The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Human P3R3URF (UniProt A0A087WWA1; gene symbol P3R3URF, HGNC:53451)

Executive summary

P3R3URF is described in the available tool-retrieved literature as an upstream open reading frame (uORF)/readthrough-associated entity located upstream of the canonical human gene PIK3R3. However, direct, P3R3URF-specific functional evidence is very limited in the accessible corpus: one study explicitly tested whether a higher-molecular-weight PIK3R3 immunoblot band reflected a P3R3URF–PIK3R3 readthrough product and found no detectable P3R3URF or P3R3URF–PIK3R3 transcripts by qRT-PCR in their neuronal model, favoring an alternative explanation (post-translational modification) for the band. Therefore, most downstream pathway conclusions from that study should be attributed to canonical PIK3R3 (p55γ) rather than P3R3URF. (tidball2023genomewidecrispriscreen pages 8-10, tidball2023genomewidecrispriscreen media aed70475)

Because of this evidence gap, the most defensible “functional annotation” at present is:
1) Identity: a putative uORF/readthrough-related product upstream of PIK3R3, distinct from PIK3R3 itself. (tidball2023genomewidecrispriscreen pages 8-10)
2) Evidence status: not robustly detected at transcript level in at least one relevant human neuronal system; no direct localization or biochemical activity data in the accessible sources. (tidball2023genomewidecrispriscreen pages 8-10)
3) Interpretation: if biologically relevant, P3R3URF may act primarily through uORF-mediated translational regulation or via a low-abundance/conditionally expressed peptide, consistent with broader 2023–2024 uORF and noncanonical ORF literature. (dasgupta2024upstreamopenreading pages 1-1, rodriguez2024evidenceforwidespread pages 1-1, yang2024widespreadstablenoncanonical pages 4-5)

1. Target verification: ensuring the correct gene/protein

1.1 Distinguishing P3R3URF from PIK3R3

In a genome-wide CRISPRi screen in human induced neurons (iNeurons), Tidball et al. report a higher-molecular-weight band on a PIK3R3 immunoblot that “fit with a known fusion readthrough protein from an open reading frame upstream of PIK3R3 called P3R3URF.” (bioRxiv preprint posted Dec 13, 2023; https://doi.org/10.1101/2023.12.13.571474). (tidball2023genomewidecrispriscreen pages 8-10)

Critically, the same study performed qRT-PCR assays intended to detect PIK3R3, P3R3URF–PIK3R3, and P3R3URF transcripts and reports that they only found detectable transcript for PIK3R3, leading them to interpret the second band as “possibly a post-translational modification.” (tidball2023genomewidecrispriscreen pages 8-10)

Thus, within accessible literature, P3R3URF appears only as a hypothesized upstream-ORF/readthrough product linked to PIK3R3, not as a separately characterized protein with independent functional annotation. (tidball2023genomewidecrispriscreen pages 8-10)

1.2 Evidence table for P3R3URF-specific claims

The following table separates what is experimentally supported in the accessible corpus from what remains speculative.

Table: This table summarizes what the available cited evidence does and does not support for human P3R3URF, clearly separating the putative upstream-ORF/readthrough annotation from experimentally demonstrated effects on canonical PIK3R3. It is useful for identity verification and for avoiding conflation with the PI3K regulatory subunit p55γ.

2. Key concepts and definitions (current understanding)

2.1 Upstream open reading frames (uORFs)

A uORF is a short open reading frame located in the 5′ untranslated region (5′ UTR; “leader sequence”) of an mRNA that initiates at a canonical AUG or non-AUG start codon and terminates upstream of—or overlapping—the main coding sequence. (dasgupta2024upstreamopenreading pages 1-1, dasgupta2024upstreamopenreading pages 1-3)

Transcriptome-wide methods have revealed ribosome occupancy outside canonical coding sequences, with uORF translation observed in upwards of ~25% of human protein-coding genes in recent summaries. (Dasgupta & Prensner, NAR Cancer, May 2024; https://doi.org/10.1093/narcan/zcae023). (dasgupta2024upstreamopenreading pages 1-1)

