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Alternative splicing

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ASlive: A database for alternative splicing atlas in livestock animals

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The precise regulation of alternative splicing is important in development and growth. Thus, the disruption of normal alternative splicing can lead to diseases such as cancers. Indeed, natural DNA variation that results in genetic variation in alternative splicing is. Part of the reason is the lack of a comprehensive annotation of alternative splicing in these agricultural species.

RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii

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RDAS for differential alternative splicing in roots. LDAS for differential alternative splicing in leaves. DAS genes related to salt stress response.. AS: Alternative splicing. DAS: Differential alternative splicing. Complexity of the alternative splicing landscape in plants. Genome-wide mapping of alternative splicing in Arabidopsis Thaliana. Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis.

Systematic evaluation of isoform function in literature reports of alternative splicing

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Search terms were: “functionally distinct splice isoforms”, “CRISPR alternative splicing”, “alterna- tive splicing knockdown” and “alternative splicing knockout.”

Differential isoform expression and alternative splicing in sex determination in mice

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Expansion of the eukaryotic proteome by alternative splicing. Temporal transcriptional profiling of somatic and germ cells reveals biased lineage priming of sexual fate in the fetal mouse gonad.. Transcriptomic analysis of mRNA expression and alternative splicing during mouse sex determination. Non-canonical and sexually dimorphic X dosage compensation states in the mouse and human germline. Epigenetic regulation of mouse sex determination by the histone demethylase Jmjd1a

Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant

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The tea plants were subjected to cold acclimation and de-acclimation with the treatments as follows: Ten well-grown plants were collected for treatments of non- acclimation (NA), CS (sampling after 10 °C for 6 h), CA1 (sampling after 10/4 °C, day/night for 7 days), and CA2 (sampling after 4/0 °C, day/night for another 7 days). 9 Regulation model of alternative splicing (AS) transcripts in cold acclimation. Characterization of alternative splicing.

Events of alternative splicing in head and neck cancer via RNA sequencing – an update

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MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. 2012;40:e61 Available from:. http://www.ncbi.nlm.nih.gov/pubmed/22266656.

Features of alternative splicing in stomach adenocarcinoma and their clinical implication: A research based on massive sequencing data

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Expansion of the eukaryotic proteome by alternative splicing. Hallmarks of alternative splicing in cancer. Survival-associated alternative splicing signatures in esophageal carcinoma. Global transcriptomic analysis identifies SERP INE1 as a prognostic biomarker associated with epithelial-to-mesenchymal transition in gastric cancer. An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer.

Gene expression and alternative splicing dynamics are perturbed in female head transcriptomes following heterospecific copulation

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Background: Despite the growing interest in the female side of copulatory interactions, the roles played by differential expression and alternative splicing mechanisms of pre-RNA on tissues outside of the reproductive tract have remained largely unknown. Here we addressed these questions in the context of con- vs heterospecific matings between Drosophila mojavensis and its sister species, D. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/..

Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala × Culter alburnus

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Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama. Results: Two reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects.

Identification of tumour immune microenvironment-related alternative splicing events for the prognostication of pancreatic adenocarcinoma

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Comprehensive characterization of the alternative splicing landscape in head and neck squamous cell carcinoma reveals novel events associated with. https://doi.org/10.7150/thno.36585.. https://doi.org/10.1 093/bioinformatics/bts452..

Alternative splicing associated with cancer stemness in kidney renal clear cell carcinoma

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We found that SASEs showed tumor heterogeneity and revealed the dynamic changes of alternative splicing in the tumor development in KIRC.. alternative splicing, suggesting splicing factors further regulate abnormal alternative splicing events.. Alternative splicing widely occurs in tumor samples and it has been proven to contribute to the generation of candidate neoantigens [15]. Here, we found that KIRC has shown a variety of specificities in alternative splicing.

Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure

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AS: Alternative splicing. Alternative splicing and the evolution of phenotypic novelty. A genomic view of alternative splicing. The Dscam homologue of the crustacean Daphnia is diversified by alternative splicing like in insects. Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity. Estimating rates of alternative splicing in mammals and invertebrates. Different levels of alternative splicing among eukaryotes.

Genome-wide profiling of the alternative splicing provides insights into development in Plutella xylostella

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Alternative splicing events. The genome-wide profiling of alternative splicing was performed using the assembled transcriptome by ASTALAVISTA algorithm and identified a total of 1804 genes showing AS events in DBM (Table 2).

Minor intron splicing revisited: Identification of new minor introncontaining genes and tissue-dependent retention and alternative splicing of minor introns

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Alternative splicing across minor introns is annotated in the Ensembl database. (B) Venn diagram showing the combined usage of AS events in annotated isoforms that are alternatively spliced across the minor introns. (C) Boxplots reflect the 5th – 95th percentile of minor intron length in minor introns that are and are not alternatively spliced.. Alternative splicing across minor introns in human tissues is dynamic. (A) Bubbleplot reflecting AS usage across minor introns in 8 human tissues.

TSVdb: A web-tool for TCGA splicing variants analysis

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Vials: Visualizing Alternative Splicing of Genes. https://doi.org/10.1109/TVCG . https://doi.org/10.1186/s z

Stress-mediated convergence of splicing landscapes in male and female rock doves

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The role of alternative splicing in the control of immune homeostasis and cellular differentiation

Genome-wide profiling of alternative splicing in glioblastoma and their clinical value

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A few key splicing factors may generate large-scale abnormal AS events. The expression levels of splicing factors were obtained from the TCGA database, and Spearman rank correlation ana- lysis was conducted between all splicing factor expres- sion levels and the PSI value of survival-related AS events (Cor >. Figure 5A illustrates that the network contains 94 splicing factors, 27 upregulated AS events and 27 downregulated AS events.

Alternative Polyadenylation in response to temperature stress contributes to gene regulation in Populus trichocarpa

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Analysis of alternative splicing and alternative polyadenylation in Populus alba var.

Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour

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Complexity of the alternative splicing landscape in plants

Systemic characterization of alternative splicing related to prognosis and immune infiltration in malignant mesothelioma

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The survival-related splicing regulatory network was established based on the correlation between survival-related AS events and splicing factors (SFs).. Results: A total of 3976 AS events associated with overall survival were identified by univariate Cox regression analysis, and ES events accounted for the greatest proportion. We constructed prognostic signatures based on survival-related AS events.