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PMID: 8202381 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Fission yeast gene structure and recognition.

Nucleic acids research ·Vol. 22 ·No. 9 ·1994-05-11 ·Pages 1750-9

Zhang MQ, Marr TG

Abstract

A database of 210 Schizosaccharomyces pombe DNA sequences (524,794 bp) was extracted from GenBank (release number 81.0) and examined by a number of methods in order to characterize statistical features of these sequences that might serve as signals or constraints for messenger RNA splicing. The statistical information compiled includes splicing signal (donor, acceptor and branch site) profiles, translational initiation start profile, exon/intron length distributions, ORF distribution, CDS size distribution, codon usage table, and 6-tuple distribution. The information content of the various signals are also presented. A rule-based interactive computer program for finding introns called INTRON.PLOT has been developed and was used to successfully analyze 7 newly sequenced genes.

MeSH Terms
Base Sequence Codon DNA, Fungal Exons Genes, Fungal Information Systems Introns Molecular Sequence Data Open Reading Frames Protein Biosynthesis RNA Splicing RNA, Fungal Schizosaccharomyces/genetics
Chemicals
Codon DNA, Fungal RNA, Fungal
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Zhang M Q
Cold Spring Harbor Laboratory, NY 11724.
Marr T G
References (49)
49 references, click to expand
  1. Spliced segments at the 5' terminus of adenovirus 2 late mRNA.
    Proc Natl Acad Sci U S A. 1977 Aug;74(8):3171-5 PMID: 269380
  2. Consensus patterns in DNA.
    Methods Enzymol. 1990;183:211-21 PMID: 2179676
  3. A catalogue of splice junction sequences.
    Nucleic Acids Res. 1982 Jan 22;10(2):459-72 PMID: 7063411
  4. The U1 small nuclear RNA-protein complex selectively binds a 5' splice site in vitro.
    Cell. 1983 Jun;33(2):509-18 PMID: 6190573
  5. A comparison of yeast ribosomal protein gene DNA sequences.
    Nucleic Acids Res. 1984 Nov 26;12(22):8295-312 PMID: 6390341
  6. Prediction of splice junctions in mRNA sequences.
    Nucleic Acids Res. 1985 Jul 25;13(14):5327-40 PMID: 4022782
  7. K-tuple frequency analysis: from intron/exon discrimination to T-cell epitope mapping.
    Methods Enzymol. 1990;183:237-52 PMID: 1690334
  8. Information content of Caenorhabditis elegans splice site sequences varies with intron length.
    Nucleic Acids Res. 1990 Mar 25;18(6):1509-12 PMID: 2326191
  9. U1 small nuclear RNA from Schizosaccharomyces pombe has unique and conserved features and is encoded by an essential single-copy gene.
    Mol Cell Biol. 1990 Jun;10(6):2874-81 PMID: 2188102
  10. gm: a practical tool for automating DNA sequence analysis.
    Comput Appl Biosci. 1990 Jul;6(3):263-70 PMID: 2242161
  11. Quantification analysis of 5'-splice signal sequences in mRNA precursors. Mutations in 5'-splice signal sequence of human beta-globin gene and beta-thalassemia.
    J Theor Biol. 1990 Aug 23;145(4):523-33 PMID: 2246900
  12. Structural features in eukaryotic mRNAs that modulate the initiation of translation.
    J Biol Chem. 1991 Oct 25;266(30):19867-70 PMID: 1939050
  13. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach.
    Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11261-5 PMID: 1763041
  14. Synonymous codon usage in Saccharomyces cerevisiae.
    Yeast. 1991 Oct;7(7):657-78 PMID: 1776357
  15. U5 snRNA interacts with exon sequences at 5' and 3' splice sites.
    Cell. 1992 Feb 21;68(4):743-54 PMID: 1739979
  16. Invariant exon skipping in the human alpha-galactosidase A pre-mRNA: Ag+1 to t substitution in a 5'-splice site causing Fabry disease.
    Genomics. 1992 Apr;12(4):643-50 PMID: 1315304
  17. Architectural features of pre-mRNA introns in the fission yeast Schizosaccharomyces pombe.
    Yeast. 1992 Mar;8(3):171-82 PMID: 1574925
  18. Recent evidence for evolution of the genetic code.
    Microbiol Rev. 1992 Mar;56(1):229-64 PMID: 1579111
  19. Mutations at the 3' splice site can be suppressed by compensatory base changes in U1 snRNA in fission yeast.
    Cell. 1992 Jun 26;69(7):1159-69 PMID: 1617727
  20. Prediction of gene structure.
