Related Experiment Video
Updated: Dec 19, 2025

08:23
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
4.0K
IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites
Jian Zhao1, Yan Li2, Cong Wang1
1Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China.
Genomics, Proteomics & Bioinformatics
|June 9, 2020
Summary
IRESbase is a new database of experimentally validated internal ribosome entry sites (IRESs). It aids research into IRES function, especially in circular RNAs (circRNAs) and non-coding RNAs.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Internal ribosome entry sites (IRESs) mediate cap-independent translation initiation.
- IRES elements are crucial for translating RNAs lacking a 5' cap, such as circular RNAs (circRNAs).
- A centralized resource for experimentally validated IRES elements is needed.
Purpose of the Study:
- To create IRESbase, a comprehensive database of functional minimal IRES elements.
- To curate and annotate IRES elements and their host RNAs from scientific literature.
- To provide a valuable resource for researchers studying translation and RNA biology.
Main Methods:
- Systematic literature curation of experimentally validated IRES elements.
- Annotation of host linear and circular RNAs associated with IRES elements.
- Bioinformatic mapping of IRES sequences to human circRNAs and long non-coding RNAs (lncRNAs).
Main Results:
- IRESbase contains 1328 experimentally validated IRES elements (774 eukaryotic, 554 viral).
- The database includes IRESs from 11 eukaryotic organisms and 198 viruses.
- Mapping revealed 2191 circRNAs and 168 lncRNAs containing IRES sequences.
Conclusions:
- IRESbase provides a unique, curated collection of functional minimal IRES elements.
- The database facilitates the study of IRES-mediated translation in various RNA types, including circRNAs and lncRNAs.
- IRESbase serves as a valuable resource for advancing research in RNA biology and translation.
Related Concept Videos
Ribosome Profiling
4.0K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.0K
Directing Proteins to the Rough Endoplasmic Reticulum
16.3K
The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
16.3K
Leaky Scanning
5.5K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.5K
Ribosomes
73.7K
Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
73.7K
Ribosomes
9.8K
Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
9.8K
Ribosomal RNA Synthesis
14.4K
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
14.4K