2.2 Mechanisms: regulation vs microprotein production

The dominant conceptual framework (2023–2024) is that uORFs can:
- Regulate translation of the downstream main coding sequence by capturing scanning ribosomes, altering reinitiation probability, or triggering mRNA surveillance such as nonsense-mediated decay (NMD), depending on uORF context and 5′ UTR structure. (dasgupta2024upstreamopenreading pages 3-3, dasgupta2024upstreamopenreading pages 3-4)
- In some cases, encode microproteins (small peptides/proteins) that can have biological functions; however, large-scale analyses indicate many upstream translation events may be unstable, lowly expressed, or non-functional (“noisy”) in aggregate. (rodriguez2024evidenceforwidespread pages 1-1, yang2024widespreadstablenoncanonical pages 4-5)

This duality is directly relevant to P3R3URF: the accessible evidence does not yet establish whether it corresponds to a stable protein product in specific tissues/conditions, so translational-regulatory interpretations remain plausible. (tidball2023genomewidecrispriscreen pages 8-10, rodriguez2024evidenceforwidespread pages 1-1)

3. P3R3URF: experimental evidence and what it implies

3.1 The Tidball et al. (2023) neuronal CRISPRi screen: what was tested

Tidball et al. used CRISPRi in human iNeurons to assess regulators of mTOR/S6 signaling and included PIK3R3 among validated hits. In immunoblots for on-target knockdown, they observed:
- 83% reduction in PIK3R3 protein abundance upon on-target perturbation. (tidball2023genomewidecrispriscreen pages 8-10)
- A second higher-molecular-weight band in the PIK3R3 blot that was reduced by the same perturbation, raising the possibility of a readthrough product (P3R3URF-related). (tidball2023genomewidecrispriscreen pages 8-10)
- By qRT-PCR, PIK3R3 mRNA reduced by 70%, but P3R3URF and P3R3URF–PIK3R3 transcripts were not detected in their assay. (tidball2023genomewidecrispriscreen pages 8-10)

The immunoblot evidence (Figure 3B) supporting the existence of a second band is shown here; importantly, the authors did not validate its identity by proteomics.

Figure evidence: PIK3R3 immunoblot showing the higher band discussed as possibly P3R3URF-readthrough. (tidball2023genomewidecrispriscreen media aed70475)

3.2 What the study does not establish about P3R3URF

From the standpoint of functional annotation for P3R3URF, the study does not provide:
- Direct demonstration of an expressed P3R3URF peptide/protein (e.g., mass spectrometry identification of a P3R3URF-unique peptide). (tidball2023genomewidecrispriscreen pages 8-10)
- Cellular localization (cytoplasm, nucleus, membranes, organelles) for a P3R3URF product. (tidball2023genomewidecrispriscreen pages 8-10)
- A biochemical function (enzyme activity, binding partners) specifically attributable to P3R3URF. (tidball2023genomewidecrispriscreen pages 8-10)

Therefore, any P3R3URF functional claims beyond “putative uORF/readthrough-associated product upstream of PIK3R3” would be speculative given the accessible evidence. (tidball2023genomewidecrispriscreen pages 8-10)

4. Recent developments (2023–2024) relevant to P3R3URF-class annotations

4.1 Evidence that many 5′UTR/uORF translation events are detectable but often weakly conserved

Rodriguez et al. (Nucleic Acids Research, Jul 2024; https://doi.org/10.1093/nar/gkae571) mined five large-scale proteomics datasets and searched against 3-frame translations of GENCODE 5′ UTRs.

