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Updated: Nov 10, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
MTSplice predicts effects of genetic variants on tissue-specific splicing
Jun Cheng1, Muhammed Hasan Çelik2, Anshul Kundaje3,4
1Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748, Germany. s6juncheng@gmail.com.
None:
We develop the free and open-source model Multi-tissue Splicing (MTSplice) to predict the effects of genetic variants on splicing of cassette exons in 56 human tissues. MTSplice combines MMSplice, which models constitutive regulatory sequences, with a new neural network that models tissue-specific regulatory sequences. MTSplice outperforms MMSplice on predicting tissue-specific variations associated with genetic variants in most tissues of the GTEx dataset, with largest improvements on brain tissues. Furthermore, MTSplice predicts that autism-associated de novo mutations are enriched for variants affecting splicing specifically in the brain. We foresee that MTSplice will aid interpreting variants associated with tissue-specific disorders.
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