Low conservation and species-specific evolution of alternative splicing in humans and mice: Comparative genomics analysis using well-annotated full-length cDNAs

Jun Ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Masahide Seki, Takuma Irie, Nono Takeuchi, Takuya Ueda, Mitsuteru Nakao, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi

研究成果: Article

21 引用 (Scopus)

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Using full-length cDNA sequences, we compared alternative splicing (AS) in humans and mice. The alignment of the human and mouse genomes showed that 86% of 199 426 total exons in human AS variants were conserved in the mouse genome. Of the 20 392 total human AS variants, however, 59% consisted of all conserved exons. Comparing AS patterns between human and mouse transcripts revealed that only 431 transcripts from 189 loci were perfectly conserved AS variants. To exclude the possibility that the full-length human cDNAs used in the present study, especially those with retained introns, were cloning artefacts or prematurely spliced transcripts, we experimentally validated 34 such cases. Our results indicate that even retained-intron type transcripts are typically expressed in a highly controlled manner and interact with translating ribosomes. We found non-conserved AS exons to be predominantly outside the coding sequences (CDSs). This suggests that non-conserved exons in the CDSs of transcripts cause functional constraint. These findings should enhance our understanding of the relationship between AS and species specificity of human genes.

元の言語English
ページ(範囲)6386-6395
ページ数10
ジャーナルNucleic acids research
36
発行部数20
DOI
出版物ステータスPublished - 2008
外部発表Yes

ASJC Scopus subject areas

  • Genetics

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    Takeda, J. I., Suzuki, Y., Sakate, R., Sato, Y., Seki, M., Irie, T., Takeuchi, N., Ueda, T., Nakao, M., Sugano, S., Gojobori, T., & Imanishi, T. (2008). Low conservation and species-specific evolution of alternative splicing in humans and mice: Comparative genomics analysis using well-annotated full-length cDNAs. Nucleic acids research, 36(20), 6386-6395. https://doi.org/10.1093/nar/gkn677