Unlike in mammals, intron retention is the major mode of alternative splicing (AS) in plants. The difference suggests distinctive regulatory mechanisms of AS between plants and animals. Chlamydomonas reinhardtii, an intron-rich green alga that shares both animal and plant traits serves a good model to study evolutionary perspective of AS and its underlying mechanisms. Moreover, rapidly increasing cDNA datasets from Next-Generation Sequencing (NGS) offers new opportunities to evaluate the true scope and type of AS. Based on all available Sanger ESTs (338,243) and new 454 pyrosequencing cDNA data (689,548), we generated AS models using GMAP and the Program to Assemble Spliced Alignment (PASA). PASA AS models were consolidated by extending structural gene annotations created by the gene-finding program, AUGUSTUS. Out of 15,935 AUGUSTUS (version u9) protein-coding genes, 4.4% were found to be subject to AS. Of all 20,654 PASA genes predicted only using cDNA-to-genome mapping evidence, 6.97% were found to have AS isoform(s). Though this web portal, you can examine closely all PASA alternatively spliced gene models. |
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