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Volumn 589, Issue 15, 2015, Pages 1766-1770

nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data

Author keywords

Alternative splicing; Differential splicing; Expression quantification; NAGNAG motif

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; COMPUTER GRAPHICS; COMPUTER PREDICTION; DATA ANALYSIS SOFTWARE; MEASUREMENT ACCURACY; NAGNAG ALTERNATIVE SPLICING; NAGNAG MOTIF; NUCLEOTIDE MOTIF; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA SEQUENCE; UNTRANSLATED REGION; PROTEIN MOTIF; SEQUENCE ANALYSIS;

EID: 84934435801     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2015.05.029     Document Type: Article
Times cited : (9)

References (34)
  • 1
    • 31544461505 scopus 로고    scopus 로고
    • Alternative splicing regulation at tandem 3' splice sites
    • M. Akerman, and Y. Mandel-Gutfreund Alternative splicing regulation at tandem 3' splice sites Nucleic Acids Res. 34 2006 23 31
    • (2006) Nucleic Acids Res. , vol.34 , pp. 23-31
    • Akerman, M.1    Mandel-Gutfreund, Y.2
  • 2
    • 84888422652 scopus 로고    scopus 로고
    • Complexity of the alternative splicing landscape in plants
    • S.N.R. Anireddy, M. Yamile, K. Maria, and B. Andrea Complexity of the alternative splicing landscape in plants Plant Cell 25 2013 3657 3683
    • (2013) Plant Cell , vol.25 , pp. 3657-3683
    • Anireddy, S.N.R.1    Yamile, M.2    Maria, K.3    Andrea, B.4
  • 3
    • 84856480471 scopus 로고    scopus 로고
    • Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution
    • R.K. Bradley, J. Merkin, N.J. Lambert, and C.B. Burge Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution PLoS Biol. 10 2012 e1001229
    • (2012) PLoS Biol. , vol.10
    • Bradley, R.K.1    Merkin, J.2    Lambert, N.J.3    Burge, C.B.4
  • 4
    • 84857128287 scopus 로고    scopus 로고
    • Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome?
    • A. Busch, and K.J. Hertel Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome? Genome Biol. 13 2012 143
    • (2012) Genome Biol. , vol.13 , pp. 143
    • Busch, A.1    Hertel, K.J.2
  • 5
    • 84901775009 scopus 로고    scopus 로고
    • Genome-wide analysis of heat-sensitive alternative splicing in Physcomitrella patens
    • C.Y. Chang, W.D. Lin, and S.L. Tu Genome-wide analysis of heat-sensitive alternative splicing in Physcomitrella patens Plant Physiol. 165 2014 826 840
    • (2014) Plant Physiol. , vol.165 , pp. 826-840
    • Chang, C.Y.1    Lin, W.D.2    Tu, S.L.3
  • 6
    • 0028244050 scopus 로고
    • Two alternatively spliced forms of the human insulin-like growth factor I receptor have distinct biological activities and internalization kinetics
    • G. Condorelli, R. Bueno, and R.J. Smith Two alternatively spliced forms of the human insulin-like growth factor I receptor have distinct biological activities and internalization kinetics J. Biol. Chem. 269 1994 8510 8516
    • (1994) J. Biol. Chem. , vol.269 , pp. 8510-8516
    • Condorelli, G.1    Bueno, R.2    Smith, R.J.3
  • 7
    • 77952997562 scopus 로고    scopus 로고
    • Prevalence of alternative splicing choices in Arabidopsis thaliana
    • A.C. English, K.S. Patel, and A.E. Loraine Prevalence of alternative splicing choices in Arabidopsis thaliana BMC Plant Biol. 10 2010 102
    • (2010) BMC Plant Biol. , vol.10 , pp. 102
    • English, A.C.1    Patel, K.S.2    Loraine, A.E.3
  • 8
