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Volumn 8, Issue , 2007, Pages

Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; ZINC FINGER PROTEIN; PROTEIN;

EID: 38049103338     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-371     Document Type: Article
Times cited : (7)

References (31)
  • 1
    • 0036314772 scopus 로고    scopus 로고
    • Studying genomes through the aeons: Protein families, pseudogenes and proteome evolution
    • 10.1016/S0022-2836(02)00109-2 12083509
    • Harrison P Gerstein M Studying genomes through the aeons: Protein families, pseudogenes and proteome evolution J Mol Biol 2002, 318(5):1155-1174. 10.1016/S0022-2836(02)00109-2 12083509
    • (2002) J Mol Biol , vol.318 , Issue.5 , pp. 1155-1174
    • Harrison, P.1    Gerstein, M.2
  • 2
    • 17844396017 scopus 로고    scopus 로고
    • Transcribed processed pseudogenes in the human genome: An intermediate form of expressed retrosequence lacking protein-coding ability
    • 1087782 15860774 10.1093/nar/gki531
    • Harrison PM Zheng D Zhang Z Carriero N Gerstein M Transcribed processed pseudogenes in the human genome: An intermediate form of expressed retrosequence lacking protein-coding ability Nucleic acids research 2005, 33:2374-2383. 1087782 15860774 10.1093/nar/gki531
    • (2005) Nucleic Acids Research , vol.33 , pp. 2374-2383
    • Harrison, P.M.1    Zheng, D.2    Zhang, Z.3    Carriero, N.4    Gerstein, M.5
  • 3
    • 0036180936 scopus 로고    scopus 로고
    • Molecular fossils in the human genome: Identification and analysis of the pseudogenes in chromosomes 21 and 22
    • 155275 11827946 10.1101/gr.207102
    • Harrison PM Hegyi H Balasubramanian S Luscombe NM Bertone P Echols N Johnson T Gerstein M Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22 Genome Res 2002, 12(2):272-280. 155275 11827946 10.1101/gr.207102
    • (2002) Genome Res , vol.12 , pp. 272-280
    • Harrison, P.M.1    Hegyi, H.2    Balasubramanian, S.3    Luscombe, N.M.4    Bertone, P.5    Echols, N.6    Johnson, T.7    Gerstein, M.8
  • 4
    • 0034079713 scopus 로고    scopus 로고
    • Human LINE retrotransposons generate processed pseudogenes
    • 10.1038/74184 10742098
    • Esnault C Maestre J Heidmann T Human LINE retrotransposons generate processed pseudogenes Nature genetics 2000, 24(4):363-367. 10.1038/74184 10742098
    • (2000) Nature Genetics , vol.24 , pp. 363-367
    • Esnault, C.1    Maestre, J.2    Heidmann, T.3
  • 6
    • 35648987151 scopus 로고    scopus 로고
    • Analysis of the role of retrotransposition in gene evolution in vertebrates
    • 10.1186/1471-2105-8-308 17718914 2048973
    • Yu Z Morais D Ivanga M Harrison PM Analysis of the role of retrotransposition in gene evolution in vertebrates BMC Bioinformatics 2007, 8:308. 10.1186/1471-2105-8-308 17718914 2048973
    • (2007) BMC Bioinformatics , vol.8 , pp. 308
    • Yu, Z.1    Morais, D.2    Ivanga, M.3    Harrison, P.M.4
  • 7
    • 0346752110 scopus 로고    scopus 로고
    • Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome
    • 403796 14656962 10.1101/gr.1429003
    • Zhang Z Harrison P Liu Y Gerstein M Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome Genome Res 2003, 13(12):2541-2558. 403796 14656962 10.1101/ gr.1429003
    • (2003) Genome Res , vol.13 , Issue.12 , pp. 2541-2558
    • Zhang, Z.1    Harrison, P.2    Liu, Y.3    Gerstein, M.4
  • 8
    • 0036796620 scopus 로고    scopus 로고
    • Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome
    • 187539 12368239 10.1101/gr.331902
    • Zhang Z Harrison P Gerstein M Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome Genome Res 2002, 12(10):1466-14482. 187539 12368239 10.1101/gr.331902
    • (2002) Genome Res , vol.12 , Issue.10 , pp. 1466-14482
    • Zhang, Z.1    Harrison, P.2    Gerstein, M.3
  • 9
    • 33644777605 scopus 로고    scopus 로고
    • Evolutionary fate of retroposed gene copies in the human genome
    • 1413932 16492757 10.1073/pnas.0511307103
    • Vinckenbosch N Dupanloup I Kaessmann H Evolutionary fate of retroposed gene copies in the human genome Proc Natl Acad Sci USA 2006, 103:3220-3225. 1413932 16492757 10.1073/pnas.0511307103
