ArticleBMC genomics2009
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Insights into the human cDNA: A descriptive study using library screening in yeast.Journal, genetic engineering & biotechnology · 2024Article
- Review
- Identification and functional analysis of a novel splice variant of AC3-33 in breast cancer.Experimental and therapeutic medicine · 2020Article
- ImmuSort, a database on gene plasticity and electronic sorting for immune cells.Scientific reports · 2015Article
- ImmuCo: a database of gene co-expression in immune cells.Nucleic acids research · 2015Article
- Beta catenin and cytokine pathway dysregulation in patients with manifestations of the "PTEN hamartoma tumor syndrome".BMC medical genetics · 2012Article
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Authors and funding
5 authors.
Funding
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Abstract
backgroundAlternative 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.
resultsIn 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.
conclusionOur 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.
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