AREsite

AREsite annotates AU-rich elements (ARE), GU-rich elements (GRE), and U-rich elements (URE) across transcriptomes of Homo sapiens, Mus musculus, Danio rerio, Caenorhabditis elegans, and Drosophila melanogaster to support analysis of their genomic context, RNA secondary structure, conservation, and RNA–protein interactions.

Key Features:

• Expanded Element Analysis: Annotates AU-rich elements, GU-rich elements, and U-rich elements across entire gene bodies, including 3' untranslated regions (UTRs) and introns.
• Multi-Species Support: Covers transcriptomic data for Homo sapiens, Mus musculus, Danio rerio, Caenorhabditis elegans, and Drosophila melanogaster.
• Genomic Contextualization: Provides genomic location and genic context for annotated motifs.
• RNA Secondary Structure Analysis: Includes data on local RNA secondary structure and stability surrounding annotated motifs.
• Conservation Data: Supplies conservation information for annotated motifs across species.
• Integration with Experimental Data: Integrates CLIP-Seq data to identify motifs with experimental evidence of RNA-binding protein interactions.
• REST Interface: Provides a REST interface for programmatic access and integration into custom workflows.

Scientific Applications:

• Post-transcriptional regulation: Supports analysis of post-transcriptional regulatory roles of AREs, GREs, and UREs.
• mRNA stability and decay: Facilitates study of mRNA stability and decay mechanisms associated with these motifs.
• Comparative conservation analysis: Enables cross-species comparison of motif conservation to infer functional importance.
• RNA–protein interaction mapping: Aids identification of motifs validated by CLIP-Seq to link sequence motifs to RNA-binding proteins.

Methodology:

Performs genome-wide scans to identify annotated motifs and locally stable RNA secondary structures across entire genes and incorporates CLIP-Seq datasets as experimental evidence.