메뉴 건너뛰기




Volumn 10, Issue , 2009, Pages

Genomic evidence for non-random endemic populations of decaying exons from mammalian genes

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; AMINO ACID SEQUENCE; ARTICLE; CODON; EXON; GENE CONTROL; GENE DUPLICATION; GENE FUNCTION; GENE STRUCTURE; HUMAN; INTRON; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; PROTEIN BINDING; PROTEIN DOMAIN; PSEUDOGENE; PSEUDOGENIZATION; RAT; ALTERNATIVE RNA SPLICING; ANIMAL; CATTLE; DNA SEQUENCE; GENETICS; GENOMICS; METHODOLOGY;

EID: 68149148966     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-309     Document Type: Article
Times cited : (3)

References (42)
  • 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 PM 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.M.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(8):2374-2383 1087782 15860774 10.1093/nar/gki531
    • (2005) Nucleic Acids Research , vol.33 , Issue.8 , pp. 2374-2383
    • Harrison, P.M.1    Zheng, D.2    Zhang, Z.3    Carriero, N.4    Gerstein, M.5
  • 3
    • 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 PM Liu Y Gerstein M Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome Genome research 2003, 13(12):2541-2558 403796 14656962 10.1101/gr.1429003
    • (2003) Genome Research , vol.13 , Issue.12 , pp. 2541-2558
    • Zhang, Z.1    Harrison, P.M.2    Liu, Y.3    Gerstein, M.4
  • 4
    • 0036430322 scopus 로고    scopus 로고
    • Digging deep for ancient relics: A survey of protein motifs in the intergenic sequences of four eukaryotic genomes
    • 10.1016/S0022-2836(02)01035-5 12417195
    • Zhang ZL Harrison PM Gerstein M Digging deep for ancient relics: A survey of protein motifs in the intergenic sequences of four eukaryotic genomes J Mol Biol 2002, 323(5):811-822 10.1016/S0022-2836(02)01035-5 12417195
    • (2002) J Mol Biol , vol.323 , Issue.5 , pp. 811-822
    • Zhang, Z.L.1    Harrison, P.M.2    Gerstein, M.3
  • 5
    • 0036262336 scopus 로고    scopus 로고
    • SNPs on human chromosomes 21 and 22 - Analysis in terms of protein features and pseudogenes
    • 10.1517/14622416.3.3.393 12052146
    • Balasubramanian S Harrison P Hegyi H Bertone P Luscombe N et al SNPs on human chromosomes 21 and 22 - analysis in terms of protein features and pseudogenes Pharmacogenomics 2002, 3(3):393-402 10.1517/14622416.3.3.393 12052146
    • (2002) Pharmacogenomics , vol.3 , Issue.3 , pp. 393-402
    • Balasubramanian, S.1    Harrison, P.2    Hegyi, H.3    Bertone, P.4    Luscombe, N.5
  • 6
    • 0142247622 scopus 로고    scopus 로고
    • 10.1016/j.jmb.2003.09.016 14583187
    • Harrison PM Carriero N Liu Y Gerstein M A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs J Mol Biol 2003, 333(5):885-892 10.1016/j.jmb.2003.09.016 14583187
    • (2003) J Mol Biol , vol.333 , Issue.5 , pp. 885-892
    • Harrison, P.M.1    Carriero, N.2    Liu, Y.3    Gerstein, M.4
  • 7
    • 34247330971 scopus 로고    scopus 로고
    • Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
    • 10.1038/nature05676 17361132
    • 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, 446(7138):926-929 10.1038/nature05676 17361132
    • (2007) Nature , vol.446 , Issue.7138 , pp. 926-929
    • Lareau, L.F.1    Inada, M.2    Green, R.E.3    Wengrod, J.C.4    Brenner, S.E.5
  • 9
    • 0345306317 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes
    • 203328 12954770 10.1093/nar/gkg745
    • Zhang Z Gerstein M Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes Nucleic acids research 2003, 31(18):5338-5348 203328 12954770 10.1093/nar/gkg745
    • (2003) Nucleic Acids Research , vol.31 , Issue.18 , pp. 5338-5348
    • Zhang, Z.1    Gerstein, M.2
  • 11
