메뉴 건너뛰기




Volumn 69, Issue 1-2, 2009, Pages 179-194

Insights into corn genes derived from large-scale cDNA sequencing

Author keywords

Alternative splicing; Corn genome; Full length cDNA; GC content; Gene prediction; Promoters

Indexed keywords

COMPLEMENTARY DNA; PRIMER DNA;

EID: 56949106781     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-008-9415-4     Document Type: Article
Times cited : (200)

References (41)
  • 1
    • 32044434957 scopus 로고    scopus 로고
    • Features of Arabidopsis genes and genome discovered using full-length cDNAs
    • 1. 10.1007/s11103-005-2564-9
    • NN Alexandrov ME Troukhan 2006 Features of Arabidopsis genes and genome discovered using full-length cDNAs Plant Mol Biol 60 1 69 85 10.1007/s11103-005-2564-9
    • (2006) Plant Mol Biol , vol.60 , pp. 69-85
    • Alexandrov, N.N.1    Troukhan, M.E.2
  • 2
    • 0030462462 scopus 로고    scopus 로고
    • Transcription-induced mutations: Increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli
    • 24. 10.1073/pnas.93.24.13919
    • A Beletskii AS Bhagwat 1996 Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli Proc Natl Acad Sci USA 93 24 13919 13924 10.1073/pnas.93.24. 13919
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13919-13924
    • Beletskii, A.1    Bhagwat, A.S.2
  • 3
    • 3042672020 scopus 로고    scopus 로고
    • Functional annotation of the Arabidopsis genome using controlled vocabularies
    • 2. 10.1104/pp.104.040071
    • TZ Berardini S Mundodi 2004 Functional annotation of the Arabidopsis genome using controlled vocabularies Plant Physiol 135 2 745 755 10.1104/pp.104.040071
    • (2004) Plant Physiol , vol.135 , pp. 745-755
    • Berardini, T.Z.1    Mundodi, S.2
  • 4
    • 0036320958 scopus 로고    scopus 로고
    • Interactions between Myxobacteria, plant pathogenic fungi, and biocontrol agents
    • 10.1094/PDIS.2002.86.8.889
    • CT Bull KG Shetty KV Subbarao 2002 Interactions between Myxobacteria, plant pathogenic fungi, and biocontrol agents Plant Dis 86 889 896 10.1094/PDIS.2002.86.8.889
    • (2002) Plant Dis , vol.86 , pp. 889-896
    • Bull, C.T.1    Shetty, K.G.2    Subbarao, K.V.3
  • 5
    • 0002232531 scopus 로고
    • Codon usage in higher plants, green algae, and cyanobacteria
    • 1
    • WH Campbell G Gowri 1990 Codon usage in higher plants, green algae, and cyanobacteria Plant Physiol 92 1 1 11
    • (1990) Plant Physiol , vol.92 , pp. 1-11
    • Campbell, W.H.1    Gowri, G.2
  • 6
    • 0037673675 scopus 로고    scopus 로고
    • Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia
    • doi: 10.1101/gr.1119703
    • Carninci P, Waki K et al (2003) Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res 13(6B):1273-1289. doi: 10.1101/gr.1119703
    • (2003) Genome Res , vol.13 , Issue.6 B , pp. 1273-1289
    • Carninci, P.1    Waki, K.2
  • 7
    • 0035430578 scopus 로고    scopus 로고
    • Plant evolution and development in a post-genomic context
    • 8. 10.1038/35084556
    • QC Cronk 2001 Plant evolution and development in a post-genomic context Nat Rev Genet 2 8 607 619 10.1038/35084556
    • (2001) Nat Rev Genet , vol.2 , pp. 607-619
    • Cronk, Q.C.1
  • 8
    • 2142738304 scopus 로고    scopus 로고
    • WebLogo: A sequence logo generator
    • 6. 10.1101/gr.849004
    • GE Crooks G Hon 2004 WebLogo: a sequence logo generator Genome Res 14 6 1188 1190 10.1101/gr.849004
    • (2004) Genome Res , vol.14 , pp. 1188-1190
    • Crooks, G.E.1    Hon, G.2
  • 9
    • 0034084035 scopus 로고    scopus 로고
    • Analysis of expressed sequence tags indicates 35, 000 human genes
    • 2. 10.1038/76115
    • B Ewing P Green 2000 Analysis of expressed sequence tags indicates 35, 000 human genes Nat Genet 25 2 232 234 10.1038/76115
