Literature DB >> 1511130

Information contents and dinucleotide compositions of plant intron sequences vary with evolutionary origin.

O White1, C Soderlund, P Shanmugan, C Fields.   

Abstract

The DNA sequence composition of 526 dicot and 345 monocot intron sequences have been characterized using computational methods. Splice site information content and bulk intron and exon dinucleotide composition were determined. Positions 4 and 5 of 5' splice sites contain different statistically significant levels of information in the two groups. Basal levels of information in introns are higher in dicots than in monocots. Two dinucleotide groups, WW (AA, AU, UA, UU) and SS (CC, CG, GC, GG) have significantly different frequencies in exons and introns of the two plant groups. These results suggest that the mechanisms of splice-site recognition and binding may differ between dicot and monocot plants.

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Year:  1992        PMID: 1511130     DOI: 10.1007/bf00040537

Source DB:  PubMed          Journal:  Plant Mol Biol        ISSN: 0167-4412            Impact factor:   4.076


  30 in total

1.  Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid.

Authors:  J JOSSE; A D KAISER; A KORNBERG
Journal:  J Biol Chem       Date:  1961-03       Impact factor: 5.157

2.  Splicing signals in Drosophila: intron size, information content, and consensus sequences.

Authors:  S M Mount; C Burks; G Hertz; G D Stormo; O White; C Fields
Journal:  Nucleic Acids Res       Date:  1992-08-25       Impact factor: 16.971

3.  Effect of 5' splice site mutations on splicing of the preceding intron.

Authors:  M Talerico; S M Berget
Journal:  Mol Cell Biol       Date:  1990-12       Impact factor: 4.272

4.  gm: a practical tool for automating DNA sequence analysis.

Authors:  C A Fields; C A Soderlund
Journal:  Comput Appl Biosci       Date:  1990-07

5.  In vivo analysis of plant pre-mRNA splicing using an autonomously replicating vector.

Authors:  A J McCullough; H Lou; M A Schuler
Journal:  Nucleic Acids Res       Date:  1991-06-11       Impact factor: 16.971

6.  Information content of binding sites on nucleotide sequences.

Authors:  T D Schneider; G D Stormo; L Gold; A Ehrenfeucht
Journal:  J Mol Biol       Date:  1986-04-05       Impact factor: 5.469

7.  Splicing of messenger RNA precursors.

Authors:  P A Sharp
Journal:  Science       Date:  1987-02-13       Impact factor: 47.728

8.  Doublet frequencies in evolutionary distinct groups.

Authors:  R Nussinov
Journal:  Nucleic Acids Res       Date:  1984-02-10       Impact factor: 16.971

9.  High mobility group chromosomal proteins bind to AT-rich tracts flanking plant genes.

Authors:  T J Pedersen; L J Arwood; S Spiker; M J Guiltinan; W F Thompson
Journal:  Plant Mol Biol       Date:  1991-01       Impact factor: 4.076

10.  Universal rule for coding sequence construction: TA/CG deficiency-TG/CT excess.

Authors:  S Ohno
Journal:  Proc Natl Acad Sci U S A       Date:  1988-12       Impact factor: 11.205

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  18 in total

Review 1.  Through a genome, darkly: comparative analysis of plant chromosomal DNA.

Authors:  Graham J King
Journal:  Plant Mol Biol       Date:  2002-01       Impact factor: 4.076

2.  A low-copy-number Sorghum DNA sequence that detects hypervariable EcoRV fragments.

Authors:  Y X Cui; G W Xu; C W Magill; K F Schertz; G E Hart
Journal:  Theor Appl Genet       Date:  1994-09       Impact factor: 5.699

3.  Viroids proper can be distinguished from hammerhead viroids and satellite RNAs through their dinucleotide composition.

Authors:  F U Gast; R L Spieker
Journal:  Arch Virol       Date:  1996       Impact factor: 2.574

Review 4.  Splicing of precursors to mRNA in higher plants: mechanism, regulation and sub-nuclear organisation of the spliceosomal machinery.

Authors:  G G Simpson; W Filipowicz
Journal:  Plant Mol Biol       Date:  1996-10       Impact factor: 4.076

5.  Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences.

Authors:  J Kleffe; K Hermann; W Vahrson; B Wittig; V Brendel
Journal:  Nucleic Acids Res       Date:  1996-12-01       Impact factor: 16.971

6.  U-richness is a defining feature of plant introns and may function as an intron recognition signal in maize.

Authors:  C H Ko; V Brendel; R D Taylor; V Walbot
Journal:  Plant Mol Biol       Date:  1998-03       Impact factor: 4.076

7.  Analysis of donor splice sites in different eukaryotic organisms.

Authors:  I B Rogozin; L Milanesi
Journal:  J Mol Evol       Date:  1997-07       Impact factor: 2.395

8.  In vivo analysis of intron processing using splicing-dependent reporter gene assays.

Authors:  J C Carle-Urioste; C H Ko; M I Benito; V Walbot
Journal:  Plant Mol Biol       Date:  1994-12       Impact factor: 4.076

9.  Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information.

Authors:  S M Hebsgaard; P G Korning; N Tolstrup; J Engelbrecht; P Rouzé; S Brunak
Journal:  Nucleic Acids Res       Date:  1996-09-01       Impact factor: 16.971

10.  RPE, a plant gene involved in early developmental steps of nematode feeding cells.

Authors:  B Favery; P Lecomte; N Gil; N Bechtold; D Bouchez; A Dalmasso; P Abad
Journal:  EMBO J       Date:  1998-12-01       Impact factor: 11.598

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