Riboseq ATLAS
First public query tool nuORFdb v1.0Every gene you know can also produce unexpected, shorter proteins from hidden reading frames. This tool lets you search which of these are actively translated in cancer — discovered by ribosome profiling (Ribo-seq), which captures ribosomes in the act of building proteins.
323,848 ORFs · 5 cancer / healthy cohorts · No other public query interface exists for this dataset · Ouspenskaia et al., Nat Biotechnol 2022 · GEO: GSE143263
What is Riboseq ATLAS? What can I find here? ▼
The core idea: Your genome encodes far more proteins than textbooks list. Beyond the ~20,000 known genes, cells — especially cancer cells — secretly translate thousands of additional short proteins from regions normally labelled "non-coding": upstream of genes, inside long non-coding RNAs, in alternative reading frames, and from pseudogenes.
How were they found? Ribosome profiling (Ribo-seq) freezes ribosomes mid-translation and sequences the mRNA they are reading. This directly proves a stretch of RNA is being turned into protein — not just transcribed. The authors applied this to cancer cell lines and patient tumours, then built nuORFdb: a catalogue of 323,848 actively translated ORFs.
Why does it matter? These hidden proteins can appear on the surface of cancer cells as neoantigens — targets the immune system (or a therapy) could recognise. Some are cancer-specific: present in tumours but absent in healthy tissue. This tool is the only public interface to query, filter, and download this dataset interactively.
Find all translated ORFs associated with any gene (e.g. TP53, EGFR, BRCA1)
Explore 5′ uORFs, lncRNA ORFs, out-of-frame, pseudogene-derived, and more
See RNA-seq expression in GBM, melanoma, CLL vs healthy tissues with boxplots
Ribo-seq TPM across 41 cell lines confirms the ORF is actively making protein
nuORFdb v1.0 — 323,848 ORFs
86,421 canonical (annotated)
237,427 novel unannotated (nuORF)
Source: ribosome profiling (Ribo-seq)
5′ uORF / 5′ Overlap uORF
3′ dORF / 3′ Overlap dORF
lncRNA-embedded
Out-of-Frame (alt reading frame)
Pseudogene-derived
Canonical (annotated CDS)
Cancer lines:
A375 (melanoma)
HCT116 (colon carcinoma)
B721.221 (92 HLA mono-allelic)
+ primary melanoma / GBM / CLL tumours
Healthy:
Primary melanocytes (Hmel rep1–3)
Active translation (ribosomes on mRNA). High TPM = actively translated in that cell line.
390 patient samples
21 healthy donor samples
172 tumour samples
473 tumour samples
777 samples across 31 tissue types
Ouspenskaia et al., Nat Biotechnol 2022.
GEO: GSE143263