Key quantitative results:
- They report 192 translated upstream regions (across 191 genes) supported by mass spectrometry, with 316 peptides mapped to these regions, and the majority representing in-frame N-terminal extensions (171/192). (rodriguez2024evidenceforwidespread pages 2-3, rodriguez2024evidenceforwidespread pages 5-6)
- They used stringent filtering to control false positives; at a conservative cutoff they estimated ~9–10 false positives among 316 peptides and required ≥2 PSM support per upstream region. (rodriguez2024evidenceforwidespread pages 3-4)
- They emphasize limited deep conservation for many upstream regions: “two thirds” of upstream reading frames not conserved beyond simians, and many start at non-canonical codons, supporting a model where a substantial fraction may be non-functional or “aberrant/noisy” translation, especially in cancer cell lines. (rodriguez2024evidenceforwidespread pages 1-1)

This provides an evidence-based context: even when upstream translation occurs, many events may not correspond to stable, conserved proteins, which is consistent with why a P3R3URF-like entity might be difficult to detect robustly. (rodriguez2024evidenceforwidespread pages 1-1, tidball2023genomewidecrispriscreen pages 8-10)

4.2 Predicting stability of noncanonical peptides (PepScore; 2024)

Yang et al. (Nature Communications, Mar 2024; https://doi.org/10.1038/s41467-024-46240-9) developed PepScore, a logistic regression model predicting the probability that a noncanonical ORF encodes a stable peptide.

Key quantitative and methodological details:
- PepScore’s major features: expected length, domain presence, and conservation (PhyloCSF), with overall reported AUROC ~0.944 and strong performance in identifying well-expressed peptides. (yang2024widespreadstablenoncanonical pages 4-5, yang2024widespreadstablenoncanonical pages 4-4)
- Using ribosome profiling across five species, they identify 58,383 noncanonical ORFs (ncORFs) in humans and report 4,812 ncORFs (13.3%) with PepScore > 0.6 (higher-confidence stability candidates). (yang2024widespreadstablenoncanonical pages 4-5, yang2024widespreadstablenoncanonical pages 1-2)
- They find noncanonical peptides are enriched for certain predicted localizations (e.g., 36.9% mitochondrial; 13.7% extracellular), indicating noncanonical products can populate diverse cellular compartments. (yang2024widespreadstablenoncanonical pages 4-5)
- They report that >80% of noncanonical peptides have low PepScores (<0.3), consistent with widespread translation that often yields unstable/undetectable products. (yang2024widespreadstablenoncanonical pages 5-6, yang2024widespreadstablenoncanonical pages 12-13)

Applied to P3R3URF: without a tool-accessible sequence record we cannot compute PepScore here, but this framework provides a state-of-the-art way to prioritize which uORF products are likely to be stable proteins versus primarily regulatory translation events. (yang2024widespreadstablenoncanonical pages 4-5, tidball2023genomewidecrispriscreen pages 8-10)

4.3 Method developments to detect microproteins: addressing Ribo-seq and proteomics limitations (2023–2024)

• Dasgupta & Prensner (NAR Cancer, May 2024) summarize uORFs as dual regulators and microprotein sources and note that uORF-derived peptides can be enriched on HLA-I; one estimate cited is that uORF peptides comprise ~7.5% of the immunopeptidome, which is relevant to real-world detection and immuno-oncology applications. (dasgupta2024upstreamopenreading pages 10-11)
• De Souza et al. (Nature Communications, Aug 2024; https://doi.org/10.1038/s41467-024-50301-4) identify a key limitation of Ribo-seq for smORFs: because footprints are short, >80% of reads can be unassigned due to multi-mapping, and featureCounts default parameters can leave ~90% unassigned in some settings. (souza2024rp3ribosomeprofilingassisted pages 3-5)
• Their Rp3 pipeline integrates proteogenomics + Ribo-seq evidence and reports, for example, 130 unannotated microproteins after excluding peptides matching annotated proteins, and 692 unannotated microproteins with strong HLA class I affinity in one analysis context. (souza2024rp3ribosomeprofilingassisted pages 2-3, souza2024rp3ribosomeprofilingassisted pages 5-7)
• Mohsen et al. (PROTEOMICS, Aug 2023; https://doi.org/10.1002/pmic.202100211) review that proteomic identification of microproteins is often based on only one tryptic peptide, and expanded search spaces inflate false positives, motivating careful database construction and FDR control. (mohsen2023microproteins—discoverystructureand pages 4-6)

