NDLI: Identification of Shadow Exons: Mining for Alternative Exons in Human, Mouse and Rat Comparative Databases

Content Provider	IEEE Xplore Digital Library
Author	Taneri, B. Novoradovsky, A. Gaasterland, T.
Copyright Year	2009
Abstract	We describe a comparative analysis of alternative exons in mammalian transcriptomes, designed to identify species-specific and conserved alternative splicing events. We mine the comparative alternative splicing databases of human, mouse and rat to identify previously unobserved alternative exons termed here as shadow exons. Using established genome synteny maps together with sequence alignment, we identify pairs of homologous genes for human and mouse (17,486 gene pairs); human and rat (13,386 gene pairs); and mouse and rat (14,416 gene pairs). Within these homologous gene pairs, we distinguish homologous exons and species-specific exons. Sequences from alternatively spliced, species-specific exons were aligned with the corresponding introns in the other species to yield 767 human, 1768 mouse and 1337 rat novel shadow exons. A surprisingly large number of alternatively spliced exons remained species-specific: 5330 human, 3841 mouse and 2912 rat exons.
Starting Page	208
Ending Page	212
File Size	333864
Page Count	5
File Format	PDF
ISBN	9780769537634
ISSN	15294188
DOI	10.1109/DEXA.2009.43
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-08-31
Publisher Place	Austria
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Humans Mice Databases Bioinformatics Genomics Splicing Sequences RNA Electronic mail Proteins species-specific alternative exons alternative splicing homologous exons mammalian transcriptomes
Content Type	Text
Resource Type	Article

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