    • 84901406102 scopus 로고    scopus 로고
    • Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues
    • L. Florea, L. Song, S.L. Salzberg. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. Res. 2 (2013), 188.
    • (2013) Res. , vol.2 , pp. 188
    • Florea, L.1    Song, L.2    Salzberg, S.L.3
  • 12
    • 33646593160 scopus 로고    scopus 로고
    • Survey of Conserved Alternative Splicing Events of mRNAs Encoding SR Proteins in Land Plants
    • K. Iida, and M. Go Survey of Conserved Alternative Splicing Events of mRNAs Encoding SR Proteins in Land Plants Mol. Biol. Evol. 23 2006 1085 1094
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1085-1094
    • Iida, K.1    Go, M.2
  • 13
    • 40849086257 scopus 로고    scopus 로고
    • Alternative splicing at NAGNAG acceptor sites shares common properties in land plants and mammals
    • K. Iida, M. Shionyu, and Y. Suso Alternative splicing at NAGNAG acceptor sites shares common properties in land plants and mammals Mol. Biol. Evol. 25 2008 709 718
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 709-718
    • Iida, K.1    Shionyu, M.2    Suso, Y.3
  • 14
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 15
    • 22244432192 scopus 로고    scopus 로고
    • Evolutionary conservation of minor U12-type spliceosome between plants and humans
    • Z.J. Lorkovic, R. Lehner, C. Forstner, and A. Barta Evolutionary conservation of minor U12-type spliceosome between plants and humans RNA 11 2005 1095 1107
    • (2005) RNA , vol.11 , pp. 1095-1107
    • Lorkovic, Z.J.1    Lehner, R.2    Forstner, C.3    Barta, A.4
  • 16
    • 34447123260 scopus 로고    scopus 로고
    • Comparative cross-species alternative splicing in plants
    • H. Ner-Gaon, N. Leviatan, E. Rubin, and R. Fluhr Comparative cross-species alternative splicing in plants Plant Physiol. 144 2007 1632 1641
    • (2007) Plant Physiol. , vol.144 , pp. 1632-1641
    • Ner-Gaon, H.1    Leviatan, N.2    Rubin, E.3    Fluhr, R.4
  • 17
    • 84883454184 scopus 로고    scopus 로고
    • Exo-endo trans splicing: a new way to link
    • C. Preußer, and A. Bindereif Exo-endo trans splicing: a new way to link Cell Res. 23 2013 1071 1072
    • (2013) Cell Res. , vol.23 , pp. 1071-1072
    • Preußer, C.1    Bindereif, A.2
  • 18
    • 84866464012 scopus 로고    scopus 로고
    • SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts
    • M.C. Ryan, J. Cleland, R. Kim, W.C. Wong, and J.N. Weinstein SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts Bioinformatics 28 2012 2385 2387
    • (2012) Bioinformatics , vol.28 , pp. 2385-2387
    • Ryan, M.C.1    Cleland, J.2    Kim, R.3    Wong, W.C.4    Weinstein, J.N.5
  • 19
    • 79951768304 scopus 로고    scopus 로고
    • Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: a emerging model biosystem for plant functional genomics
    • G. Sablok, P.K. Gupta, J.M. Baek, F. Vazquez, and X.J. Min Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: a emerging model biosystem for plant functional genomics Biotechnol. Lett. 33 2011 629 636
    • (2011) Biotechnol. Lett. , vol.33 , pp. 629-636
    • Sablok, G.1    Gupta, P.K.2    Baek, J.M.3    Vazquez, F.4    Min, X.J.5
  • 21
    • 50949105626 scopus 로고    scopus 로고
    • A general definition and nomenclature for alternative splicing events
    • M. Sammeth, S. Foissac, and R. Guigó A general definition and nomenclature for alternative splicing events PLoS Comput. Biol. 4 8 2008 e1000147