Collectively, these 2023–2024 developments explain why P3R3URF-like microproteins are challenging to validate and why negative qRT-PCR and ambiguous immunoblot bands are common in early-stage characterization. (mohsen2023microproteins—discoverystructureand pages 4-6, tidball2023genomewidecrispriscreen pages 8-10, souza2024rp3ribosomeprofilingassisted pages 3-5)

5. Current applications and real-world implementations relevant to P3R3URF

Although there are no direct P3R3URF-targeted applications in the accessible evidence, uORF/microprotein research has multiple real-world implementations that could apply if P3R3URF translation is confirmed:

1) Variant interpretation in 5′UTRs/uORFs: uORF-creating/disrupting variants can modulate protein output and may contribute to disease mechanisms, motivating inclusion of 5′UTR/uORF annotations in genomic interpretation pipelines. (dasgupta2024upstreamopenreading pages 11-12)

2) Cancer immunopeptidomics/neoantigen discovery: uORF-derived peptides can appear on HLA-I and may constitute a nontrivial fraction of the immunopeptidome (~7.5% estimate), supporting exploration of noncanonical ORFs as tumor antigens. (dasgupta2024upstreamopenreading pages 10-11)

3) Proteogenomics pipelines for biopharma cell lines and impurity detection: improvements in noncanonical ORF annotation and microprotein detection have downstream relevance to identifying unexpected peptides/proteins in production contexts and in therapeutic products (conceptual link via 2024 method papers and the general push toward expanded ORF catalogs). (souza2024rp3ribosomeprofilingassisted pages 3-5)

6. Expert opinions and analysis (authoritative sources)

6.1 uORFs as major translational regulatory elements

Dasgupta & Prensner (2024) emphasize uORFs as “new players” in gene regulation, arguing that ribosome activity in 5′ leaders is common and functionally relevant in cancer, but that systematic cancer-wide studies remain incomplete—supporting a cautious interpretation of any single uORF/microprotein candidate until validated. (dasgupta2024upstreamopenreading pages 3-4)

6.2 Functionality vs translational noise

Rodriguez et al. (2024) argue that while translation from 5′ UTRs is widespread, many upstream regions are GC-rich, start from noncanonical codons, lack purifying selection, and are disproportionately detected in cancer cell lines—consistent with a substantial component of nonfunctional/aberrant initiation. (rodriguez2024evidenceforwidespread pages 1-1)

Yang et al. (2024) provide a complementary “stability prioritization” lens: the majority of noncanonical peptides are predicted to be low-stability (low PepScore), and they show experimentally that some peptides can be stabilized by proteasome/lysosome inhibition while very low-score peptides remain undetectable. (yang2024widespreadstablenoncanonical pages 6-8)

Applied to P3R3URF, these perspectives support an evidence-based stance that a putative P3R3URF protein product should not be assumed to exist or be stable without direct peptide-level validation. (tidball2023genomewidecrispriscreen pages 8-10, rodriguez2024evidenceforwidespread pages 1-1, yang2024widespreadstablenoncanonical pages 6-8)

7. What can be said today about P3R3URF function, pathways, and localization

7.1 Primary function

Unknown in the accessible corpus. The only P3R3URF-relevant study investigated whether a PIK3R3 immunoblot band could represent a P3R3URF readthrough product but did not detect P3R3URF transcripts and did not establish any P3R3URF-specific activity. (tidball2023genomewidecrispriscreen pages 8-10)

7.2 Cellular localization

Unknown for P3R3URF in the accessible corpus. Broader 2024 work indicates noncanonical peptides can localize to diverse compartments (e.g., mitochondrial enrichment reported for some classes), but this cannot be assigned to P3R3URF specifically without sequence- or experiment-based evidence. (yang2024widespreadstablenoncanonical pages 4-5)

