P-GRe: An efficient pipeline to maximised pseudogene prediction in plants/eucaryotes

S Cabanac, C Mathe, C Dunand - bioRxiv, 2023 - biorxiv.org
Formerly considered as part of" junk DNA", pseudogenes are nowadays known for their role
in the post-transcriptional regulation of functional genes. In addition, their identification …

Pseudogenes and their genome-wide prediction in plants

J Xiao, MK Sekhwal, P Li, R Ragupathy… - International Journal of …, 2016 - mdpi.com
Pseudogenes are paralogs generated from ancestral functional genes (parents) during
genome evolution, which contain critical defects in their sequences, such as lacking a …

Gauging the trends of pseudogenes in plants

N Garewal, N Goyal, S Pathania, J Kaur… - Critical Reviews in …, 2021 - Taylor & Francis
Pseudogenes, the debilitated parts of ancient genes, were previously scrapped off as junk or
discarded genes with no functional significance. Pseudogenes have come under scrutiny for …

GENCODE pseudogenes

C Sisu - Pseudogenes: Functions and Protocols, 2021 - Springer
Pseudogenes have long been considered nonfunctional elements. The influx of large-scale
sequencing projects over the last decade have provided rich sources of evidence that …

Current trends in pseudogene detection and characterization

EC Rouchka, IE Cha - Current Bioinformatics, 2009 - ingentaconnect.com
Pseudogenes are homologous relatives of known genes that have lost their ability to
function as a transcriptional unit. Three classes of pseudogenes are known to exist …

GENCODE pseudogenes

A Frankish, J Harrow - Pseudogenes: Functions and Protocols, 2014 - Springer
Historically pseudogenes were believed to represent nonfunctional genomic fossils;
however, there is emerging evidence that many of them could be biologically active. This …

Unravelling the due importance of pseudogenes and their resurrection in plants

S Yadav, G Kalwan, S Meena, SS Gill… - Plant Physiology and …, 2023 - Elsevier
The complexities of a genome are underpinned to the vast expanses of the intergenic
region, which constitutes∼ 97–98% of the genome. This region is essentially composed of …

Pseudogene. org: a comprehensive database and comparison platform for pseudogene annotation

JE Karro, Y Yan, D Zheng, Z Zhang… - Nucleic acids …, 2007 - academic.oup.com
The Pseudogene. org knowledgebase serves as a comprehensive repository for
pseudogene annotation. The definition of a pseudogene varies within the literature, resulting …

Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice

C Zou, MD Lehti-Shiu, F Thibaud-Nissen… - Plant …, 2009 - academic.oup.com
Pseudogenes (Ψ) are nonfunctional genomic sequences resembling functional genes.
Knowledge of Ψs can improve genome annotation and our understanding of genome …

Regulatory roles of novel small RNAs from pseudogenes

X Guo, D Zheng - Non Coding RNAs in Plants, 2011 - Springer
Arising from gene duplications or retrotranspositions, pseudogenes are genomic sequences
with high sequence similarity to functional genes but unable to encode the same type of …