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Open Access Research article

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site

Pingzhang Wang123, Peng Yu1, Peng Gao1, Taiping Shi123 and Dalong Ma123*

Author Affiliations

1 Chinese National Human Genome Center, #3-707 North YongChang Road BDA, Beijing 100176, PR China

2 Laboratory of Medical Immunology, School of Basic Medical Science, Peking University Health Science Center, 38# Xueyuan Road, Beijing, 100083, PR China

3 Peking University Center for Human Disease Genomics, 38# Xueyuan Road, Beijing, 100083, PR China

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BMC Genomics 2009, 10:518  doi:10.1186/1471-2164-10-518

Published: 12 November 2009

Abstract

Background

Alternative polyadenylation sites within a gene can lead to alternative transcript variants. Although bioinformatic analysis has been conducted to detect polyadenylation sites using nucleic acid sequences (EST/mRNA) in the public databases, one special type, single-block EST is much less emphasized. This bias leaves a large space to discover novel transcript variants.

Results

In the present study, we identified novel transcript variants in the human genome by detecting intronic polyadenylation sites. Poly(A/T)-tailed ESTs were obtained from single-block ESTs and clustered into 10,844 groups standing for 5,670 genes. Most sites were not found in other alternative splicing databases. To verify that these sites are from expressed transcripts, we analyzed the supporting EST number of each site, blasted representative ESTs against known mRNA sequences, traced terminal sequences from cDNA clones, and compared with the data of Affymetrix tiling array. These analyses confirmed about 84% (9,118/10,844) of the novel alternative transcripts, especially, 33% (3,575/10,844) of the transcripts from 2,704 genes were taken as high-reliability. Additionally, RT-PCR confirmed 38% (10/26) of predicted novel transcript variants.

Conclusion

Our results provide evidence for novel transcript variants with intronic poly(A) sites. The expression of these novel variants was confirmed with computational and experimental tools. Our data provide a genome-wide resource for identification of novel human transcript variants with intronic polyadenylation sites, and offer a new view into the mystery of the human transcriptome.