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Int. J. Mol. Sci. 2015, 16(5), 10376-10388; doi:10.3390/ijms160510376

Identification and Validation of Evolutionarily Conserved Unusually Short Pre-mRNA Introns in the Human Genome

1
Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
2
Matsunami Research Park (Sosai-kouseikai), 10 Izumi-cho, Kasamatsu-cho, Hashima-gun, Gifu 501-6061, Japan
*
Authors to whom correspondence should be addressed.
Academic Editor: Bing Yan
Received: 23 March 2015 / Revised: 13 April 2015 / Accepted: 13 April 2015 / Published: 7 May 2015
(This article belongs to the Special Issue Pre-mRNA Splicing 2015)
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Abstract

According to the length distribution of human introns, there is a large population of short introns with a threshold of 65 nucleotides (nt) and a peak at 85 nt. Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the identities of which are scarcely known. Here, we provide for the first time a list of bona fide human ultra-short introns, which have never been characterized elsewhere. By conducting BLAST searches of the databases, we screened 22 introns (37–65 nt) with conserved lengths and sequences among closely related species. We then provide experimental and bioinformatic evidence for the splicing of 15 introns, of which 12 introns were remarkably G-rich and 9 introns contained completely inefficient splice sites and/or branch sites. These unorthodox characteristics of ultra-short introns suggest that there are unknown splicing mechanisms that differ from the well-established mechanism. View Full-Text
Keywords: G-rich sequence; H-InvDB; human genome; human transcriptome; intron length; pre-mRNA splicing; splice sites; ultra-short intron G-rich sequence; H-InvDB; human genome; human transcriptome; intron length; pre-mRNA splicing; splice sites; ultra-short intron
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Shimada, M.K.; Sasaki-Haraguchi, N.; Mayeda, A. Identification and Validation of Evolutionarily Conserved Unusually Short Pre-mRNA Introns in the Human Genome. Int. J. Mol. Sci. 2015, 16, 10376-10388.

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