    • 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 research 2002, 12(10):1466-1482 187539 12368239 10.1101/gr.331902
    • (2002) Genome Research , vol.12 , Issue.10 , pp. 1466-1482
    • Zhang, Z.1    Harrison, P.2    Gerstein, M.3
  • 12
    • 11144239489 scopus 로고    scopus 로고
    • Comprehensive analysis of pseudogenes in prokaryotes: Widespread gene decay and failure of putative horizontally transferred genes
    • 522871 15345048 10.1186/gb-2004-5-9-r64
    • Liu Y Harrison PM Kunin V Gerstein M Comprehensive analysis of pseudogenes in prokaryotes: Widespread gene decay and failure of putative horizontally transferred genes Genome biology 2004, 5(9):R64 522871 15345048 10.1186/gb-2004-5-9-r64
    • (2004) Genome Biology , vol.5 , Issue.9
    • Liu, Y.1    Harrison, P.M.2    Kunin, V.3    Gerstein, M.4
  • 13
    • 40749101072 scopus 로고    scopus 로고
    • hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions
    • 2266713 18215318 10.1186/1471-2148-8-19
    • Brocchieri L Conway de Macario E Macario AJ hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions BMC evolutionary biology 2008, 8:19 2266713 18215318 10.1186/1471-2148-8-19
    • (2008) BMC Evolutionary Biology , vol.8 , pp. 19
    • Brocchieri, L.1    Conway de Macario, E.2    Macario, A.J.3
  • 14
    • 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 et al Molecular fossils in the human genome: Identification and analysis of the pseudogenes in chromosomes 21 and 22 Genome research 2002, 12(2):272-280 155275 11827946 10.1101/gr.207102
    • (2002) Genome Research , vol.12 , Issue.2 , pp. 272-280
    • Harrison, P.M.1    Hegyi, H.2    Balasubramanian, S.3    Luscombe, N.M.4    Bertone, P.5
  • 15
    • 0036300794 scopus 로고    scopus 로고
    • A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution
    • 10.1006/jmbi.2001.5343 11866506
    • Harrison P Kumar A Lan N Echols N Snyder M et al A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution J Mol Biol 2002, 316(3):409-419 10.1006/ jmbi.2001.5343 11866506
    • (2002) J Mol Biol , vol.316 , Issue.3 , pp. 409-419
    • Harrison, P.1    Kumar, A.2    Lan, N.3    Echols, N.4    Snyder, M.5
  • 16
    • 0037047628 scopus 로고    scopus 로고
    • Recent segmental duplications in the human genome
    • 10.1126/science.1072047 12169732
    • Bailey JA Gu Z Clark RA Reinert K Samonte RV et al Recent segmental duplications in the human genome Science 2002, 297(5583):1003-1007 10.1126/science.1072047 12169732
    • (2002) Science , vol.297 , Issue.5583 , pp. 1003-1007
    • Bailey, J.A.1    Gu, Z.2    Clark, R.A.3    Reinert, K.4    Samonte, R.V.5
  • 17
    • 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 et al 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
  • 18
    • 44349159416 scopus 로고    scopus 로고
    • Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes
    • 10.1038/nature06904 18404147
    • Tam OH Aravin AA Stein P Girard A Murchison EP et al Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes Nature 2008, 453(7194):534-538 10.1038/nature06904 18404147
    • (2008) Nature , vol.453 , Issue.7194 , pp. 534-538
    • Tam, O.H.1    Aravin, A.A.2    Stein, P.3    Girard, A.4    Murchison, E.P.5
  • 19
    • 44349130233 scopus 로고    scopus 로고
    • Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes
    • 10.1038/nature06908 18404146
    • Watanabe T Totoki Y Toyoda A Kaneda M Kuramochi-Miyagawa S et al Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes Nature 2008, 453(7194):539-543 10.1038/nature06908 18404146
    • (2008) Nature , vol.453 , Issue.7194 , pp. 539-543
    • Watanabe, T.1    Totoki, Y.2    Toyoda, A.3    Kaneda, M.4    Kuramochi-Miyagawa, S.5
  • 20
    • 0030983025 scopus 로고    scopus 로고
