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lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...

piRNA - Piwi-interacting RNAs

piRNA - Piwi-interacting RNAs

PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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Related Experiment Video

Updated: Apr 20, 2026

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

Published on: January 21, 2020

PNRD: a plant non-coding RNA database.

Xin Yi¹, Zhenhai Zhang¹, Yi Ling¹

¹State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.

Nucleic Acids Research

|November 16, 2014

Summary

This summary is machine-generated.

The plant ncRNA database (PNRD) now offers comprehensive data on 11 non-coding RNA types across 150 species. This updated platform enhances plant research with improved usability and extensive data for agronomic trait discovery.

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A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

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Published on: January 21, 2020

mRNA Interactome Capture from Plant Protoplasts

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RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs

Published on: July 11, 2020

Area of Science:

Plant biology
Genomics
Bioinformatics

Background:

Non-coding RNAs (ncRNAs) play crucial roles in various biological processes.
Research on plant ncRNAs primarily focuses on improving agronomic traits.
The predecessor Plant miRNA Database (PMRD) was established in 2010 to support plant miRNA research.

Purpose of the Study:

To develop an updated and enhanced platform for plant ncRNA research.
To consolidate and expand upon existing plant ncRNA data.
To provide a user-friendly, comprehensive resource for fundamental research on plant ncRNAs.

Main Methods:

Construction of the Plant ncRNA Database (PNRD) based on PMRD.
Collection and integration of diverse plant ncRNA data, including miRNA targets and expression profiles.
Incorporation of user-friendly features and prevalent bioinformatics toolkits.

Main Results:

PNRD now contains 25,739 entries of 11 ncRNA types from 150 plant species.
Data includes 178,138 miRNA-target pairs and 35 miRNA expression profiles.
The platform features a more user-friendly interface, enhanced browsing, and downloadable background data.

Conclusions:

PNRD serves as a valuable, one-stop resource for plant ncRNA research.
The database facilitates fundamental research and the utilization of public resources for agronomic improvement.
Continuous updates and integrated tools strengthen PNRD's capability for scientific users.