UTR reconstruction and analysis using genomically aligned EST sequences.
Untranslated regions (UTR) play important roles in the posttranscriptional regulation of mRNA processing. There is a wealth of UTR-related information to be mined from the rapidly accumulating EST collections. A computational tool, UTR-extender, has been developed to infer UTR sequences from genomically aligned ESTs. It can completely and accurately reconstruct 72% of the 3' UTRs and 15% of the 5' UTRs when tested using 908 functionally cloned transcripts. In addition, it predicts extensions for 11% of the 5' UTRs and 28% of the 3' UTRs. These extension regions are validated by examining splicing frequencies and conservation levels. We also developed a method called polyadenylation site scan (PASS) to precisely map polyadenylation sites in human genomic sequences. A PASS analysis of 908 genic regions estimates that 40-50% of human genes undergo alternative polyadenylation. Using EST redundancy to assess expression levels, we also find that genes with short 3' UTRs tend to be highly expressed.
Kan
Z
Z
Institute for Biomedical Computing, Washington University, St. Louis, MO 63110, USA. zkan@ibc.wustl.edu
Gish
W
W
Rouchka
E
E
Glasscock
J
J
States
D
D
D000465:Algorithms; D003198:Computer Simulation; D015894:Genome, Human; D006801:Humans; D011237:Predictive Value of Tests; D017421:Sequence Analysis / Q000379:methods*; D020506:Untranslated Regions
D020506:Untranslated Regions