    • Chemical synthesis, structural modeling, and biological activity of the epidermal growth factor-like domain of human cripto
    • 10.1021/bi961542p 9092813
    • Lohmeyer M Harrison PM Kannan S DeSantis M O'Reilly NJ et al Chemical synthesis, structural modeling, and biological activity of the epidermal growth factor-like domain of human cripto Biochemistry 1997, 36(13):3837-3845 10.1021/bi961542p 9092813
    • (1997) Biochemistry , vol.36 , Issue.13 , pp. 3837-3845
    • Lohmeyer, M.1    Harrison, P.M.2    Kannan, S.3    DeSantis, M.4    O'Reilly, N.J.5
  • 21
    • 0026817136 scopus 로고
    • Stein and Moore Award address. Reconstructing history with amino acid sequences
    • 2142198 1339026
    • Doolittle RF Stein and Moore Award address. Reconstructing history with amino acid sequences Protein Sci 1992, 1(2):191-200 2142198 1339026
    • (1992) Protein Sci , vol.1 , Issue.2 , pp. 191-200
    • Doolittle, R.F.1
  • 22
    • 21444445084 scopus 로고    scopus 로고
    • BABELOMICS: A suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments
    • 1160217 15980512 10.1093/nar/gki456
    • Al-Shahrour F Minguez P Vaquerizas JM Conde L Dopazo J BABELOMICS: A suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments Nucleic acids research 2005, 33:WEb Server W460-464 1160217 15980512 10.1093/nar/gki456
    • (2005) Nucleic Acids Research
    • Al-Shahrour, F.1    Minguez, P.2    Vaquerizas, J.M.3    Conde, L.4    Dopazo, J.5
  • 23
    • 33748596625 scopus 로고    scopus 로고
    • Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons
    • 1569180 16938881 10.1073/pnas.0603042103
    • Zhang XH Chasin LA Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons Proceedings of the National Academy of Sciences of the United States of America 2006, 103(36):13427-13432 1569180 16938881 10.1073/pnas.0603042103
    • (2006) Proceedings of the National Academy of Sciences of the United States of America , vol.103 , Issue.36 , pp. 13427-13432
    • Zhang, X.H.1    Chasin, L.A.2
  • 24
    • 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
    • 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 , Issue.2 , pp. 177-180
    • Modrek, B.1    Lee, C.J.2
  • 27
    • 10744227931 scopus 로고    scopus 로고
    • Mammalian overlapping genes: The comparative perspective
    • 327103 14762064 10.1101/gr.1590904
    • Veeramachaneni V Makalowski W Galdzicki M Sood R Makalowska I Mammalian overlapping genes: The comparative perspective Genome research 2004, 14(2):280-286 327103 14762064 10.1101/gr.1590904
    • (2004) Genome Research , vol.14 , Issue.2 , pp. 280-286
    • Veeramachaneni, V.1    Makalowski, W.2    Galdzicki, M.3    Sood, R.4    Makalowska, I.5
  • 29
    • 24344459435 scopus 로고    scopus 로고
    • The evolutionary fate of MULE-mediated duplications of host gene fragments in rice
    • 1199544 16140995 10.1101/gr.4064205
    • Juretic N Hoen DR Huynh ML Harrison PM Bureau TE The evolutionary fate of MULE-mediated duplications of host gene fragments in rice Genome research 2005, 15(9):1292-1297 1199544 16140995 10.1101/gr.4064205
    • (2005) Genome Research , vol.15 , Issue.9 , pp. 1292-1297
    • Juretic, N.1    Hoen, D.R.2    Huynh, M.L.3    Harrison, P.M.4    Bureau, T.E.5
  • 30
    • 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
  • 31
    • 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 et al 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
  • 32
    • 38049103338 scopus 로고    scopus 로고
    • Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures
    • 2194788 17937804 10.1186/1471-2164-8-371
    • Harrison P Yu Z Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures BMC genomics 2007, 8:371 2194788 17937804 10.1186/1471-2164-8-371
