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  • mRNA
  • In the nucleoplasm, the U1 snRNP along with other small nuclear ribonucleoproteins (U2, U4-U6, and U5) assemble into SPLICEOSOMES that remove introns from pre-mRNA by splicing. (labome.org)
  • mutation
  • Strains expressing RNAPII with a K 1246 R mutation showed reduced co-transcriptional splicing. (elifesciences.org)
  • Mutation of both the splice donor and acceptor sites was necessary for RNAs to be edited efficiently. (biochemj.org)
  • Genetic correction of splice site mutation in purified and enriched myoblasts isolated from mdx5cv mice. (nih.gov)
  • AG-dependent 3'-splice sites are predisposed to aberrant splicing due to a mutation at the first nucleotide of an exon. (nih.gov)
  • A series of artificial mutations in the polypyrimidine tracts of GH1, FECH, EYA1, LPL and HEXA disclosed that a stretch of at least 10-15 pyrimidines is required to ensure normal splicing in the presence of a mutation at E(+1). (nih.gov)
  • Our studies suggest that a mutation at the AG-dependent 3'-splice site that requires U2AF(35) for spliceosome assembly causes exon skipping, whereas one at the AG-independent 3'-splice site that does not require U2AF(35) gives rise to normal splicing. (nih.gov)
  • Less efficient effects of U2AF35-siRNA on GH1, FECH and EYA1 (Figure 2B) compared to the mutant constructs (Figure 1B) were likely because the mutation abolished binding of U2AF35 in all the cells, whereas substantial numbers of cells failed to incorporate U2AF35-siRNA and gave rise to normally spliced products.Figure 2. (nih.gov)
  • The pseudoknot structure is very similar in influenzavirus A and influenzavirus B. A unique point mutation occurring in the strains of influenza A virus subtype H5N1 after 2001 has been suggested to result in RNA conformational shift, favouring an alternative hairpin structure instead of the pseudoknot. (wikipedia.org)
  • They distances are then assigned percentile ranks to estimate the likelihood of a splicing mutation. (wikipedia.org)
  • genome
  • Group I introns may also insert into the natural intron insertion site at the RNA level, and subsequently become stably integrated into the host genome. (biomedsearch.com)
  • RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo. (wikipedia.org)
  • Some types of RNA editing repair or correct the information encoded by the genome, whereas others act to diversify this information, offering an organism the potential for greater complexity. (pubmedcentralcanada.ca)
  • The Influenza virus pseudoknot is an RNA pseudoknot structure formed in one of the non-structural coding segments (NS) of influenza virus genome. (wikipedia.org)
  • In order to investigate further the distribution of wobble splicing events within the human genome, we have performed an in-depth computational analysis using a well known database--the Alternative Splicing Database (ASD) . (nih.gov)
  • Furthermore, based on the statistics of splice signal sequences, Senapathy has developed a functional genome-wide fingerprinting method. (wikipedia.org)
  • RSeQC RSeQC analyzes diverse aspects of RNA-Seq experiments: sequence quality, sequencing depth, strand specificity, GC bias, read distribution over the genome structure and coverage uniformity. (wikipedia.org)
  • conserved RNA secondary structure
  • On the basis of conserved RNA secondary structure with predicted high thermodynamic stability, putative structures were identified that contain splice sites in segment 8 of influenza B and segments 6 and 7 of influenza C. The sequence in segment 6 also contains three unused AUG start codon sites that are sequestered within a hairpin structure. (beds.ac.uk)
  • Conformation
  • In particular, influenza 3′ splice sites are predicted to form secondary structures that can switch conformation to regulate splicing. (beds.ac.uk)
  • Thus, these RNA structures present attractive targets for therapeutics aimed at targeting one or the other conformation. (beds.ac.uk)
  • Each conformation places important splicing regulatory sites in different structural environments, which has implications for the modulation of splicing of the segment 7 transcript. (wikipedia.org)
  • For example, the splice site, polypyrimidine tract, branch point, and ASF/SF2 exonic enhancer binding sites are expected to be more accessible in the hairpin conformation and less accessible in the pseudoknot (Figure 1). (wikipedia.org)
  • catalytic
  • Here, we identify a site of ubiquitination (K1246) in the catalytic subunit of RNAPII close to the DNA entry path. (elifesciences.org)
  • Most attention has focused on modifications of the regulatory C-terminal domain (CTD) of the large, catalytic subunit of RNAPII, which promote the ordered recruitment of numerous RNA packaging and processing factors to the nascent pre-mRNAs. (elifesciences.org)
  • regulatory
  • Matching genomic and transcriptomic data allows us to identify putative regulatory variants associated with changes in splicing patterns. (nih.gov)
  • Both pseudoknots have the possibility of alternating between hairpin loop and pseudoknot conformations, which place splicing regulatory motifs in different structural contexts. (wikipedia.org)
  • alternatively
  • Alternatively spliced introns are better conserved overall than are constitutively spliced introns (23), as is reflected by the enrichment in alternatively spliced introns (of 30%, P = 2 × 10-7) observed in the control set when splice sites were rewired (alternative to alternative and constitutive to constitutive). (nih.gov)
  • It may make it possible to perform CRISPR cutting on both RNA and DNA at once, or alternatively just on single-stranded messenger RNA without affecting genomic regions at all. (scoop.it)
  • U2AF
  • RNA-EMSA revealed that wild-type FECH requires U2AF(35) but wild-type LPL does not. (nih.gov)
  • genomes
  • Influenza A, B, and C viruses belong to the family Orthomyxoviridae and are characterized by segmented, single-stranded, negative-sense (−) RNA genomes. (beds.ac.uk)
  • Pseudoknots are commonly found in viral genomes, especially RNA viruses, where they incorporate an RNA splice site and can have a wide range of functions. (wikipedia.org)
  • vivo
  • B) RT-PCR of in vivo splicing assay performed in HEK293T transfected with the indicated minigenes, Flag-SRSF1 and increasing amounts of GFP-PTBP1. (nih.gov)