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Volumn 91, Issue 2, 2008, Pages 186-194

Case study for identification of potentially indel-caused alternative expression isoforms in the rice subspecies japonica and indica by integrative genome analysis

Author keywords

Alternative splicing; InDel; Indica; Japonica; Polyadenylation signal

Indexed keywords

MESSENGER RNA; PEROXIDASE; POLYADENYLIC ACID;

EID: 38149063766     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2007.10.001     Document Type: Article
Times cited : (6)

References (44)
  • 1
    • 0034256020 scopus 로고    scopus 로고
    • Alternative pre-mRNA splicing: the logic of combinatorial control
    • Smith C.W., and Valcarcel J. Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci. 25 (2000) 381-388
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 381-388
    • Smith, C.W.1    Valcarcel, J.2
  • 2
    • 0035904279 scopus 로고    scopus 로고
    • Co-transcriptional splicing of pre-messenger RNAs: considerations for the mechanism of alternative splicing
    • Goldstrohm A.C., Greenleaf A.L., and Garcia-Blanco M.A. Co-transcriptional splicing of pre-messenger RNAs: considerations for the mechanism of alternative splicing. Gene 277 (2001) 31-47
    • (2001) Gene , vol.277 , pp. 31-47
    • Goldstrohm, A.C.1    Greenleaf, A.L.2    Garcia-Blanco, M.A.3
  • 3
    • 0036337915 scopus 로고    scopus 로고
    • A genomic view of alternative splicing
    • Modrek B., and Lee C. A genomic view of alternative splicing. Nat. Genet. 30 (2002) 13-19
    • (2002) Nat. Genet. , vol.30 , pp. 13-19
    • Modrek, B.1    Lee, C.2
  • 5
    • 0037041395 scopus 로고    scopus 로고
    • An extensive network of coupling among gene expression machines
    • Maniatis T., and Reed R. An extensive network of coupling among gene expression machines. Nature 416 (2002) 499-506
    • (2002) Nature , vol.416 , pp. 499-506
    • Maniatis, T.1    Reed, R.2
  • 6
    • 3843111257 scopus 로고    scopus 로고
    • The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome
    • Leipzig J., Pevzner P., and Heber S. The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res. 32 (2004) 3977-3983
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3977-3983
    • Leipzig, J.1    Pevzner, P.2    Heber, S.3
  • 8
    • 33745394130 scopus 로고    scopus 로고
    • Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes
    • Xing Y., and Lee C. Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes. Nat. Rev. 7 (2006) 499-509
    • (2006) Nat. Rev. , vol.7 , pp. 499-509
    • Xing, Y.1    Lee, C.2
  • 9
    • 33645651622 scopus 로고    scopus 로고
    • Alternative first exon splicing regulates subcellular distribution of methionine sulfoxide reductases
    • Kim H.Y., and Gladyshev V.N. Alternative first exon splicing regulates subcellular distribution of methionine sulfoxide reductases. BMC Mol. Biol. 7 (2006) 11
    • (2006) BMC Mol. Biol. , vol.7 , pp. 11
    • Kim, H.Y.1    Gladyshev, V.N.2
  • 10
    • 33846681383 scopus 로고    scopus 로고
    • Different levels of alternative splicing among eukaryotes
    • Kim E., Magen A., and Ast G. Different levels of alternative splicing among eukaryotes. Nucleic Acids Res. 35 (2007) 125-131
    • (2007) Nucleic Acids Res. , vol.35 , pp. 125-131
    • Kim, E.1    Magen, A.2    Ast, G.3
  • 11
    • 34250813107 scopus 로고    scopus 로고
    • Alternative splicing of pre-messenger RNAs in plants in the genomic era
    • Reddy A.S. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu. Rev. Plant Biol. 58 (2007) 267-294
    • (2007) Annu. Rev. Plant Biol. , vol.58 , pp. 267-294
    • Reddy, A.S.1
  • 12
    • 0018263844 scopus 로고
    • Why genes in pieces?
    • Gilbert W. Why genes in pieces?. Nature 271 (1978) 501
    • (1978) Nature , vol.271 , pp. 501
    • Gilbert, W.1
  • 13
    • 0035036534 scopus 로고    scopus 로고
    • Gene structure prediction and alternative splicing analysis using genomically aligned ESTs
    • Kan Z., Rouchka E.C., Gish W.R., and States D.J. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 11 (2001) 889-900
    • (2001) Genome Res. , vol.11 , pp. 889-900
    • Kan, Z.1    Rouchka, E.C.2    Gish, W.R.3    States, D.J.4
  • 14
    • 0242594493 scopus 로고    scopus 로고
    • Database and analyses of known alternatively spliced genes in plants
    • Zhou Y., Zhou C., Ye L., Dong J., Xu H., Cai L., Zhang L., and Wei L. Database and analyses of known alternatively spliced genes in plants. Genomics 82 (2003) 584-595
