IRESite

IRESite curates a database of experimentally validated internal ribosome entry site (IRES) regions in eukaryotic viral and cellular RNAs to support analysis of translational regulation.

Key Features:

• Database content: Over 600 records of experimentally validated IRESs from eukaryotic viral and cellular RNAs.
• Curated experimental evidence: Entries are populated with experimentally validated data documenting IRES regions and their functional backgrounds.
• Annotations: Detailed annotations include RNA secondary structures and interactions with trans-acting factors (IRES-TAFs).
• Concluding evaluations: Each entry contains concluding remarks that synthesize experimental findings and evaluations of reported IRES functions.
• In-house analyses and plasmid verification: The resource incorporates in-house bioinformatic analyses and plasmid DNA verification by DNA sequencing and restriction endonuclease mapping.
• RNA secondary structure visualization: Computational visualization of RNA secondary structures for annotated IRESs.
• Structure search capability: Searchable repository of stored RNA secondary structures to support comparative analyses and motif identification.

Scientific Applications:

• Molecular biology: Investigating the role of IRES elements in viral replication and cellular translation processes.
• Structural biology: Analyzing RNA secondary structures to infer structural determinants of IRES function.
• Genomics and bioinformatics: Using curated experimental data for computational modeling and prediction of IRES activity.

Methodology:

In-house bioinformatic analyses include in silico replication of published cloning experiments and computational RNA secondary-structure visualization and structure-based searching.