Alternative splicing (AS) modulates many physiological and pathological processes. For instance, AS of the BCL-X gene balances cell survival and apoptosis in development and cancer. Herein, we identified the polypyrimidine tract binding protein (PTBP1) as a direct regulator of BCL-X AS. Overexpression of PTBP1 promotes selection of the distal 5' splice site in BCL-X exon 2, generating the pro-a...

The GluN1 subunit of the N-methyl-D-aspartate (NMDA) receptor shows age-related changes in its expression pattern, some of which correlate with spatial memory performance in mice. Aged C57BL/6 mice show an age-related increase in mRNA expression of GluN1 subunit splice variants that lack the N terminal splice cassette, GluN1(0XX) (GluN1-a). This increase in expression is associated with good pe...

To identify untranslated regions (UTR) splice sites more accurately and efficiently, a method for the recognition of UTR splice sites using both splicing sequences and secondary structures of flank sequence information based on combination statistical method with support vector machine was proposed. The method consists of two stages: a statistical method is used in the first stage and a support...

The integrin β1 subfamily of adhesion receptors consists of 12 members and forms the biggest subfamily among integrins. Human integrin subunit β1 has five cytoplasmic splice variants (β1A, β1B, β1C-1, β1-C2, β1D). Even though cytoplasmic splice variants do not change the ligand-specificity of a β1 integrin, clustering of these different splice variants triggers signaling pathways that lead to a...

We mapped the collection of The Institute of Physical and Chemical Research (Japan) (RIKEN) 21,076 full-length mouse cDNA clone sequences and the mouse RefSeq sequences to the recently completed draft of the mouse genome. Using this mapping, we identified 3674 mouse genes with multiple transcripts, of which 1098 have splice variants. All but 532 of 21,076 clones (97.5%) mapped to the genome ass...

The natural cytotoxicity receptors NKp46/NCR1, NKp44/NCR2 and NKp30/NCR3 are critical for natural killer (NK) cell functions. Their genes are transcribed into several splice variants whose physiological relevance is not yet fully understood. Here we report that decidua basalis NK (dNK) cells of the pregnant uterine mucosa and peripheral blood NK (pNK) cells, two functionally distinct subsets of...

Glutamic acid decarboxylase (GAD) is a major inhibitory neurotransmitter in the brain, which catalyses the reaction of L-glutamate to gamma-aminobutyric acid. There are two isoforms of GAD, a 65-kDa form and a 67-kDa form, which are encoded by two different genes. As previous studies suggested a role for GAD67 splice variants during fetal pancreas development, we have investigated the mRNA expr...

Results A method for predicting trans-splicing sites must be able to identify more than one likely splice site in a given trans-splicing region if the conditions warrant such a prediction. Otherwise, the predictive ability of the method would be limited to identifying one of several possible splice sites. Therefore, we wished to assess our method’s predictive ability on a set of known trans-spl...

The regulatory and accessory proteins of human immunodeficiency virus type 1 (HIV-1) are produced from singly or multiply spliced mRNAs. We have used HIV-1-specific oligonucleotide primer pairs in a polymerase chain reaction procedure on RNA from lymphocyte cell lines infected with HIV-1(228,200). The amplified products were analysed by hybridization with splice junction-specific oligonucleotid...

We present a novel classification method for splice sites prediction using support vector machine (SVM). The method first represents input sequences by sequence-based features, including the information of the distribution of tri-nucleotides and the conserved features surrounding the splice sites characterized by Markov model. An F-score based feature selection method is then used to select inf...