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 3220-3225
    • Vinckenbosch, N.1    Dupanloup, I.2    Kaessmann, H.3
  • 10
    • 0038617729 scopus 로고    scopus 로고
    • Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss
    • 180 10.1038/ng1159 12730695
    • Modrek B Lee CJ Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss Nat Genet 2003, 34(2):177-180. 10.1038/ng1159 12730695
    • (2003) Nat Genet , vol.34 , pp. 177-180
    • Modrek, B.1    Lee, C.J.2
  • 11
    • 0037422575 scopus 로고    scopus 로고
    • Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans
    • 140922 12502788 10.1073/pnas.0136770100
    • Lewis BP Green RE Brenner SE Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans Proc Natl Acad Sci USA 2003, 100:189-192. 140922 12502788 10.1073/ pnas.0136770100
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 189-192
    • Lewis, B.P.1    Green, R.E.2    Brenner, S.E.3
  • 12
    • 0037096758 scopus 로고    scopus 로고
    • Common exon duplication in animals and its role in alternative splicing
    • 10.1093/hmg/11.13.1561 12045209
    • Letunic I Copley RR Bork P Common exon duplication in animals and its role in alternative splicing Hum Mol Genet 2002, 11:1561-1567. 10.1093/ hmg/11.13.1561 12045209
    • (2002) Hum Mol Genet , vol.11 , pp. 1561-1567
    • Letunic, I.1    Copley, R.R.2    Bork, P.3
  • 13
    • 32044464524 scopus 로고    scopus 로고
    • A genome-wide study of dual coding regions in human alternatively spliced genes
    • 1361714 16365380 10.1101/gr.4246506
    • Liang H Landweber L A genome-wide study of dual coding regions in human alternatively spliced genes Genome Res 2006, 16:190-196. 1361714 16365380 10.1101/gr.4246506
    • (2006) Genome Res , vol.16 , pp. 190-196
    • Liang, H.1    Landweber, L.2
  • 14
    • 22144499539 scopus 로고    scopus 로고
    • Functional divergence of proteins through frameshift mutations
    • 10.1016/j.tig.2005.05.013 15951050
    • Raes J Van de Peer Y Functional divergence of proteins through frameshift mutations Trends Genet 2005, 21:428-431. 10.1016/ j.tig.2005.05.013 15951050
    • (2005) Trends Genet , vol.21 , pp. 428-431
    • Raes, J.1    Van de Peer, Y.2
  • 15
    • 33750962721 scopus 로고    scopus 로고
    • Frequent appearance of novel protein-coding sequences by frameshift translation
    • 10.1016/j.ygeno.2006.06.009 16890400
    • Okamura K Feuk L Marques-Bonet T Navarro A Scherer SW Frequent appearance of novel protein-coding sequences by frameshift translation Genomics 2006, 88:690-697. 10.1016/j.ygeno.2006.06.009 16890400
    • (2006) Genomics , vol.88 , pp. 690-697
    • Okamura, K.1    Feuk, L.2    Marques-Bonet, T.3    Navarro, A.4    Scherer, S.W.5
  • 17
    • 0036064148 scopus 로고    scopus 로고
    • Alu-containing exons are alternatively spliced
    • 186627 12097342 10.1101/gr.229302
    • Sorek R Ast G Graur D Alu-containing exons are alternatively spliced Genome Res 2002, 12:1060-1070. 186627 12097342 10.1101/gr.229302
    • (2002) Genome Res , vol.12 , pp. 1060-1070
    • Sorek, R.1    Ast, G.2    Graur, D.3
  • 18
    • 0742323558 scopus 로고    scopus 로고
    • Nonsense-mediated mRNA decay: Splicing, translation and mRNP dynamics
    • 10.1038/nrm1310 15040442
    • Maquat LE Nonsense-mediated mRNA decay: Splicing, translation and mRNP dynamics Nat Rev Mol Cell Biol 2004, 5:89-99. 10.1038/nrm1310 15040442
    • (2004) Nat Rev Mol Cell Biol , vol.5 , pp. 89-99
    • Maquat, L.E.1
  • 19
    • 32944474841 scopus 로고    scopus 로고
    • Ebs1p, a negative regulator of gene expression controlled by the Upf proteins in the yeast Saccharomyces cerevisiae
    • 1405902 16467471 10.1128/EC.5.2.301-312.2006
    • Ford AS Guan Q Neeno-Eckwall E Culbertson MR Ebs1p, a negative regulator of gene expression controlled by the Upf proteins in the yeast Saccharomyces cerevisiae Eukaryot Cell 2006, 5:301-312. 1405902 16467471 10.1128/EC.5.2.301-312.2006
    • (2006) Eukaryot Cell , vol.5 , pp. 301-312
    • Ford, A.S.1    Guan, Q.2    Neeno-Eckwall, E.3    Culbertson, M.R.4
  • 20
    • 12144285746 scopus 로고    scopus 로고
