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Nucleic Acids Research 2005 33(Web Server Issue):W681-W685; doi:10.1093/nar/gki407
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The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

ASePCR: alternative splicing electronic RT–PCR in multiple tissues and organs

Namshin Kim1, Dajeong Lim, Sanghyuk Lee1 and Heebal Kim*

School of Agricultural Biotechnology, Seoul National University Seoul 151-742, Korea 1Division of Molecular Life Sciences, Ewha Womans University Seoul 120-750, Korea

*To whom correspondence should be addressed. Tel: +82 28804803; Fax: +82 28732271; Email: heebal{at}snu.ac.kr

Received February 14, 2005. Revised March 21, 2005. Accepted March 21, 2005.

RT–PCR is one of the most powerful and direct methods to detect transcript variants due to alternative splicing (AS) that increase transcript diversity significantly in vertebrates. ASePCR is an efficient web-based application that emulates RT–PCR in various tissues. It estimates the amplicon size for a given primer pair based on the transcript models identified by the reverse e-PCR program of the NCBI. The tissue specificity of each PCR band is deduced from the tissue information of expressed sequence tag (EST) sequences compatible with each transcript structure. The output page shows PCR bands like a gel electrophoresis in various tissues. Each band in the output picture represents a putative isoform that could happen in a tissue-specific manner. It also shows the EST alignment and tissue information in the genome browser. Furthermore, the user can compare the AS patterns of orthologous genes in other species. The ASePCR, available at http://genome.ewha.ac.kr/ASePCR/, supports the transcriptome models of the RefSeq, Ensembl, ECgene and AceView for human, mouse, rat and chicken genomes. It will be a valuable web resource to explore the transcriptome diversity associated with different tissues and organs in multiple species.

The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors


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