46 results about "Splice Site SNP" patented technology

The present invention relates to methods for identifying target nucleic acid molecules differing by one or more single-base changes, insertions, deletions, or translocations; and identifying one or more target mRNA molecules differing by one or more splice site variations in a plurality of mRNA molecules. Also disclosed is a method of generating a linearly amplified representation of a whole genome. Other aspects of the present invention relate to labeled detection oligonucleotide probes and translational oligonucleotide probes as well as to methods of designing such probes.

Disclosed herein are point mutations in the LMNA gene that cause HGPS. These mutations activate a cryptic splice site within the LMNA gene, which leads to deletion of part of exon 11 and generation of a mutant Lamin A protein product that is 50 amino acids shorter than the normal protein. In addition to the novel Lamin A variant protein and nucleic acids encoding this variant, methods of using these molecules in detecting biological conditions associated with a LMNA mutation in a subject (e.g., HGPS, arteriosclerosis, and other age-related diseases), methods of treating such conditions, methods of selecting treatments, methods of screening for compounds that influence Lamin A activity, and methods of influencing the expression of LMNA or LMNA variants are also described. Oligonucleotides and other compounds for use in examples of the described methods are also provided, as are protein-specific binding agents, such as antibodies, that bind specifically to at least one epitope of a Lamin A variant protein preferentially compared to wildtype Lamin A, and methods of using such antibodies in diagnosis, treatment, and screening. Also provided are kits for carrying out the methods described herein.

The invention is directed to a method of preparing a nucleic acid sequence with a modified splice site usage profile, which employs the use of a nucleic acid sequence comprising a cryptic splice donor site. The invention also provides a method of producing an alternate form of an RNA molecule encoded by a nucleic acid sequence, which nucleic acid sequence comprises a cryptic splice donor site, a heterologous nucleic acid sequence, and a splice acceptor site.

The present invention relates to riboswitches that have been engineered to regulate pre-mRNA splicing. In particular, the insertion of a high affinity theophylline binding aptamer into the 3′ splice site region, 5′ splice site region, or branchpoint sequence (BPS) of a pre-mRNA modulates RNA splicing in the presence of theophylline. Accordingly, the aspects of the present invention include, but are not limited to, theophylline-dependent riboswitches which modulate RNA splicing, methods of modulating RNA splicing using theophylline and its corresponding riboswitches, methods of improving/identifying theophylline-dependent riboswitches, methods of treating diseases associated with or caused by abnormal RNA splicing.

The invention relates to a method for performing gene interference on non-coding RNA (lncRNA) through targeting eukaryocyte genome splicing sites.

The invention belongs to the technical field of biology, and particularly relates to an EZH2 variable splicing site and an application thereof. Specific siRNA is used for knocking down two subtypes ofEZH2-L and EZH2-S respectively, and myocardial hypertrophy and heart failure models are established at the cellular level and the animal level respectively. Results show that after the EZH2-L is knocked down, the expression level of a myocardial hypertrophy pathological gene is obviously reduced, the myocardial cell area is reduced, and the heart weight is reduced; and after the EZH2-S is knockeddown, the expression level of the myocardial hypertrophy pathological gene is remarkably increased, the myocardial cell area is increased, the heart weight is increased, and the situation prompts that the EZH2-L and the EZH2-S have the effects of promoting and inhibiting myocardial hypertrophy and heart failure respectively. In addition, after the EZH2-L is knocked down, tumor cell proliferationis inhibited, and knock-down of the EZH2-S has no influence on tumor cell proliferation. The invention provides a new target and a new strategy for research and development of medicines for treating EZH2 gene related diseases.

A method of regulating RNA splicing by inducing splice site base mutation or polypyrimidine region base substitution is disclosed, the method comprises expressing targeted cytidine deaminase in cellsto induce AG to AA mutation of 3' splicing site of intron of interested of gene of interested in the cells, or GT to AT mutation of 5' splicing site of the intron of interested of the gene of interested in the cells, or respective mutation of multiple C in a polypyrimidine region of the intron of interested of the gene of interested to T. The method can specifically block the exon recognition process, regulates the alternative splicing process of endogenous mRNA, induces exon skipping, activates alternative splicing sites, induces mutual exclusive exon conversion, induces intron retention andenhances exon retention.

The present invention concerns a modified nucleic acid molecule comprising a nucleotide sequence coding for a full length hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, this molecule having at least one nucleotide alteration, wherein, due to this alteration, at least one RNA splice site selected from the group consisting of RNA splice acceptor and RNA splice donor sites is eliminated from the coding sequence. The invention is also directed to methods for expressing on the surface of a cell and a pseudovirion an HCV glycoprotein, wherein the majority of the glycoprotein is full length. The invention further provides a cell and a pseudovirion expressing such glycoprotein. The invention still further provides a method for determining whether an agent inhibits HCV fusion with and entry into a target cell. The invention also provides an agent that inhibits HCV fusion with and entry into a target cell. The invention further provides methods for treating a subject afflicted with an HCV-associated disorder, for preventing an HCV infection in a subject, and for inhibiting in a subject the onset of an HCV-associated disorder.

The invention discloses a double-end paired splicing site prediction method. The method comprises the following steps: acquiring a double-end paired splicing site sample sequence as a reference data set and an independent data set; coding the base sequence through a plurality of feature extraction modes based on the sequence, physicochemical properties and the like; combining a plurality of features as a multi-channel multi-dimensional vector representation; training a convolutional neural network model; and finally, evaluating. The prediction method can be combined with multiple feature representation modes of the sample to help the convolutional neural network to fully learn the intrinsic mode of the sample, and the accuracy of predicting the splicing sites with the paired two ends is improved.

The invention relates to a method for repairing aberrant splicing in Pompe patients that carry the IVS1 variant, wherein such aberrant splicing is caused by the expression of a natural pseudo exon present in GAA intron 1, comprising blocking of either the natural cryptic 3′ splice site or the natural cryptic 5′ splice site of said natural pseudo exon with an antisense oligomeric compound (AON). Further, the invention comprises an antisense oligomeric compound targeting SEQ ID NO: 1 or SEQ ID NO: 180, preferably selected from the sequences of SEQ ID NO: 91-179, sequences that are complementary to said sequences or sequences that have an identity of 80% with said sequences or the complementary sequences and a second AON from the sequences of SEQ ID NO: 346-508, sequences that are complementary to said sequences or sequences that have an identity of 80% with said sequences or the complementary sequences.

The invention discloses a third-generation sequencing RNA-seq comparison method based on a WFA algorithm. The method comprises the following steps: acquiring a data set containing a target sequence and a query sequence; then indexing the reference genome; carrying out region selection and graph mapping; searching the longest common subsequence LCSk of the k-length substring, and then carrying out anchor point filtering and anchor point comparison; and introducing an annotation file to obtain a comparison result, and finally evaluating the comparison result. Experiments prove that the method provided by the invention effectively improves the accuracy of sequence alignment, especially the accuracy of splicing site alignment, and reduces the alignment time to a certain extent.

A method, including identifying, in a nucleotide string, at least two exons, at least one acceptor, at least one donor, and at least one intron between the at least two exons, is provided. The method includes identifying, in the nucleotide string, a cryptic splice site comprising a sequence of nucleotides based on a similarity score with at least one of the acceptor or the donor, and graphically marking, in a display for a user, the nucleotide string at a location indicative of an exon, an intron, a true splice site, and optionally a cryptic splice site when the similarity score is higher than a pre-selected threshold. A system and a non-transitory, computer-readable medium including instructions to cause the system to perform the method are also provided.