7.3 Pathways

No pathway can be attributed to P3R3URF specifically with current evidence. Tidball et al. show that canonical PIK3R3 knockdown affects PI3K/AKT/mTOR/S6 signaling (e.g., increased AKT phosphorylation after PIK3R3 knockdown), but because P3R3URF transcripts were not detected, these results should be interpreted as PIK3R3 biology rather than P3R3URF biology. (tidball2023genomewidecrispriscreen pages 8-10, tidball2023genomewidecrispriscreen pages 10-12)

8. Recommended evidence needed for confident functional annotation (evidence-based guidance)

Based on 2023–2024 methodological consensus for microproteins/uORFs, P3R3URF functional annotation would require at least one of the following types of direct evidence:
- Peptide-level identification by mass spectrometry with stringent FDR control and ideally multiple peptides or orthogonal validation (Rodriguez 2024; Mohsen 2023). (rodriguez2024evidenceforwidespread pages 3-4, mohsen2023microproteins—discoverystructureand pages 4-6)
- Ribo-seq/TIS evidence showing consistent translation initiation at the P3R3URF start with strong periodicity and mapping confidence, including strategies to handle multi-mapping reads (Rp3 highlights the importance of this). (souza2024rp3ribosomeprofilingassisted pages 3-5, souza2024rp3ribosomeprofilingassisted pages 9-10)
- Genetic perturbation specifically targeting the P3R3URF ORF without perturbing PIK3R3 coding sequence and showing a phenotype rescued by supplying the microprotein in trans (a pattern used in microprotein validation literature as summarized in reviews). (dasgupta2024upstreamopenreading pages 11-12)

Limitations of this report

• Curated database annotations (UniProt/HGNC/Ensembl) for A0A087WWA1/P3R3URF were not retrievable within the tool-accessible corpus; thus, protein length, domains, isoforms, and predicted localization from those resources are not cited here.
• Direct P3R3URF-specific literature was sparse in retrieved sources; conclusions about P3R3URF are therefore necessarily cautious and largely limited to what Tidball et al. tested and concluded.

Key referenced sources (URLs and publication dates)

• Tidball AM et al. Genome-wide CRISPRi Screen in Human iNeurons to Identify Novel Focal Cortical Dysplasia Genes. bioRxiv (posted 2023-12-13). https://doi.org/10.1101/2023.12.13.571474 (tidball2023genomewidecrispriscreen pages 8-10)
• Dasgupta A, Prensner JR. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer (2024-05). https://doi.org/10.1093/narcan/zcae023 (dasgupta2024upstreamopenreading pages 1-1)
• Rodriguez JM et al. Evidence for widespread translation of 5′ untranslated regions. Nucleic Acids Research (2024-07). https://doi.org/10.1093/nar/gkae571 (rodriguez2024evidenceforwidespread pages 1-1)
• Yang H et al. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features. Nature Communications (2024-03). https://doi.org/10.1038/s41467-024-46240-9 (yang2024widespreadstablenoncanonical pages 1-2)
• de Souza EV et al. Rp3: Ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery. Nature Communications (2024-08). https://doi.org/10.1038/s41467-024-50301-4 (souza2024rp3ribosomeprofilingassisted pages 1-2)
• Mohsen JJ et al. Microproteins—Discovery, structure, and function. PROTEOMICS (2023-08). https://doi.org/10.1002/pmic.202100211 (mohsen2023microproteins—discoverystructureand pages 4-6)

References

1. (tidball2023genomewidecrispriscreen pages 8-10): Andrew M. Tidball, Jinghui Luo, J. Clayton Walker, Taylor N. Takla, Gemma L. Carvill, and Jack M. Parent. Genome-wide crispri screen in human ineurons to identify novel focal cortical dysplasia genes. bioRxiv, Dec 2023. URL: https://doi.org/10.1101/2023.12.13.571474, doi:10.1101/2023.12.13.571474. This article has 1 citations.

