ArticleGenome research2004
Ordered partitioning reveals extended splice-site consensus information.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- MEMO1 drives cranial endochondral ossification and palatogenesis.Developmental biology · 2016Article
- Cis-acting signals modulate the efficiency of programmed DNA elimination in Paramecium tetraurelia.Nucleic acids research · 2015Article
- RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts.Genome research · 2015Article
- A simple model to explain evolutionary trends of eukaryotic gene architecture and expression: how competition between splicing and cleavage/polyadenylation factors may affect gene expression and splice-site recognition in eukaryotes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2013Review
- Article
- Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons.Genome research · 2012Article
- Conservation and sex-specific splicing of the doublesex gene in the economically important pest species Lucilia cuprina.Journal of genetics · 2010Article
- TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites.EURASIP journal on bioinformatics & systems biology · 2010Article
- Sexual development in Lucilia cuprina (Diptera, Calliphoridae) is controlled by the transformer gene.Genetics · 2009Article
- A DNA damage signal activates and derepresses exon inclusion in Drosophila TAF1 alternative splicing.RNA (New York, N.Y.) · 2008Article
- Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes.Genome research · 2008Article
- Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis.Journal of molecular evolution · 2007Article
- Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns.BMC genomics · 2006Article
- Challenging the spliceosome machine.Genome biology · 2006Article
- Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements.Genetics · 2005Article
- Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing.Genome research · 2005Article
- Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project.Chromosoma · 2004Article
- Relational databases: a transparent framework for encouraging biology students to think informatically.Cell biology education · 2004Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using recently available cDNA and genomic data (Berkeley Drosophila Genome Project; http://www.fruitfly.org), we computed a large sample of 10,057 Drosophila splice sites. An information-theoretic analysis of the nucleotide sequences adjacent to these splice sites showed a strong correlation between the sizes of introns and exons and the levels of information, which is a measure of sequence conservation. The strong correlation permitted us to determine extensive consensus sequences at the donor and acceptor sites of longer introns. These sequences were further refined and extended by examining the information in regions around splice sites that only partially matched the consensus. The correlation between length and information provided the basis for determining alternative consensus arrangements associated with shorter introns, as well as general base-composition preferences that likely promote spliceosome function. We also observed a correlation between information near splice sites and the lengths of nonadjacent introns, indicating that there are long-range effects spanning multiple introns. The ordered partitioning approach used in this analysis may become increasingly useful as large genomic data sets become available.
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