ArticleBMC bioinformatics2021
SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 21 citations in OpenAlex.
- PKR engages viral RNA and intron-retained host transcripts during poxvirus infection.Cell reports · 2026Article
- Nucleotide resolution 4-thiouridine sequencing by SNU-Seq and sf4sU-Seq reveals the transcriptional responsiveness of an epigenetically primed human genome.Nucleic acids research · 2026Article
- Efficient co-transcriptional splicing enforces rapid microexon definition and inclusion by SRRM4.bioRxiv : the preprint server for biology · 2026Article
- Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib.Science advances · 2026Article
- The exon junction complex coordinates the cotranscriptional inclusion of blocks of neighboring exons.Genes & development · 2026Article
- Reduced Cas9 transgene silencing by incorporation of intron sequences.Nature communications · 2025Article
- Global impact of unproductive splicing on human gene expression.Nature genetics · 2024Article
- Metabolic labeling based methylome profiling enables functional dissection of histidine methylation in C3H1 zinc fingers.Nature communications · 2024Article
- LINE-1 transcription activates long-range gene expression.Nature genetics · 2024Article
- A systematic screen identifies Saf5 as a link between splicing and transcription in fission yeast.PLoS genetics · 2024Article
- Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation.Molecular cell · 2023Article
- Global impact of aberrant splicing on human gene expression levels.bioRxiv : the preprint server for biology · 2023Article
- Inefficient splicing of long non-coding RNAs is associated with higher transcript complexity in human and mouse.RNA biology · 2023Article
- Introns: the "dark matter" of the eukaryotic genome.Frontiers in genetics · 2023Review
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Authors and funding
5 authors at 5 institutions in 3 countries.
Funding
Abstract
backgroundIntrons are generally removed from primary transcripts to form mature RNA molecules in a post-transcriptional process called splicing. An efficient splicing of primary transcripts is an essential step in gene expression and its misregulation is related to numerous human diseases. Thus, to better understand the dynamics of this process and the perturbations that might be caused by aberrant transcript processing it is important to quantify splicing efficiency.
resultsHere, we introduce SPLICE-q, a fast and user-friendly Python tool for genome-wide SPLICing Efficiency quantification. It supports studies focusing on the implications of splicing efficiency in transcript processing dynamics. SPLICE-q uses aligned reads from strand-specific RNA-seq to quantify splicing efficiency for each intron individually and allows the user to select different levels of restrictiveness concerning the introns' overlap with other genomic elements such as exons of other genes. We applied SPLICE-q to globally assess the dynamics of intron excision in yeast and human nascent RNA-seq. We also show its application using total RNA-seq from a patient-matched prostate cancer sample.
conclusionsOur analyses illustrate that SPLICE-q is suitable to detect a progressive increase of splicing efficiency throughout a time course of nascent RNA-seq and it might be useful when it comes to understanding cancer progression beyond mere gene expression levels. SPLICE-q is available at: https://github.com/vrmelo/SPLICE-q.
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