Spliceator: multi-species splice site prediction using convolutional neural networks

N Scalzitti, A Kress, R Orhand, T Weber, L Moulinier… - BMC …, 2021 - Springer
Background Ab initio prediction of splice sites is an essential step in eukaryotic genome
annotation. Recent predictors have exploited Deep Learning algorithms and reliable gene …

Sequence and evolutionary features for the alternatively spliced exons of eukaryotic genes

SY Chen, C Li, X Jia, SJ Lai - International Journal of Molecular Sciences, 2019 - mdpi.com
Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in
eukaryotes without requiring a considerable increase of genes in the number. Due to rapid …

Comprehensive discovery of salt-responsive alternative splicing events based on Iso-Seq and RNA-seq in grapevine roots

Z Jin, X Lv, Y Sun, Z Fan, G Xiang, Y Yao - Environmental and experimental …, 2021 - Elsevier
Alternative splicing (AS) can enhance the adaptive capacity of organisms to respond to
abiotic stresses via transcriptome plasticity; however, the mechanism underlying the …

The Nix locus on the male-specific homologue of chromosome 1 in Aedes albopictus is a strong candidate for a male-determining factor

LM Gomulski, M Mariconti, A Di Cosimo, F Scolari… - Parasites & vectors, 2018 - Springer
Background Global concern over the rapid expansion of the Asian tiger mosquito, Aedes
albopictus, and its vector competence has highlighted an urgent need to improve currently …

Transcriptome-Wide Detection of Intron/Exon Definition in the Endogenous Pre-mRNA Transcripts of Mammalian Cells and Its Regulation by Depolarization

L Liu, U Das, S Ogunsola, J Xie - International Journal of Molecular …, 2022 - mdpi.com
Pairing of splice sites across an intron or exon is the central point of intron or exon definition
in pre-mRNA splicing with the latter mode proposed for most mammalian exons. However …

Widespread separation of the polypyrimidine tract from 3′ AG by G tracts in association with alternative exons in metazoa and plants

H Nguyen, J Xie - Frontiers in genetics, 2019 - frontiersin.org
At the end of introns, the polypyrimidine tract (Py) is often close to the 3′ AG in a consensus
(Y) 20NC AG gt in humans. Interestingly, we have found that they could also be separated …

ESI mutagenesis: A one-step method for introducing point mutations into bacterial artificial chromosome transgenes

A Rondelet, A Pozniakovsky, M Leuschner, I Poser… - bioRxiv, 2019 - biorxiv.org
Bacterial artificial chromosome (BAC)-based transgenes have emerged as a powerful tool
for controlled and conditional interrogation of protein function in higher eukaryotes. While …

[图书][B] The Impact of Pre-mRNA Splice Site Selection on mRNA Stability and Splicing Fidelity in Methionine-Dependent Cancer Cells

FG Carranza - 2023 - search.proquest.com
Eukaryotic gene expression is an essential process for proper cell differentiation,
development, and the cell's response to environmental signals. Pre-mRNA splicing is an …

Genome-wide evolution of wobble base-pairing nucleotides of branchpoint motifs with increasing organismal complexity

H Nguyen, U Das, J Xie - RNA biology, 2020 - Taylor & Francis
How have the branchpoint motifs evolved in organisms of different complexity? Here we
identified and examined the consensus motifs (R1C2T3R4A5Y6, R: A or G, Y: C or T) of 898 …

ESI mutagenesis: a one-step method for introducing mutations into bacterial artificial chromosomes

A Rondelet, A Pozniakovsky… - Life science …, 2021 - life-science-alliance.org
Bacterial artificial chromosome (BAC)–based transgenes have emerged as a powerful tool
for controlled and conditional interrogation of protein function in higher eukaryotes. Although …