in rodents
    • Wen Wang,
    • Hongkun Zheng,
    • Shuang Yang,
    • Haijing Yu,
    • Jun Li,
    • Huifeng Jiang,
    • Jianning Su,
    • Lei Yang,
    • Jianguo Zhang,
    • Jason McDermott,
    • Ram Samudrala,
    • Jian Wang,
    • Huanming Yang,
    • Jun Yu,
    • Karsten Kristiansen,
    • Gane Ka-Shu Wong,
    • and Jun Wang
    Genome Res. September 2005 15: 1258-1264; Published in Advance August 18, 2005, doi:10.1101/gr.3929705
    ...Sequencing Project Consortium. 2004 . Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428 : 493 -521. ↵ Sorek, R., Ast, G., and Graur, D. 2002 . Alu -containing exons are alternatively spliced. Genome Res. 12 : 1060 -1067. ↵ Springer, M.S., Murphy, W.J., Eizirik, E...
  3. Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
    • Luis Ferrández-Peral,
    • Xiaoyu Zhan,
    • Marina Alvarez-Estape,
    • Cristina Chiva,
    • Paula Esteller-Cucala,
    • Raquel García-Pérez,
    • Eva Julià,
    • Esther Lizano,
    • Òscar Fornas,
    • Eduard Sabidó,
    • Qiye Li,
    • Tomàs Marquès-Bonet,
    • David Juan,
    • and Guojie Zhang
    Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
    ...) and percentage of splice site combinations associated with each AS class (right). (SE) Skipping exons, (RI) retained introns, (A5SS) alternative 5′ splice sites, (A3SS) alternative 3′ splice sites, (MEX) mutually exclusive exons. (C) Number of annotated genes with novel detected peptides in each species for Uni...
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  4. Research: RNA editing in nascent RNA affects pre-mRNA splicing
    • Yun-Hua Esther Hsiao,
    • Jae Hoon Bahn,
    • Yun Yang,
    • Xianzhi Lin,
    • Stephen Tran,
    • Ei-Wen Yang,
    • Giovanni Quinones-Valdez,
    • and Xinshu Xiao
    Genome Res. June 2018 28: 812-823; Published in Advance May 3, 2018, doi:10.1101/gr.231209.117
    ...examined the sequence conservation of non-Alu-containing exons with 3′ss editing sites across 46 vertebrates spanning primates to fish (Siepel et al. 2005). Since these exons demonstrated multiple types of alternative splicing in the RNA-seq data (Fig. 3B) and because different types of alternative...
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  5. Research: HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo
    • Jonathan M. Howard,
    • Hai Lin,
    • Andrew J. Wallace,
    • Garam Kim,
    • Jolene M. Draper,
    • Maximilian Haeussler,
    • Sol Katzman,
    • Masoud Toloue,
    • Yunlong Liu,
    • and Jeremy R. Sanford
    Genome Res. May 2018 28: 689-698; Published in Advance April 12, 2018, doi:10.1101/gr.229062.117
    ...; Zorio and Blumenthal 1999). These early steps in spliceosome assembly play critical roles in defining exon–intron boundaries.HNRNPA1 is a well-characterized regulator of alternative splicing. One of the primary functions of HNRNPA1 is to prevent inclusion of specific exons (Mayeda and Krainer 1992...
  6. Research: Alu insertion variants alter gene transcript levels
    • Lindsay M. Payer,
    • Jared P. Steranka,
    • Maria S. Kryatova,
    • Giacomo Grillo,
    • Mathieu Lupien,
    • Pedro P. Rocha,
    • and Kathleen H. Burns
    Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
    ...Alu sequences. Recently, we showed that a subset of those mapping to introns can alter mRNA splicing of nearby exons (Payer et al. 2019), and that is likely just one of many functional consequences of polymorphic Alu elements.Retrotransposons have intrinsic sequences that regulate expression...
  7. Research: Gene length and expression level shape genomic novelties
    • Vladislav Grishkevich and
    • Itai Yanai
    Genome Res. September 2014 24: 1497-1503; Published in Advance July 11, 2014, doi:10.1101/gr.169722.113
    ...of short (black), medium (dark gray), and long (light gray) genes (boxes indicate exons). (B) An inverse relationship between a gene’s number of alternatively spliced variants and its family size, as previously characterized (Kopelmanet al. 2005). Theboxplot indicates themedian,mean (circle), and25%and75...
  8. Methods: A Non-EST-Based Method for Exon-Skipping Prediction
    • Rotem Sorek,
    • Ronen Shemesh,
    • Yuval Cohen,
    • Ortal Basechess,
    • Gil Ast,
    • and Ron Shamir
    Genome Res. August 2004 14: 1617-1623; doi:10.1101/gr.2572604
    ...Acids Res. 31 : 1067 –1074. ↵ Sorek, R., Ast, G., and Graur, D. 2002 . Alu-containing exons are alternatively spliced. Genome Res. 12 : 1060 –1067. ↵ Sorek, R., Shamir, R., and Ast, G. 2004 . How prevalent is functional alternative splicing in the human ? Trends Genet. 20 : 68 –71. ↵ Thanaraj, T...
  9. Research: The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages
    • Musa A. Hassan,
    • Vincent Butty,
    • Kirk D.C. Jensen,
    • and Jeroen P.J. Saeij
    Genome Res. March 2014 24: 377-389; Published in Advance November 18, 2013, doi:10.1101/gr.166033.113
    ...). Thus, treating each macrophage condition (nonstimulated, IFNG/TNF-stimulated, CpG-stimulated, and Toxoplasma-infected) as an independent cohort, we calculated the PSI values for each splicing event in each of the 28 samples. Of the 16,974 annotated exon-centric and 39 UTR alternative events (Wang et al...
  10. LETTER: Evolution of exon–intron structure and alternative splicing in fruit flies and malarial mosquito genomes
    • Dmitry B. Malko,
    • Vsevolod J. Makeev,
    • Andrey A. Mironov,
    • and Mikhail S. Gelfand
    Genome Res. April 2006 16: 505-509; Published in Advance March 6, 2006, doi:10.1101/gr.4236606
    .... ( 2005 ) Comparative sequencing of Drosophila pseudoobscura : Chromosomal, gene, and cis -element evolution. Genome Res. 15 : 1 – 18 . ↵ Sorek R. , Ast G. , Graur D. ( 2002 ) Alu -containing exons are alternatively spliced. Genome Res. 12 : 1060 – 1067 . ↵ Stolc V. , Gauhar Z. , Mason C. , Halasz G...
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