    • (2008) PLoS Comput. Biol. , vol.4 , Issue.8
    • Sammeth, M.1    Foissac, S.2    Guigó, R.3
  • 24
    • 84919936245 scopus 로고    scopus 로고
    • RMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
    • S. Shen, J.W. Park, Z.X. Lu, L. Lin, M.D. Henry, Y.N. Wu, Q. Zhou, and Y. Xing RMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data PNAS 111 2014 E5593 E5601
    • (2014) PNAS , vol.111 , pp. E5593-E5601
    • Shen, S.1    Park, J.W.2    Lu, Z.X.3    Lin, L.4    Henry, M.D.5    Wu, Y.N.6    Zhou, Q.7    Xing, Y.8
  • 25
    • 84891599115 scopus 로고    scopus 로고
    • Genome-wide study of NAGNAG alternative splicing in Arabidopsis
    • Y. Shi, G. Sha, and X. Sun Genome-wide study of NAGNAG alternative splicing in Arabidopsis Planta 239 2014 127 138
    • (2014) Planta , vol.239 , pp. 127-138
    • Shi, Y.1    Sha, G.2    Sun, X.3
  • 28
    • 84903643218 scopus 로고    scopus 로고
    • Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA
    • X. Sun, S.M. Lin, and X. Yan Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA Biomed. Res. Int. 2014 2014 736798
    • (2014) Biomed. Res. Int. , vol.2014 , pp. 736798
    • Sun, X.1    Lin, S.M.2    Yan, X.3
  • 29
    • 25444516516 scopus 로고    scopus 로고
    • 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
    • K. Tadokoro, M. Yamazaki-Inoue, M. Tachibana, M. Fujishiro, K. Nagao, M. Toyoda, M. Ozaki, and M. Ono 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. 50 2005 382 394
    • (2005) J. Hum. Genet. , vol.50 , pp. 382-394
    • Tadokoro, K.1    Yamazaki-Inoue, M.2    Tachibana, M.3    Fujishiro, M.4    Nagao, K.5    Toyoda, M.6    Ozaki, M.7    Ono, M.8
  • 30
    • 0029860454 scopus 로고    scopus 로고
    • An alternative splicing event in the Pax-3 paired domain identifies the linker region as a key determinant of paired domain DNA-binding activity
    • K.J. Vogan, D.A. Underhill, and P. Gros 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. 16 1996 6677 6686
    • (1996) Mol. Cell. Biol. , vol.16 , pp. 6677-6686
    • Vogan, K.J.1    Underhill, D.A.2    Gros, P.3
  • 31
    • 84879157497 scopus 로고    scopus 로고
    • Genome-wide landscape of alternative splicing events in Brachypodium distachyon
    • B. Walters, G. Lum, G. Sablok, and X.J. Min Genome-wide landscape of alternative splicing events in Brachypodium distachyon DNA Res. 20 2013 163 171
    • (2013) DNA Res. , vol.20 , pp. 163-171
    • Walters, B.1    Lum, G.2    Sablok, G.3    Min, X.J.4
  • 32
    • 84878787698 scopus 로고    scopus 로고
    • Alt event finder: a tool for extracting alternative splicing events from RNA-Seq data
    • A. Zhou, M.R. Breese, Y. Hao, H.J. Edenberg, L. Li, T.C. Skaar, and Y. Liu Alt event finder: a tool for extracting alternative splicing events from RNA-Seq data BMC Genomics 13 2012 S10
    • (2012) BMC Genomics , vol.13 , pp. S10
    • Zhou, A.1    Breese, M.R.2    Hao, Y.3    Edenberg, H.J.4    Li, L.5    Skaar, T.C.6    Liu, Y.7
  • 33
    • 0038349624 scopus 로고    scopus 로고
    • Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome
    • M. Zavolan, S. Kondo, C. Schonbach, J. Adachi, and D.A. Hume Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome Genome Res. 13 2003 1290 1300
    • (2003) Genome Res. , vol.13 , pp. 1290-1300
    • Zavolan, M.1    Kondo, S.2    Schonbach, C.3    Adachi, J.4    Hume, D.A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.