    • (2007) BMC Genomics , vol.8 , pp. 371
    • Harrison, P.1    Yu, Z.2
  • 33
    • 0028186046 scopus 로고
    • Using the FASTA program to search protein and DNA sequence databases
    • 8205202
    • Pearson WR Using the FASTA program to search protein and DNA sequence databases Methods Mol Biol 1994, 24:307-331 8205202
    • (1994) Methods Mol Biol , vol.24 , pp. 307-331
    • Pearson, W.R.1
  • 34
    • 2442713832 scopus 로고    scopus 로고
    • GeneWise and Genomewise
    • 479130 15123596 10.1101/gr.1865504
    • Birney E Clamp M Durbin R GeneWise and Genomewise Genome research 2004, 14(5):988-995 479130 15123596 10.1101/gr.1865504
    • (2004) Genome Research , vol.14 , Issue.5 , pp. 988-995
    • Birney, E.1    Clamp, M.2    Durbin, R.3
  • 35
    • 18144417788 scopus 로고    scopus 로고
    • Integrated pseudogene annotation for human chromosome 22: Evidence for transcription
    • 10.1016/j.jmb.2005.02.072 15876366
    • Zheng D Zhang Z Harrison PM Karro J Carriero N et al Integrated pseudogene annotation for human chromosome 22: Evidence for transcription J Mol Biol 2005, 349(1):27-45 10.1016/j.jmb.2005.02.072 15876366
    • (2005) J Mol Biol , vol.349 , Issue.1 , pp. 27-45
    • Zheng, D.1    Zhang, Z.2    Harrison, P.M.3    Karro, J.4    Carriero, N.5
  • 37
    • 0032964297 scopus 로고    scopus 로고
    • BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences
    • 10.1111/j.1574-6968.1999.tb13575.x 10339815
    • Tatusova TA Madden TL BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences FEMS Microbiol Lett 1999, 174(2):247-250 10.1111/j.1574-6968.1999.tb13575.x 10339815
    • (1999) FEMS Microbiol Lett , vol.174 , Issue.2 , pp. 247-250
    • Tatusova, T.A.1    Madden, T.L.2
  • 38
    • 35648987151 scopus 로고    scopus 로고
    • Analysis of the role of retrotransposition in gene evolution in vertebrates
    • 2048973 17718914 10.1186/1471-2105-8-308
    • Yu Z Morais D Ivanga M Harrison PM Analysis of the role of retrotransposition in gene evolution in vertebrates BMC Bioinformatics 2007, 8:308 2048973 17718914 10.1186/1471-2105-8-308
    • (2007) BMC Bioinformatics , vol.8 , pp. 308
    • Yu, Z.1    Morais, D.2    Ivanga, M.3    Harrison, P.M.4
  • 39
    • 24044522270 scopus 로고    scopus 로고
    • BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis
    • 10.1093/bioinformatics/bti525 16082012
    • Durinck S Moreau Y Kasprzyk A Davis S De Moor B et al BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis Bioinformatics 2005, 21(16):3439-3440 10.1093/ bioinformatics/bti525 16082012
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3439-3440
    • Durinck, S.1    Moreau, Y.2    Kasprzyk, A.3    Davis, S.4    De Moor, B.5
  • 40
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • 9367129
    • Yang Z PAML: A program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 1997, 13(5):555-556 9367129
    • (1997) Comput Appl Biosci , vol.13 , Issue.5 , pp. 555-556
    • Yang, Z.1
  • 41
    • 33747847779 scopus 로고    scopus 로고
    • PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
    • 1538804 16845082 10.1093/nar/gkl315
    • Suyama M Torrents D Bork P PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments Nucleic acids research 2006, 34:WEb Server W609-612 1538804 16845082 10.1093/nar/ gkl315
    • (2006) Nucleic Acids Research
    • Suyama, M.1    Torrents, D.2    Bork, P.3
  • 42
    • 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(13):1561-1567 10.1093/hmg/11.13.1561 12045209
    • (2002) Hum Mol Genet , vol.11 , Issue.13 , pp. 1561-1567
    • Letunic, I.1    Copley, R.R.2    Bork, P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.