We propose a novel method to detect 5' splice sites of eukaryotic mRNA. We have grouped the 5' splice splice sites into various classes. The clustered sites are represented by a set of PWMs. The clustering algorithm is similar to k-means clustering algorithm but the distance definition and the training score function were arranged. The clustered PWMs were applied to 5' splice site detection. Th...

The problem of identifying splice sites consists of two sub-problems: finding their boundaries, and characterizing their sequence markers. Other splicing elements—including, enhancers and silencers—that occur in the intronic and exonic regions play an important role in splicing activity. Existing methods for detecting splicing elements are limited to finding either splice sites or enhancers and...

BACKGROUND We developed and validated a real-time reverse transcription (RT)-PCR for the quantification of 4 individual human telomerase reverse transcriptase (TERT) splice variants (alpha+beta+, alpha-beta+, alpha+beta-, alpha-beta-) in tumor cell lines and non-small cell lung cancer (NSCLC). METHODS We used in silico designed primers and a common TaqMan probe for highly specific amplificati...

The Narumi-Katayama index of a graph G, denoted by NK(G), is equal to the product of the degrees of the vertices of G. In this paper we compute this index for Splice and Link of two graphs. At least with use of Link of two graphs, we compute this index for a class of dendrimers. With this method, the NK index for other class of dendrimers can be computed similarly.

While the majority of multiexonic human genes show some evidence of alternative splicing, it is unclear what fraction of observed splice forms is functionally relevant. In this study, we examine the extent of alternative splicing in human cells using deep RNA sequencing and de novo identification of splice junctions. We demonstrate the existence of a large class of low abundance isoforms, encom...

Alternative splicing is widespread in mammalian gene expression, and variant splice patterns are often specific to different stages of development, particular tissues or a disease state. There is a need to systematically collect data on alternatively spliced exons, introns and splice isoforms, and to annotate this data. The Alternative Splicing Database consortium has been addressing this need,...

To investigate the mechanisms underlying accurate pre-mRNA splicing, we developed an in vitro assay sensitive to proofreading of 5' splice site cleavage. We inactivated spliceosomes by disrupting a metal-ligand interaction at the catalytic center and discovered that, when the DEAH box ATPase Prp16 was disabled, these spliceosomes catalyzed 5' splice site cleavage but at a reduced rate. Although...

Bovine papillomavirus type 1 (BPV-1) late pre-mRNAs are spliced in keratinocytes in a differentiation-specific manner: the late leader 5' splice site alternatively splices to a proximal 3' splice site (at nucleotide 3225) to express L2 or to a distal 3' splice site (at nucleotide 3605) to express L1. Two exonic splicing enhancers, each containing two ASF/SF2 (alternative splicing factor/splicin...

INTRODUCTION The presence of a variety of MDM2 splice variants has been reported in a range of different tumor types and is associated with poor patient prognosis. Furthermore, several MDM2 variants have been shown to have oncogenic properties. Despite this, MDM2 splice variants have not been comprehensively characterized in oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS MDM2 spli...