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  • genome
  • MapSplice - map RNA-seq data to reference genome for splice junction discovery. (github.com)
  • Using data for more than 4,000 cancer patients from The Cancer Genome Atlas (TCGA project), a team led by Eduardo Eyras, ICREA research professor at the Department for Experimental and Health Sciences of the Pompeu Fabra University (DCEXS-UPF), has analyzed the changes in alternative splicing that occur in each tumor patient and studied how these changes could impact the function of genes. (eurekalert.org)
  • Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. (jcvi.org)
  • Alternative splicing (AS) can add significantly to genome complexity. (plantphysiol.org)
  • EST pairs gapped alignment was first evaluated in Arabidopsis ( Arabidopsis thaliana ), rice ( Oryza sativa ), and tomato ( Solanum lycopersicum ) for which annotated genome sequence is available and was shown to accurately predict splicing events. (plantphysiol.org)
  • undergo
  • We identified 95 AS events that undergo robust splicing transitions during C2C12 differentiation. (nih.gov)
  • Western analyses demonstrated that several splicing regulators undergo dynamic changes in nuclear abundance during differentiation. (nih.gov)
  • B ) The number of splicing events (out of 117 total validated events) that undergo splicing transitions of ≥20 percentage points. (nih.gov)
  • occurs
  • Variation of the splicing process occurs during tumor progression and may play a major role in tumorigenesis. (hindawi.com)
  • regulators
  • Computational analyses revealed enrichment of many sequence motifs within the upstream and downstream intronic regions near the alternatively spliced regions corresponding to binding sites of splicing regulators. (nih.gov)
  • In addition to describing the cis -acting RNA elements on the pre-mRNA molecules that respond to changes of intracellular calcium levels, we will summarize how splicing regulators change and affect alternative splicing in this process. (frontiersin.org)
  • biological
  • However, each gene can lead to several RNA molecules through alternative splicing, an essential mechanism for multiple biological processes that can be altered in disease conditions. (eurekalert.org)
  • However, regulated splicing changes are likely to be important in biological transitions such as cellular differentiation, or response to environmental stimuli. (nih.gov)
  • patterns
  • The majority of splicing transitions during C2C12 differentiation fall into four temporal patterns and were dependent on the myogenic program, suggesting that they are integral components of myogenic differentiation. (nih.gov)
  • RNA splicing patterns in antibody-secreting cells are shaped by endoplasmic reticulum stress, ELL2 (eleven-nineteen lysine-rich leukemia gene 2) induction, and changes in the levels of snRNA s. (mdpi.com)
  • large-scale changes in mRNA content and splicing patterns result. (mdpi.com)
  • Inhibition of the mRNA-degradation function of Ire1 is correlated with further differences in the splicing patterns and a reduction in the mRNA factors for snRNA transcription. (mdpi.com)