Computational analysis of 3′-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat
J Yan, TG Marr - Genome research, 2005 - genome.cshlp.org
Alternative initiation, splicing, and polyadenylation are key mechanisms used by many
organisms to generate diversity among mature mRNA transcripts originating from the same …
organisms to generate diversity among mature mRNA transcripts originating from the same …
Predictive modeling of plant messenger RNA polyadenylation sites
Background One of the essential processing events during pre-mRNA maturation is the post-
transcriptional addition of a polyadenine [poly (A)] tail. The 3'-end poly (A) track protects …
transcriptional addition of a polyadenine [poly (A)] tail. The 3'-end poly (A) track protects …
Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation
J Mata - RNA biology, 2013 - Taylor & Francis
Regulatory elements in the 3′ untranslated regions (UTRs) of eukaryotic mRNAs influence
mRNA localization, translation, and stability. 3′-UTR length is determined by the location at …
mRNA localization, translation, and stability. 3′-UTR length is determined by the location at …
Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
Alternative polyadenylation (APA) enables a gene to generate multiple transcripts with
different 3′ ends, which is dynamic across different cell types or conditions. Many …
different 3′ ends, which is dynamic across different cell types or conditions. Many …
Fast-Find: a novel computational approach to analyzing combinatorial motifs
M Hamady, E Peden, R Knight, R Singh - BMC bioinformatics, 2006 - Springer
Background Many vital biological processes, including transcription and splicing, require a
combination of short, degenerate sequence patterns, or motifs, adjacent to defined …
combination of short, degenerate sequence patterns, or motifs, adjacent to defined …
Identification and characterization of polyadenylation signal (PAS) variants in human genomic sequences based on modified EST clustering
M Kamasawa, J Horiuchi - In silico biology, 2008 - content.iospress.com
A large-scale analysis of human polyadenylation signals was carried out in silico. The most
canonical AAUAAA hexamer and its 11 single-nucleotide variants that are most frequent in …
canonical AAUAAA hexamer and its 11 single-nucleotide variants that are most frequent in …
PAS-seq 2: A fast and sensitive method for global profiling of polyadenylated RNAs
Alternative polyadenylation (APA) is a widespread phenomenon in eukaryotes that
contributes to regulating gene expression and generating proteomic diversity. APA plays …
contributes to regulating gene expression and generating proteomic diversity. APA plays …
Identification of experimentally-supported poly (A) sites in single-cell RNA-seq data with SCINPAS
Y Moon, D Burri, M Zavolan - NAR genomics and bioinformatics, 2023 - academic.oup.com
Alternative polyadenylation is a main driver of transcriptome diversity in mammals,
generating transcript isoforms with different 3'ends via cleavage and polyadenylation at …
generating transcript isoforms with different 3'ends via cleavage and polyadenylation at …
Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing
Alternative cleavage and polyadenylation (APA) generates diverse mRNA isoforms. We
developed 3′ region extraction and deep sequencing (3′ READS) to address mispriming …
developed 3′ region extraction and deep sequencing (3′ READS) to address mispriming …
Alternative cleavage and polyadenylation: extent, regulation and function
The 3′ end of most protein-coding genes and long non-coding RNAs is cleaved and
polyadenylated. Recent discoveries have revealed that a large proportion of these genes …
polyadenylated. Recent discoveries have revealed that a large proportion of these genes …