    J Mol Biol. 1992 Jul 5;226(1):141-57 PMID: 1619647
  21. The prediction of exons through an analysis of spliceable open reading frames.
    Nucleic Acids Res. 1992 Jul 11;20(13):3453-62 PMID: 1321415
  22. Splicing takes a holliday.
    Science. 1992 Aug 14;257(5072):888-9 PMID: 1386941
  23. Splicing signals in Drosophila: intron size, information content, and consensus sequences.
    Nucleic Acids Res. 1992 Aug 25;20(16):4255-62 PMID: 1508718
  24. The genetics of nuclear pre-mRNA splicing: a complex story.
    Antonie Van Leeuwenhoek. 1992 Aug;62(1-2):35-46 PMID: 1444335
  25. Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli.
    J Mol Biol. 1985 Nov 5;186(1):117-28 PMID: 3908689
  26. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes.
    Cell. 1986 Jan 31;44(2):283-92 PMID: 3943125
  27. Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications.
    Proc Natl Acad Sci U S A. 1986 Apr;83(7):2133-7 PMID: 3457379
  28. Schizosaccharomyces pombe and Saccharomyces cerevisiae: a look at yeasts divided.
    Cell. 1986 Jun 20;45(6):781-2 PMID: 3518949
  29. Information content of binding sites on nucleotide sequences.
    J Mol Biol. 1986 Apr 5;188(3):415-31 PMID: 3525846
  30. Assessment of protein coding measures.
    Nucleic Acids Res. 1992 Dec 25;20(24):6441-50 PMID: 1480466
  31. mRNA splicing and autocatalytic introns: distant cousins or the products of chemical determinism?
    Cell. 1993 Jan 29;72(2):161-4 PMID: 8425215
  32. Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks.
    Nucleic Acids Res. 1993 Feb 11;21(3):607-13 PMID: 8441672
  33. A 13 kb resolution cosmid map of the 14 Mb fission yeast genome by nonrandom sequence-tagged site mapping.
    Cell. 1993 Apr 9;73(1):121-32 PMID: 8462095
  34. Scanning and competition between AGs are involved in 3' splice site selection in mammalian introns.
    Mol Cell Biol. 1993 Aug;13(8):4939-52 PMID: 8336728
  35. Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing.
    Nature. 1993 Sep 23;365(6444):364-8 PMID: 8397340
  36. A weight array method for splicing signal analysis.
    Comput Appl Biosci. 1993 Oct;9(5):499-509 PMID: 8293321
  37. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes.
    Nucleic Acids Res. 1986 Jul 11;14(13):5125-43 PMID: 3526280
  38. Splicing of messenger RNA precursors.
    Annu Rev Biochem. 1986;55:1119-50 PMID: 2943217
  39. Accurate in vitro splicing of two pre-mRNA plant introns in a HeLa cell nuclear extract.
    EMBO J. 1986 Nov;5(11):2749-58 PMID: 2431897
  40. Pre-mRNA splicing.
    Annu Rev Genet. 1986;20:671-708 PMID: 2880558
  41. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression.
    Nucleic Acids Res. 1987 Sep 11;15(17):7155-74 PMID: 3658675
  42. Sequence and structural features associated with translational initiator regions in yeast--a review.
    Gene. 1987;59(1):1-18 PMID: 3325335
  43. Structure of vertebrate genes: a statistical analysis implicating selection.
    J Mol Evol. 1988;27(1):45-55 PMID: 3133487
  44. A survey on intron and exon lengths.
    Nucleic Acids Res. 1988 Nov 11;16(21):9893-908 PMID: 3057449
  45. The 5' splice site: phylogenetic evolution and variable geometry of association with U1RNA.
    Nucleic Acids Res. 1989 Mar 25;17(6):2159-80 PMID: 2704616
  46. U2 small nuclear RNA is remarkably conserved between Schizosaccharomyces pombe and mammals.
    Mol Cell Biol. 1988 Dec;8(12):5575-80 PMID: 3244367
  47. Introduction of functional artificial introns into the naturally intronless ura4 gene of Schizosaccharomyces pombe.
    Mol Cell Biol. 1989 Apr;9(4):1526-35 PMID: 2725514
  48. Nuclear pre-mRNA splicing in yeast.
    Yeast. 1989 Nov-Dec;5(6):439-57 PMID: 2694677
  49. Codon selection in yeast.
    J Biol Chem. 1982 Mar 25;257(6):3026-31 PMID: 7037777
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/22.9.1750
Published
1994-05-11
Pages
1750-9
Language
English
Region
England
NLM ID
0411011
PMCID
PMC308059
Subset
IM
Grants
NHGRI NIH HHS · 1K01 HG00010-01 · United States
NHGRI NIH HHS · 1R01 HG00203-01A1 · United States
External Links
PubMed source DOI: 10.1093/nar/22.9.1750 PMC Full Text View journal details
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