    • (2000) Nat Genet , vol.25 , pp. 232-234
    • Ewing, B.1    Green, P.2
  • 10
    • 38549146894 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Finn RD, Tate J et al (2007) The Pfam protein families database. Nucleic Acids Res 36(Database issue):D281-288
    • (2007) Nucleic Acids Res , vol.36 , Issue.DATABASE ISSUE
    • Finn, R.D.1    Tate, J.2
  • 11
    • 25444443669 scopus 로고    scopus 로고
    • GC-compositional strand bias around transcription start sites in plants and fungi
    • 1. 10.1186/1471-2164-6-26
    • S Fujimori T Washio 2005 GC-compositional strand bias around transcription start sites in plants and fungi BMC Genomics 6 1 26 10.1186/1471-2164-6-26
    • (2005) BMC Genomics , vol.6 , pp. 26
    • Fujimori, S.1    Washio, T.2
  • 12
    • 0022358896 scopus 로고
    • Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli
    • 1. 10.1016/0022-2836(85)90262-1
    • DJ Galas M Eggert 1985 Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli J Mol Biol 186 1 117 128 10.1016/0022-2836(85)90262-1
    • (1985) J Mol Biol , vol.186 , pp. 117-128
    • Galas, D.J.1    Eggert, M.2
  • 14
    • 0029962302 scopus 로고    scopus 로고
    • The first intron of the Arabidopsis thaliana gene coding for elongation factor 1 beta contains an enhancer-like element
    • 2. 10.1016/0378-1119(95)00837-3
    • M Gidekel B Jimenez 1996 The first intron of the Arabidopsis thaliana gene coding for elongation factor 1 beta contains an enhancer-like element Gene 170 2 201 206 10.1016/0378-1119(95)00837-3
    • (1996) Gene , vol.170 , pp. 201-206
    • Gidekel, M.1    Jimenez, B.2
  • 15
    • 56949107274 scopus 로고    scopus 로고
    • Gish W (1996-2004) http://blast.wustl.edu
    • (1996)
    • Gish, W.1
  • 16
    • 13444252847 scopus 로고    scopus 로고
    • Rfam: Annotating non-coding RNAs in complete genomes
    • doi: 10.1093/nar/gki081
    • Griffiths-Jones S, Moxon S et al (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33(Database issue):D121-D124. doi: 10.1093/nar/gki081
    • (2005) Nucleic Acids Res , vol.33 , Issue.DATABASE ISSUE
    • Griffiths-Jones, S.1    Moxon, S.2
  • 17
    • 0032524384 scopus 로고    scopus 로고
    • Analyzing genomes with cumulative skew diagrams
    • 10. 10.1093/nar/26.10.2286
    • A Grigoriev 1998 Analyzing genomes with cumulative skew diagrams Nucleic Acids Res 26 10 2286 2290 10.1093/nar/26.10.2286
    • (1998) Nucleic Acids Res , vol.26 , pp. 2286-2290
    • Grigoriev, A.1
  • 18
    • 33344470688 scopus 로고    scopus 로고
    • Structure and architecture of the maize genome
    • 4. 10.1104/pp.105.068718
    • G Haberer S Young 2005 Structure and architecture of the maize genome Plant Physiol 139 4 1612 1624 10.1104/pp.105.068718
    • (2005) Plant Physiol , vol.139 , pp. 1612-1624
    • Haberer, G.1    Young, S.2
  • 19
    • 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
    • 4. 10.1104/pp.106.091900
    • M Jain A Nijhawan 2007 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 4 1467 1483 10.1104/pp.106.091900
    • (2007) Plant Physiol , vol.143 , pp. 1467-1483
    • Jain, M.1    Nijhawan, A.2
  • 20
    • 33751021416 scopus 로고    scopus 로고
    • Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings
    • 5
    • J Jia J Fu 2006 Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings Plant J 48 5 710 727
    • (2006) Plant J , vol.48 , pp. 710-727
    • Jia, J.1    Fu, J.2
  • 21
    • 0024844260 scopus 로고
    • Insertion sequence IS10 anti-sense pairing initiates by an interaction between the 5′ end of the target RNA and a loop in the anti-sense RNA
    • 3. 10.1016/0022-2836(89)90132-0
