3 results about "Splice Site SNP" patented technology

The technology disclosed relates to splice site prediction and aberrant splicing detection. In particular, it relates to a splice site predictor that includes a convolutional neural network trained on training examples of donor splice sites, acceptor splice sites, and non-splicing sites. An input stage of the convolutional neural network feeds an input sequence of nucleotides for evaluation of target nucleotides in the input sequence. An output stage of the convolutional neural network translates analysis by the convolutional neural network into classification scores for likelihoods that each of the target nucleotides is a donor splice site, an acceptor splice site, and a non-splicing site.

This disclosure provides a DNA construct comprising: (a) a start exon encoding a start codon; (b) a first frameshift exon downstream of the start exon, the first frameshift exon including a first receptor splice site, wherein inclusion or exclusion of the first frameshift exon in alternative splicing determines the downstream reading frame of a mature mRNA transcript; and (c) a first specific exon downstream of the first frameshift exon, the first specific exon including a second receptor splice site, a first reporter gene, and a second reporter gene, wherein the first reporter gene is located upstream or downstream of the second reporter gene, and wherein the first reporter gene and the second reporter gene are in different reading frames, wherein exclusion of the first frameshift exon causes the first reporter gene to be in the same reading frame as the start codon, and wherein inclusion of the first frameshift exon causes the second reporter gene to be in the same reading frame as the start codon.

Provided herein are polynucleotides, vectors, complexes, compositions, systems, kits, methods and uses for enriching for gene editing in a cell. Some aspects of the disclosure relate to the use of a polynucleotide cassette comprising a coding sequence of a selection marker gene that is disrupted by a synthetic intron sequence to prevent gene expression of the selection marker. The synthetic intron further comprises a defective splice site that is correctable by a base edit such that when the splice site is corrected by a gene editor, the intron is removed by the endogenous slicing system of the cell and expression of the selection marker gene can occur. Methods described herein screen for the presence of active gene editors within the cell by subjecting the cell to the selection pressure of the selection marker.