Genetic regulation of organisms involves complicated RNA–RNA interactions (RRIs) among messenger RNA (mRNA), microRNA (miRNA), and long non-coding (lncRNA). Detecting RRIs is beneficial for discovering biological mechanisms as well designing new drugs. In recent years, with more experimentally verified being deposited into databases, statistical machine learning, especially deep-learning-based ...

Impairment of RNA editing at a handful of coding sites causes severe disorders, prompting the view that coding RNA editing is highly advantageous. Recent genomic studies have expanded the list of human coding RNA editing sites by more than 100 times, raising the question of how common advantageous RNA editing is. Analyzing 1,783 human coding A-to-G editing sites, we show that both the frequency...

The simian virus 40 (SV40)-associated small RNA (SAS-RNA), approximately 64 nucleotides, is virally encoded within a region of the viral late (+) DNA strand which encodes no known protein. The SAS-RNA arises in abundance late in SV40 lytic infection. Previous data indicate that the synthesis of the SAS-RNA may be under the control of the normal late viral promoter; i.e., inhibition of transcrip...

The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. The TAIR10 annotation update had a profound impact on Arabidopsis research but was...

Emerging evidence implicates that a large fraction of human genome was transcribed but the transcripts known as long non coding RNA are not translated into proteins. They are contributing in different cellular processes, including cellular proliferation and apoptosis. LncRNAs were found to play critical roles in many diseases and act as key regulators in malignancies. In this study, we investig...

Precise interpretation of the transcriptome sequences in the several species showed that the major part of genome has been transcribed; however, just a few amounts of the transcription sequences have open-reading frames which are conversed during the evolution. So, it is unlikely that many of the transcribed sequences code the proteins. Among the all human non-coding transcripts, at least 10000...