NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants

Abstract

NONCODE (http://www.noncode.org/) is a comprehensive database of collection and annotation of noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. NONCODEV6 is dedicated to providing the full scope of lncRNAs across plants and animals. The number of lncRNAs in NONCODEV6 has increased from 548 640 to 644 510 since the last update in 2017. The number of human lncRNAs has increased from 172 216 to 173 112. The number of mouse lncRNAs increased from 131 697 to 131 974. The number of plant lncRNAs is 94 697. The relationship between lncRNAs in human and cancer were updated with transcriptome sequencing profiles. Three important new features were also introduced in NONCODEV6: (i) updated human lncRNA-disease relationships, especially cancer; (ii) lncRNA annotations with tissue expression profiles and predicted function in five common plants; iii) lncRNAs conservation annotation at transcript level for 23 plant species. NONCODEV6 is accessible through http://www.noncode.org/.

From “Dark Matter” to “Star”: Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs

“…However, until present, only a small number of these lncRNAs have been validated by the low-throughput experimental analysis. For example, Plant Long Non-Coding RNA Database version 2.0 (Jin et al, 2020 ) has 1,246,372 lncRNAs and predicted lncRNA targets in 80 species, and NONCODEV6 contains 94,697 lncRNAs in 23 plant species (Zhao et al, 2020 ). According to the experimentally validated functional lncRNA (EVLncRNA) predictions, nearly 30% of lncRNAs obtained by high-throughput sequencing have biological functions (Zhou et al, 2019 ).…”

Methylation and Noncoding RNAs in Gastric Cancer: Everything Is Connected

“…However, there are also several important differences, including shorter length with a smaller number of exons, lower expression level, much higher tissue-specificity, and absence of an open reading frame (ORF) [ 54 ]. The NONCODE database estimates 96,411 lncRNA genes and 173,112 lncRNA transcripts in the human genome [ 55 ].…”

RNAs as Regulators of Cellular Matchmaking

“…Estimates in the human genome suggest between 20 and 60k loci in the human genome transcribe lncRNA (Iyer et al, 2015;Hon et al, 2017), with over 170k distinct lncRNA transcripts now reported (Zhao et al, 2021). A considerable challenge in the field lies in discriminating transcriptional noise from functional lncRNA molecules that may act as scaffolds or decoys.…”