    • JD Kittle RW Simons 1989 Insertion sequence IS10 anti-sense pairing initiates by an interaction between the 5′ end of the target RNA and a loop in the anti-sense RNA J Mol Biol 210 3 561 572 10.1016/0022-2836(89)90132-0
    • (1989) J Mol Biol , vol.210 , pp. 561-572
    • Kittle, J.D.1    Simons, R.W.2
  • 22
    • 0040289054 scopus 로고    scopus 로고
    • Statistical analysis of the exon-intron structure of higher eukaryote genes
    • 4
    • EV Kriventseva V Makeev 1999 Statistical analysis of the exon-intron structure of higher eukaryote genes Biofizika 44 4 595 600
    • (1999) Biofizika , vol.44 , pp. 595-600
    • Kriventseva, E.V.1    Makeev, V.2
  • 23
    • 5144219921 scopus 로고    scopus 로고
    • Characterization of the maize endosperm transcriptome and its comparison to the rice genome
    • doi: 10.1101/gr.2780504
    • Lai J, Dey N et al (2004) Characterization of the maize endosperm transcriptome and its comparison to the rice genome. Genome Res 14(10A):1932-1937. doi: 10.1101/gr.2780504
    • (2004) Genome Res , vol.14 , Issue.10 A , pp. 1932-1937
    • Lai, J.1    Dey, N.2
  • 24
    • 35348896591 scopus 로고    scopus 로고
    • The Chlamydomonas genome reveals the evolution of key animal and plant functions
    • 5848. 10.1126/science.1143609
    • SS Merchant SE Prochnik 2007 The Chlamydomonas genome reveals the evolution of key animal and plant functions Science 318 5848 245 250 10.1126/science.1143609
    • (2007) Science , vol.318 , pp. 245-250
    • Merchant, S.S.1    Prochnik, S.E.2
  • 26
    • 33846101405 scopus 로고    scopus 로고
    • The TIGR Rice Genome Annotation Resource: Improvements and new features
    • doi: 10.1093/nar/gkl976
    • Ouyang S, Zhu W et al (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35(Database issue):D883-D887. doi: 10.1093/nar/gkl976
    • (2007) Nucleic Acids Res , vol.35 , Issue.DATABASE ISSUE
    • Ouyang, S.1    Zhu, W.2
  • 27
    • 0033573925 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution in Drosophila and mammalian genomes
    • 4. 10.1073/pnas.96.4.1475
    • DA Petrov DL Hartl 1999 Patterns of nucleotide substitution in Drosophila and mammalian genomes Proc Natl Acad Sci USA 96 4 1475 1479 10.1073/pnas.96.4.1475
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 1475-1479
    • Petrov, D.A.1    Hartl, D.L.2
  • 28
    • 0030012861 scopus 로고    scopus 로고
    • An essential domain in Saccharomyces cerevisiae U14 snoRNA is absent in vertebrates, but conserved in other yeasts
    • 11. 10.1093/nar/24.11.2059
    • DA Samarsky GS Schneider 1996 An essential domain in Saccharomyces cerevisiae U14 snoRNA is absent in vertebrates, but conserved in other yeasts Nucleic Acids Res 24 11 2059 2066 10.1093/nar/24.11.2059
    • (1996) Nucleic Acids Res , vol.24 , pp. 2059-2066
    • Samarsky, D.A.1    Schneider, G.S.2
  • 29
    • 33745638358 scopus 로고    scopus 로고
    • Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction
    • doi: 10.1371/journal.pgen.0010013
    • Seoighe C, Gehring C et al (2005) Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction. PLoS Genet 1(2):e13. doi: 10.1371/journal.pgen.0010013
    • (2005) PLoS Genet , vol.1 , Issue.2
    • Seoighe, C.1    Gehring, C.2
  • 30
    • 0028049832 scopus 로고
    • Construction and characterization of a normalized cDNA library
    • 20. 10.1073/pnas.91.20.9228
    • MB Soares MF Bonaldo 1994 Construction and characterization of a normalized cDNA library Proc Natl Acad Sci USA 91 20 9228 9232 10.1073/pnas.91.20.9228
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 9228-9232
    • Soares, M.B.1    Bonaldo, M.F.2
  • 31
    • 0026092757 scopus 로고
    • Transposon-facilitated DNA sequencing
    • 4. 10.1073/pnas.88.4.1247
