RibORF-DB: comprehensive catalogs of translated open reading frames (ORFs) from Ribosome profiling

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Example: SLC35A4, ATF4
RibORF-DB: comprehensive catalogs of translated open reading frames (ORFs) from Ribosome profiling

Ribosome profiling has revealed dozens of functional peptides in putative ‘noncoding’ regions and raised the question of how many proteins are encoded by noncanonical open reading frames (ORFs) and how many peptides are stable with biological functions. Our recent study comprehensively annotated genome-wide translated ORFs across five eukaryote species, which was based on a large cohort of published ribosome profiling datasets and high-quality reads showing strong 3-nt periodicity. For the first time, we developed a logistic regression model, PepScore, to calculate the peptide functional probability in humans. In ncORF, we will deliver a comprehensive list of ORFs annotated in human and mouse species. ncORFs expect to provide a valuable resource and a quantitative guide for future functional characterization of noncanonical peptides during development and disease, leading to biological insights that offer avenues for the development of promising new therapies.

References

  1. Ji, Z., Song, R., Regev, A. & Struhl, K. Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins. eLife 4, e08890 (2015).
  2. Ji, Z. RibORF: Identifying Genome-Wide Translated Open Reading Frames Using Ribosome Profiling. Curr Protoc Mol Biol 124, e67 (2018).
  3. xxx(2023).

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