The Drosophila fruitless (fru) gene encodes a transcription factor that essentially regulates all aspects of male courtship behavior. The use of alternative 5'-splice sites generates fru isoforms that determine gender-appropriate sexual behaviors. Alternative splicing of fru is regulated by TRA and TRA2 and depends on an exonic splicing enhancer (fruRE) consisting of three 13-nucleotide repeat ...

Auxiliary splicing signals play a major role in the regulation of constitutive and alternative pre-mRNA splicing, but their relative importance in selection of mutation-induced cryptic or de novo splice sites is poorly understood. Here, we show that exonic sequences between authentic and aberrant splice sites that were activated by splice-site mutations in human disease genes have lower frequen...

Mutations in the Caenorhabditis elegans sup-39 gene cause allele-specific suppression of the uncoordination defect of unc-73(e936). e936 is a point mutation that changes the canonical G at the 5' end of intron 16 to a U. This mutation activates three splice donors, two of which define introns beginning with the canonical GU. Use of these two cryptic splice sites causes loss of reading frame; in...

As a result of large-scale sequencing projects and recent splicing-microarray studies, estimates of mammalian genes expressing multiple transcripts continue to increase. This expansion of transcript information makes it possible to better characterize alternative splicing events and gain insights into splicing mechanisms and regulation. Here, we describe a class of splice sites that we call dua...

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...