biostudies-literatureUnknown23(Suppl 3)Fahmi N<h4>Background</h4> The eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3′-untranslated region (3′-UTR) of mRNA produces transcripts with shorter or longer 3′-UTR. Often, 3′-UTR serves as a binding platform for microRNAs and RNA-binding proteins, which affect the fate of the mRNA transcript. Thus, 3′-UTR APA is known to modulate translation and provides a mean to regulate gene expression at the post-transcriptional level. Current bioinformatics pipelines have limited capability in profiling 3′-UTR APA events due to incomplete annotations and a low-resolution analyzing power: widely available bioinformatics pipelines do not reference actionable polyadenylation (cleavage) sites but simulate 3′BMC bioinformaticshttps://www.ebi.ac.uk/biostudies/studies/S-EPMC9520800biostudies-literatureAPA-Scan: detection and visualization of 3′-UTR alternative polyadenylation with RNA-seq and 3′-end-seq dataPMC9520800Zhang WFahmi NYong JAhmed KChang JNassereddeen HFan DfalseAPA-Scan: detection and visualization of 3′-UTR alternative polyadenylation with RNA-seq and 3′-end-seq data<h4>Background</h4> The eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3′-untranslated region (3′-UTR) of mRNA produces transcripts with shorter or longer 3′-UTR. Often, 3′-UTR serves as a binding platform for microRNAs and RNA-binding proteins, which affect the fate of the mRNA transcript. Thus, 3′-UTR APA is known to modulate translation and provides a mean to regulate gene expression at the post-transcriptional level. Current bioinformatics pipelines have limited capability in profiling 3′-UTR APA events due to incomplete annotations and a low-resolution analyzing power: widely available bioinformatics pipelines do not reference actionable polyadenylation (cleavage) sites but simulate 3′2022-01-01T00:00:00Z2022 Jan2025-05-29T22:02:11.281Z2025-05-29T22:02:11.281ZS-EPMC9520800