ASePCR: Alternative splicing electronic RT-PCR in multiple tissues and organs

Namshin Kim, Dajeong Lim, Sanghyuk Lee, Heebal Kim

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


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://, 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.

Original languageEnglish
Pages (from-to)W681-W685
JournalNucleic Acids Research
Issue numberSUPPL. 2
StatePublished - Jul 2005

Bibliographical note

Funding Information:
We thank Dr Robert Klein for helpful comments and English editing on the manuscript. This work was supported by the Bioinformatics Research Program of the Ministry of Science and Technology of Korea (to S.L., grant 2005-00201) and the BioGreen 21 Program of the Korean Rural Development Administration (to H.K.) and the Brain Korea 21 Project of the Ministry of Education (to H.K.). Funding to pay the Open Access publication charges for this article was provided by BioGreen 21 Program.


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