    • (2003) Genomics , vol.82 , pp. 584-595
    • Zhou, Y.1    Zhou, C.2    Ye, L.3    Dong, J.4    Xu, H.5    Cai, L.6    Zhang, L.7    Wei, L.8
  • 15
    • 4444346326 scopus 로고    scopus 로고
    • Estimating rates of alternative splicing in mammals and invertebrates
    • (author reply 916-917)
    • Kim H., Klein R., Majewski J., and Ott J. Estimating rates of alternative splicing in mammals and invertebrates. Nat. Genet. 36 (2004) 915-916 (author reply 916-917)
    • (2004) Nat. Genet. , vol.36 , pp. 915-916
    • Kim, H.1    Klein, R.2    Majewski, J.3    Ott, J.4
  • 16
    • 3042675114 scopus 로고    scopus 로고
    • Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes
    • Itoh H., Washio T., and Tomita M. Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes. RNA (New York) 10 (2004) 1005-1018
    • (2004) RNA (New York) , vol.10 , pp. 1005-1018
    • Itoh, H.1    Washio, T.2    Tomita, M.3
  • 17
    • 4444270781 scopus 로고    scopus 로고
    • Genome wide identification and classification of alternative splicing based on EST data
    • Gupta S., Zink D., Korn B., Vingron M., and Haas S.A. Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics (Oxford) 20 (2004) 2579-2585
    • (2004) Bioinformatics (Oxford) , vol.20 , pp. 2579-2585
    • Gupta, S.1    Zink, D.2    Korn, B.3    Vingron, M.4    Haas, S.A.5
  • 18
    • 31144458029 scopus 로고    scopus 로고
    • Extraction of transcript diversity from scientific literature
    • Shah P.K., Jensen L.J., Boue S., and Bork P. Extraction of transcript diversity from scientific literature. PLoS Comput. Biol. 1 (2005) e10
    • (2005) PLoS Comput. Biol. , vol.1
    • Shah, P.K.1    Jensen, L.J.2    Boue, S.3    Bork, P.4
  • 21
    • 34250666605 scopus 로고    scopus 로고
    • Plant gene and alternatively spliced variant annotator: a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species
    • Chen F.C., Wang S.S., Chaw S.M., Huang Y.T., and Chuang T.J. Plant gene and alternatively spliced variant annotator: a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species. Plant Physiol. 143 (2007) 1086-1095
    • (2007) Plant Physiol. , vol.143 , pp. 1086-1095
    • Chen, F.C.1    Wang, S.S.2    Chaw, S.M.3    Huang, Y.T.4    Chuang, T.J.5
  • 22
    • 34447123260 scopus 로고    scopus 로고
    • Comparative cross-species alternative splicing in plants
    • Ner-Gaon H., Leviatan N., Rubin E., and Fluhr R. 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
  • 24
    • 33646484347 scopus 로고    scopus 로고
    • Genomewide comparative analysis of alternative splicing in plants
    • Wang B.B., and Brendel V. Genomewide comparative analysis of alternative splicing in plants. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 7175-7180
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 7175-7180
    • Wang, B.B.1    Brendel, V.2
  • 25
    • 0026661101 scopus 로고
    • Insertion of non-intron sequence into maize introns interferes with splicing
    • Luehrsen K.R., and Walbot V. Insertion of non-intron sequence into maize introns interferes with splicing. Nucleic Acids Res. 20 (1992) 5181-5187
    • (1992) Nucleic Acids Res. , vol.20 , pp. 5181-5187
    • Luehrsen, K.R.1    Walbot, V.2
  • 26
    • 0026885574 scopus 로고
    • Alternative splicing induced by insertion of retrotransposons into the maize waxy gene
    • Varagona M.J., Purugganan M., and Wessler S.R. Alternative splicing induced by insertion of retrotransposons into the maize waxy gene. Plant Cell 4 (1992) 811-820
    • (1992) Plant Cell , vol.4 , pp. 811-820
    • Varagona, M.J.1    Purugganan, M.2    Wessler, S.R.3
  • 27
    • 0034787902 scopus 로고    scopus 로고
    • Retrotransposons of the Tnt1B family are mobile in Nicotiana plumbaginifolia and can induce alternative splicing of the host gene upon insertion
    • Leprinc A.S., Grandbastien M.A., and Christian M. Retrotransposons of the Tnt1B family are mobile in Nicotiana plumbaginifolia and can induce alternative splicing of the host gene upon insertion. Plant Mol. Biol. 47 (2001) 533-541
    • (2001) Plant Mol. Biol. , vol.47 , pp. 533-541
    • Leprinc, A.S.1    Grandbastien, M.A.2    Christian, M.3
  • 28
    • 0035102828 scopus 로고    scopus 로고
    • The use of the Monsanto draft rice genome sequence in research
