EST comparison indicates 38% of human mRNAs contain possible alternative splice forms

Abstract

Expressed sequence tag (EST) databases represent a large volume of information on expressed genes including tissue type, expression profile and exon structure. In this study we create an extensive data set of human alternative splicing. We report the analysis of 7867 non-redundant mRNAs, 3011 of which contained alternative splice forms (38% of all mRNAs analysed). From a total of 12 572 ESTs 4560 different possible alternative splice forms were detected. Interestingly, 70% of the alternative splice forms correspond to exon deletion events with only 30% exonic insertions. We experimentally verified 19 different splice forms from 16 genes in a total subset of 20 studied; all of the respective genes are of medical relevance.z 2000 Federation of European Biochemical Societies.

Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment

“…In all, 87% variants contained less than 16 ESTs, and 58% were represented by the EST singletons. If the singletons were excluded from the database, then only 66% genes were alternatively spliced, which is consistent with previous reports (Mironov et al, 1999;Brett et al, 2000;Kan et al, 2002).…”

“…A higher percentage of alternative splicing (81%) than the reported ratio of 30-65% (Mironov et al, 1999;Brett et al, 2000;Kan et al, 2002) is suggested. This is mainly due to the inclusion of EST singletons in the BASD, since 58% of splicing variants are supported by one EST in our database.…”

“…When the EST singletons are excluded from BASD, the percentage of genes with alternative splicing sites becomes comparable (66%) to the percentage in the previous reports. Splicing variants represented by singleton EST were sometimes considered noninformative (Mironov et al, 1999;Brett et al, 2000), since the singleton ESTs may introduce nonnative splicing events. However, we retained these variants because six of eight single-EST-supported variants (75%) were confirmed by RT-PCR in our study (Table 2), demonstrating the value of these single-EST-supported variants in mining genomic information.…”

“…Discussions about the almost inestimable complex function produced by those limited number of genes were focused on transcription regulation and alternative splicing (Black, 2000;Claverie, 2001), in addition to post-translation modification, such as phosphoration and glycosylation, which presumably contributes to the diversified functions of proteins. Alternative splicing is an important mechanism in higher eukaryotes for producing proteomic complexity, since approximately 30-65% genes are alternatively spliced as estimated by genomically aligned expressed sequence tags (ESTs) (Mironov et al, 1999;Brett et al, 2000;Kan et al, 2002). Combining these mechanisms, the human organism could conceivably produce hundreds of thousands of different proteins by the estimated 35 000 human genes.…”

Molecular analysis of the glyoxylate reductase (GRHPR) gene and description of mutations underlying primary hyperoxaluria type 2

“…The transcript was present in a variety of tissues as demonstrated by RT-PCR and also by searching for identical sequences in ESTs (http://www.ncbi.nlm.nih.gov/BLAST). Recent studies have shown that 35-38% of human RNAs contain possible alternative splice forms by comparison of multiple EST sequences (Mironov et al, 1999;Brett et al, 2000). Some of these will include exon or intron isoforms where alternative donor or acceptor sites have been used, others include skipped exons or intron retention.…”