    • M Strathmann BA Hamilton 1991 Transposon-facilitated DNA sequencing Proc Natl Acad Sci USA 88 4 1247 1250 10.1073/pnas.88.4.1247
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 1247-1250
    • Strathmann, M.1    Hamilton, B.A.2
  • 32
    • 38549144806 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): Gene structure and function annotation
    • Swarbreck D, Wilks C et al (2007). The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36(Database issue):D1009-1014
    • (2007) Nucleic Acids Res , vol.36 , Issue.DATABASE ISSUE
    • Swarbreck, D.1    Wilks, C.2
  • 33
    • 4944234699 scopus 로고    scopus 로고
    • Skew in CG content near the transcription start site in Arabidopsis thaliana
    • doi: 10.1093/bioinformatics/btg1043
    • Tatarinova T, Brover V et al (2003) Skew in CG content near the transcription start site in Arabidopsis thaliana. Bioinformatics 19(Suppl 1):i313-i314. doi: 10.1093/bioinformatics/btg1043
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Tatarinova, T.1    Brover, V.2
  • 34
    • 33745583768 scopus 로고    scopus 로고
    • A genetic signature of interspecies variations in gene expression
    • 7. 10.1038/ng1819
    • I Tirosh A Weinberger 2006 A genetic signature of interspecies variations in gene expression Nat Genet 38 7 830 834 10.1038/ng1819
    • (2006) Nat Genet , vol.38 , pp. 830-834
    • Tirosh, I.1    Weinberger, A.2
  • 35
    • 33847305025 scopus 로고    scopus 로고
    • Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage
    • 5. 10.1007/s11103-006-9112-0
    • H Walia C Wilson 2007 Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage Plant Mol Biol 63 5 609 623 10.1007/s11103-006-9112-0
    • (2007) Plant Mol Biol , vol.63 , pp. 609-623
    • Walia, H.1    Wilson, C.2
  • 36
    • 33646484347 scopus 로고    scopus 로고
    • Genomewide comparative analysis of alternative splicing in plants
    • 18. 10.1073/pnas.0602039103
    • BB Wang V Brendel 2006 Genomewide comparative analysis of alternative splicing in plants Proc Natl Acad Sci USA 103 18 7175 7180 10.1073/pnas. 0602039103
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 7175-7180
    • Wang, B.B.1    Brendel, V.2
  • 37
    • 34248184632 scopus 로고    scopus 로고
    • Rapid divergence of codon usage patterns within the rice genome
    • doi: 10.1186/1471-2148-7-S1-S6
    • Wang HC, Hickey DA (2007) Rapid divergence of codon usage patterns within the rice genome. BMC Evol Biol 7(Suppl 1):S6. doi: 10.1186/1471-2148-7-S1-S6
    • (2007) BMC Evol Biol , vol.7 , Issue.SUPPL. 1
    • Wang, H.C.1    Hickey, D.A.2
  • 38
    • 1242284665 scopus 로고    scopus 로고
    • Mutational bias affects protein evolution in flowering plants
    • 1. 10.1093/molbev/msh003
    • HC Wang GA Singer 2004 Mutational bias affects protein evolution in flowering plants Mol Biol Evol 21 1 90 96 10.1093/molbev/msh003
    • (2004) Mol Biol Evol , vol.21 , pp. 90-96
    • Wang, H.C.1    Singer, G.A.2
  • 39
    • 56949085476 scopus 로고    scopus 로고
    • Sequence and assembly of the maize B73 genome
    • Washington, D.C.
    • Wilson R (2008) Sequence and assembly of the maize B73 genome. In: 50th Annual Maize Genetics Conference, Washington, D.C.
    • (2008) 50th Annual Maize Genetics Conference
    • Wilson, R.1
  • 40
    • 2342483696 scopus 로고    scopus 로고
    • Simple cDNA normalization using kamchatka crab duplex-specific nuclease
    • doi: 10.1093/nar/gnh031
    • Zhulidov PA, Bogdanova EA et al (2004) Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res 32(3):e37. doi: 10.1093/nar/gnh031
    • (2004) Nucleic Acids Res , vol.32 , Issue.3
    • Zhulidov, P.A.1    Bogdanova, E.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.