UTRdb

UTRdb provides a curated repository of 5' and 3' untranslated regions (UTRs) of eukaryotic mRNAs with annotations of experimentally validated functional motifs, miRNA targets, and conserved sequence elements for studies of post-transcriptional regulation.

Key Features:

• Curated Data: Compiles 5' and 3' untranslated sequences for eukaryotic mRNAs from multiple primary data sources.
• Functional Motif Annotation: Annotates experimentally validated functional motifs within UTRs.
• UTRsite Integration: Links functional motifs to the UTRsite database with cross-references to interacting regulatory proteins.
• Gene-Centric Structure: Organizes entries around genes to represent 5' and 3' UTR variants arising from alternative transcription initiation and termination and alternative splicing.
• miRNA Target Annotation: Annotates experimentally validated microRNA (miRNA) targets within UTRs.
• Conserved Sequence Elements: Includes annotations of conserved sequence elements to identify evolutionarily preserved regulatory regions.

Scientific Applications:

• Post-transcriptional regulation analysis: Investigate how specific 5' or 3' UTR variants affect mRNA stability, translation efficiency, nucleo-cytoplasmic transport, and subcellular localization.
• miRNA–mRNA interaction studies: Analyze experimentally validated miRNA targets within UTRs to study miRNA-mediated regulation.
• Comparative regulatory element discovery: Explore conserved sequence elements across species to identify evolutionarily preserved regulatory regions.

Methodology:

Integration with genomic data and an annotation system is used to parse UTR sequences and annotate experimentally validated functional motifs, miRNA targets, and conserved sequence elements.