Ribo-uORF

Ribo-uORF catalogs and analyzes upstream open reading frames (uORFs) and upstream translation initiation sites (uTIS) using ribosome profiling (Ribo-seq) and quantitative translation initiation sequencing (QTI-seq) data to support studies of translational regulation across human, mouse, rat, zebrafish, fruit fly, and worm.

Key Features:

• Extensive Data Repository: Aggregates 1495 Ribo-seq datasets and 77 QTI-seq datasets across human, mouse, rat, zebrafish, fruit fly, and worm.
• Identification of uORFs and uTIS: Identifies 501,554 actively translated uORFs and 107,914 upstream translation initiation sites (uTIS).
• Integrated Genomic Annotations: Maps cis-regulatory elements, genetic variations, expression quantitative trait loci (eQTLs), genome-wide association study (GWAS) associations, RNA modifications, and RNA editing to uORFs.
• mRNAbrowse visualization: Provides mRNAbrowse for integrated visualization of uORFs and associated genomic features.
• uORFscan: Enables precise identification of uORFs from user-uploaded datasets.
• UTR5var: Analyzes the impact of genetic mutations on uORFs.

Scientific Applications:

• Translation and posttranscriptional regulation studies: Enables analysis of how uORFs modulate downstream coding sequence (CDS) translation and posttranscriptional gene expression control.
• Genetic variation impact analysis: Supports exploration of how genetic variants, eQTLs, and GWAS associations affect uORF-mediated translational regulation.
• Multi-species uORF research: Facilitates comparative analysis of uORF translation across human, mouse, rat, zebrafish, fruit fly, and worm.

Methodology:

Aggregates 1495 Ribo-seq and 77 QTI-seq datasets to identify translated uORFs and uTIS (501,554 uORFs and 107,914 uTIS), provides uORFscan for uORF identification from user data, UTR5var for mutation-impact analysis, and mRNAbrowse for visualization of cis-regulatory elements, genetic variations, eQTLs, GWAS associations, RNA modifications, and RNA editing.