Transcriptome and genome conservation of alternative splicing events in humans and mice - PubMed (original) (raw)
Comparative Study
Transcriptome and genome conservation of alternative splicing events in humans and mice
C W Sugnet et al. Pac Symp Biocomput. 2004.
Free article
Abstract
Combining mRNA and EST data in splicing graphs with whole genome alignments, we discover alternative splicing events that are conserved in both human and mouse transcriptomes. 1,964 of 19,156 (10%) loci examined contain one or more such alternative splicing events, with 2,698 total events. These events represent a lower bound on the amount of alternative splicing in the human genome. Also, as these alternative splicing events are conserved between the human and mouse transcriptomes they should be enriched for functionally significant alternative splicing events, free from much of the noise found in the EST libraries. Further classification of these alternative splicing events reveals that 1,037 (38.4%) are due to exon skipping, 497 (18.4%) are due to alternative 3' splice sites, 214 (7.9%) are due to alternative 5' splice sites, 75 (2.8%) are due to intron retention and the other 875 (32.4%) are due to other, more complicated, alternative splicing events. In addition, genomic sequences nearby these alternative splicing events display increased sequence conservation. Both the alternatively spliced exons and the proximal intron show increased levels of genomic conservation relative to constitutively spliced exons. For exon skipping events both intron regions flanking the exon are conserved while for alternative 5' and 3' splicing events the conservation is greater near the alternative splice site.
Similar articles
- Conservation of human alternative splice events in mouse.
Thanaraj TA, Clark F, Muilu J. Thanaraj TA, et al. Nucleic Acids Res. 2003 May 15;31(10):2544-52. doi: 10.1093/nar/gkg355. Nucleic Acids Res. 2003. PMID: 12736303 Free PMC article. - Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a.
Gulledge AA, Roberts AD, Vora H, Patel K, Loraine AE. Gulledge AA, et al. Am J Bot. 2012 Feb;99(2):219-31. doi: 10.3732/ajb.1100355. Epub 2012 Jan 30. Am J Bot. 2012. PMID: 22291167 - How prevalent is functional alternative splicing in the human genome?
Sorek R, Shamir R, Ast G. Sorek R, et al. Trends Genet. 2004 Feb;20(2):68-71. doi: 10.1016/j.tig.2003.12.004. Trends Genet. 2004. PMID: 14746986 Review. - Bioinformatics detection of alternative splicing.
Kim N, Lee C. Kim N, et al. Methods Mol Biol. 2008;452:179-97. doi: 10.1007/978-1-60327-159-2_9. Methods Mol Biol. 2008. PMID: 18566765 Review. - Selecting for functional alternative splices in ESTs.
Kan Z, States D, Gish W. Kan Z, et al. Genome Res. 2002 Dec;12(12):1837-45. doi: 10.1101/gr.764102. Genome Res. 2002. PMID: 12466287 Free PMC article.
Cited by
- The Role of mRNA Alternative Splicing in Macrophages Infected with Mycobacterium tuberculosis: A Field Needing to Be Discovered.
Hong W, Yang H, Wang X, Shi J, Zhang J, Xie J. Hong W, et al. Molecules. 2024 Apr 16;29(8):1798. doi: 10.3390/molecules29081798. Molecules. 2024. PMID: 38675618 Free PMC article. Review. - Exitrons: offering new roles to retained introns-the novel regulators of protein diversity and utility.
Shamnas V M, Singh A, Kumar A, Mishra GP, Sinha SK. Shamnas V M, et al. AoB Plants. 2024 Mar 20;16(2):plae014. doi: 10.1093/aobpla/plae014. eCollection 2024 Feb. AoB Plants. 2024. PMID: 38566894 Free PMC article. Review. - Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts.
Khalifah BA, Alghamdi SA, Alhasan AH. Khalifah BA, et al. Front Bioeng Biotechnol. 2023 Nov 16;11:1244377. doi: 10.3389/fbioe.2023.1244377. eCollection 2023. Front Bioeng Biotechnol. 2023. PMID: 38047291 Free PMC article. Review. - The role of alternative splicing in lung cancer.
Ning X, Fu Z, Zhang J, Gao S, Cui Z, Cong M, Guo Q, Sun X, Li J, Zhang M, Wang S. Ning X, et al. Cancer Chemother Pharmacol. 2023 Aug;92(2):83-95. doi: 10.1007/s00280-023-04553-4. Epub 2023 Jun 19. Cancer Chemother Pharmacol. 2023. PMID: 37335335 Review. - Poly(A) capture full length cDNA sequencing improves the accuracy and detection ability of transcript quantification and alternative splicing events.
Ura H, Togi S, Niida Y. Ura H, et al. Sci Rep. 2022 Jun 22;12(1):10599. doi: 10.1038/s41598-022-14902-7. Sci Rep. 2022. PMID: 35732903 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Research Materials