    • Barry G.F. The use of the Monsanto draft rice genome sequence in research. Plant Physiol. 125 (2001) 1164-1165
    • (2001) Plant Physiol. , vol.125 , pp. 1164-1165
    • Barry, G.F.1
  • 33
    • 0036077888 scopus 로고    scopus 로고
    • Insights into cereal genomes from two draft genome sequences of rice
    • (REVIEWS1015)
    • Bancroft I. Insights into cereal genomes from two draft genome sequences of rice. Genome Biol. 3 (2002) (REVIEWS1015)
    • (2002) Genome Biol. , vol.3
    • Bancroft, I.1
  • 34
    • 0037394626 scopus 로고    scopus 로고
    • Genome-wide intraspecific DNA-sequence variations in rice
    • Han B., and Xue Y. Genome-wide intraspecific DNA-sequence variations in rice. Curr. Opin. Plant Biol. 6 (2003) 134-138
    • (2003) Curr. Opin. Plant Biol. , vol.6 , pp. 134-138
    • Han, B.1    Xue, Y.2
  • 36
    • 33645938294 scopus 로고    scopus 로고
    • Plant genome organisation and diversity: the year of the junk!
    • Morgante M. Plant genome organisation and diversity: the year of the junk!. Curr. Opin. Biotechnol. 17 (2006) 168-173
    • (2006) Curr. Opin. Biotechnol. , vol.17 , pp. 168-173
    • Morgante, M.1
  • 37
    • 34249819663 scopus 로고    scopus 로고
    • F-box proteins in rice: genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress
    • Jain M., Nijhawan A., Arora R., Agarwal P., Ray S., Sharma P., Kapoor S., Tyagi A.K., and Khurana J.P. F-box proteins in rice: genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol. 143 (2007) 1467-1483
    • (2007) Plant Physiol. , vol.143 , pp. 1467-1483
    • Jain, M.1    Nijhawan, A.2    Arora, R.3    Agarwal, P.4    Ray, S.5    Sharma, P.6    Kapoor, S.7    Tyagi, A.K.8    Khurana, J.P.9
  • 38
    • 34547884302 scopus 로고    scopus 로고
    • Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice (Oryza sativa L.)
    • Li M., Xu W., Yang W., Kong Z., and Xue Y. Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice (Oryza sativa L.). Plant Physiol. 144 (2007) 1797-1812
    • (2007) Plant Physiol. , vol.144 , pp. 1797-1812
    • Li, M.1    Xu, W.2    Yang, W.3    Kong, Z.4    Xue, Y.5
  • 39
    • 0000379882 scopus 로고
    • Catalase, peroxidase, and polyphenoloxidase activities during rice leaf senescence
    • Kar M., and Mishra D. Catalase, peroxidase, and polyphenoloxidase activities during rice leaf senescence. Plant Physiol. 57 (1976) 315-319
    • (1976) Plant Physiol. , vol.57 , pp. 315-319
    • Kar, M.1    Mishra, D.2
  • 40
    • 0031239680 scopus 로고    scopus 로고
    • Differential induction of a peroxidase gene family during infection of rice by Xanthomonas oryzae pv. oryzae
    • Chittoor J.M., Leach J.E., and White F.F. Differential induction of a peroxidase gene family during infection of rice by Xanthomonas oryzae pv. oryzae. Mol. Plant-Microb. Interact. 10 (1997) 861-871
    • (1997) Mol. Plant-Microb. Interact. , vol.10 , pp. 861-871
    • Chittoor, J.M.1    Leach, J.E.2    White, F.F.3
  • 42
    • 3242672609 scopus 로고    scopus 로고
    • A probabilistic model of 3′ end formation in Caenorhabditis elegans
    • Hajarnavis A., Korf I., and Durbin R. A probabilistic model of 3′ end formation in Caenorhabditis elegans. Nucleic Acids Res. 32 (2004) 3392-3399
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3392-3399
    • Hajarnavis, A.1    Korf, I.2    Durbin, R.3
  • 43
    • 0031982649 scopus 로고    scopus 로고
    • Martinson, Poly(A)-driven and poly(A)-assisted termination: two different modes of poly(A)-dependent transcription termination
    • Yeung G., Choi L.M., Chao L.C., Park N.J., Liu D., and Jamil A. Martinson, Poly(A)-driven and poly(A)-assisted termination: two different modes of poly(A)-dependent transcription termination. Mol. Cell. Biol. 18 (1998) 276-289
    • (1998) Mol. Cell. Biol. , vol.18 , pp. 276-289
    • Yeung, G.1    Choi, L.M.2    Chao, L.C.3    Park, N.J.4    Liu, D.5    Jamil, A.6
  • 44
    • 0142211310 scopus 로고    scopus 로고
    • Poly(A)-dependent transcription termination: continued communication of the poly(A) signal with the polymerase is required long after extrusion in vivo
    • Kim S.J., and Martinson H.G. Poly(A)-dependent transcription termination: continued communication of the poly(A) signal with the polymerase is required long after extrusion in vivo. J. Biol. Chem. 278 (2003) 41691-41701
    • (2003) J. Biol. Chem. , vol.278 , pp. 41691-41701
    • Kim, S.J.1    Martinson, H.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.