    • Molecular mechanism for distinct neurological phenotypes conveyed by allelic truncating mutations
    • 10.1038/ng1322 15004559
    • Inoue K Khajavi M Ohyama T Hirabayashi S Wilson J Reggin JD Mancias P Butler IJ Wilkinson MF Wegner M Lupski JR Molecular mechanism for distinct neurological phenotypes conveyed by allelic truncating mutations Nat Genet 2004, 36:361-369. 10.1038/ng1322 15004559
    • (2004) Nat Genet , vol.36 , pp. 361-369
    • Inoue, K.1    Lupski, J.R.2
  • 21
    • 0033568856 scopus 로고    scopus 로고
    • Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene
    • 10479675
    • Korneev SA Park JH O'Shea M Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene J Neurosci 1999, 19(18):7711-7720. 10479675
    • (1999) J Neurosci , vol.19 , Issue.18 , pp. 7711-7720
    • Korneev, S.A.1    Park, J.H.2    O'Shea, M.3
  • 22
    • 33846635882 scopus 로고    scopus 로고
    • High-throughput identification of catalytic redox-active cysteine residues
    • 10.1126/science.1133114 17234949
    • Fomenko DE Xing W Adair BM Thomas DJ Gladyshev VN High-throughput identification of catalytic redox-active cysteine residues Science 2007, 315:387-389. 10.1126/science.1133114 17234949
    • (2007) Science , vol.315 , pp. 387-389
    • Fomenko, D.E.1    Xing, W.2    Adair, B.M.3    Thomas, D.J.4    Gladyshev, V.N.5
  • 23
    • 33745134398 scopus 로고    scopus 로고
    • Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes
    • 1457049 16606703 10.1101/gr.4843906
    • Hamilton AT Huntley S Tran-Gyamfi M Baggott DM Gordon L Stubbs L Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes Genome Res 2006, 16:584-594. 1457049 16606703 10.1101/gr.4843906
    • (2006) Genome Res , vol.16 , pp. 584-594
    • Hamilton, A.T.1    Huntley, S.2    Tran-Gyamfi, M.3    Baggott, D.M.4    Gordon, L.5    Stubbs, L.6
  • 24
    • 34047207053 scopus 로고    scopus 로고
    • Position of the final intron in full-length transcripts: Determined by NMD?
    • 10.1093/molbev/msm010 17244600
    • Scofield DG Hong X Lynch M Position of the final intron in full-length transcripts: Determined by NMD? Mol Biol Evol 2007, 24:896-899. 10.1093/ molbev/msm010 17244600
    • (2007) Mol Biol Evol , vol.24 , pp. 896-899
    • Scofield, D.G.1    Hong, X.2    Lynch, M.3
  • 26
    • 34247330971 scopus 로고    scopus 로고
    • Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
    • e-pub
    • Lareau LF Inada M Green RE Wengrod JC Brenner SE Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements Nature 2007 e-pub
    • (2007) Nature
    • Lareau, L.F.1    Inada, M.2    Green, R.E.3    Wengrod, J.C.4    Brenner, S.E.5
  • 28
    • 6944256813 scopus 로고    scopus 로고
    • Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise
    • 10.1038/ng1429 15448691
    • Mendell JT Sharif NA Meyers J Martinez F Dietz HC Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise Nat Genet 2004, 36:1073-1078. 10.1038/ng1429 15448691
    • (2004) Nat Genet , vol.36 , pp. 1073-1078
    • Mendell, J.T.1    Sharif, N.A.2    Meyers, J.3    Martinez, F.4    Dietz, H.C.5
  • 29
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • 146917 9254694 10.1093/nar/25.17.3389
    • Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic acids research 1997, 25(17):3389-3402. 146917 9254694 10.1093/nar/25.17.3389
    • (1997) Nucleic Acids Research , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 30
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • 8743706
    • Wootton JC Federhen S Analysis of compositionally biased regions in sequence databases Methods Enzymol 1996, 266:554-571. 8743706
    • (1996) Methods Enzymol , vol.266 , pp. 554-571
    • Wootton, J.C.1    Federhen, S.2
  • 31
    • 0033990061 scopus 로고    scopus 로고
    • Flexible sequence similarity searching with the FASTA3 program package
    • 10547837
    • Pearson WR Flexible sequence similarity searching with the FASTA3 program package Methods Mol Biol 2000, 132:185-219. 10547837
    • (2000) Methods Mol Biol , vol.132 , pp. 185-219
    • Pearson, W.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.