2. (tidball2023genomewidecrispriscreen media aed70475): Andrew M. Tidball, Jinghui Luo, J. Clayton Walker, Taylor N. Takla, Gemma L. Carvill, and Jack M. Parent. Genome-wide crispri screen in human ineurons to identify novel focal cortical dysplasia genes. bioRxiv, Dec 2023. URL: https://doi.org/10.1101/2023.12.13.571474, doi:10.1101/2023.12.13.571474. This article has 1 citations.

3. (dasgupta2024upstreamopenreading pages 1-1): Anwesha Dasgupta and John R. Prensner. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer, May 2024. URL: https://doi.org/10.1093/narcan/zcae023, doi:10.1093/narcan/zcae023. This article has 18 citations and is from a peer-reviewed journal.

4. (rodriguez2024evidenceforwidespread pages 1-1): Jose Manuel Rodriguez, Federico Abascal, Daniel Cerdán-Vélez, Laura Martínez Gómez, Jesús Vázquez, and Michael L Tress. Evidence for widespread translation of 5′ untranslated regions. Nucleic Acids Research, 52:8112-8126, Jul 2024. URL: https://doi.org/10.1093/nar/gkae571, doi:10.1093/nar/gkae571. This article has 9 citations and is from a highest quality peer-reviewed journal.

5. (yang2024widespreadstablenoncanonical pages 4-5): Haiwang Yang, Qianru Li, Emily K. Stroup, Sheng Wang, and Zhe Ji. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and orf features. Nature Communications, Mar 2024. URL: https://doi.org/10.1038/s41467-024-46240-9, doi:10.1038/s41467-024-46240-9. This article has 72 citations and is from a highest quality peer-reviewed journal.

6. (tidball2023genomewidecrispriscreen pages 12-15): Andrew M. Tidball, Jinghui Luo, J. Clayton Walker, Taylor N. Takla, Gemma L. Carvill, and Jack M. Parent. Genome-wide crispri screen in human ineurons to identify novel focal cortical dysplasia genes. bioRxiv, Dec 2023. URL: https://doi.org/10.1101/2023.12.13.571474, doi:10.1101/2023.12.13.571474. This article has 1 citations.

7. (tidball2023genomewidecrispriscreen pages 10-12): Andrew M. Tidball, Jinghui Luo, J. Clayton Walker, Taylor N. Takla, Gemma L. Carvill, and Jack M. Parent. Genome-wide crispri screen in human ineurons to identify novel focal cortical dysplasia genes. bioRxiv, Dec 2023. URL: https://doi.org/10.1101/2023.12.13.571474, doi:10.1101/2023.12.13.571474. This article has 1 citations.

8. (dasgupta2024upstreamopenreading pages 1-3): Anwesha Dasgupta and John R. Prensner. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer, May 2024. URL: https://doi.org/10.1093/narcan/zcae023, doi:10.1093/narcan/zcae023. This article has 18 citations and is from a peer-reviewed journal.

9. (dasgupta2024upstreamopenreading pages 3-3): Anwesha Dasgupta and John R. Prensner. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer, May 2024. URL: https://doi.org/10.1093/narcan/zcae023, doi:10.1093/narcan/zcae023. This article has 18 citations and is from a peer-reviewed journal.

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11. (rodriguez2024evidenceforwidespread pages 2-3): Jose Manuel Rodriguez, Federico Abascal, Daniel Cerdán-Vélez, Laura Martínez Gómez, Jesús Vázquez, and Michael L Tress. Evidence for widespread translation of 5′ untranslated regions. Nucleic Acids Research, 52:8112-8126, Jul 2024. URL: https://doi.org/10.1093/nar/gkae571, doi:10.1093/nar/gkae571. This article has 9 citations and is from a highest quality peer-reviewed journal.

12. (rodriguez2024evidenceforwidespread pages 5-6): Jose Manuel Rodriguez, Federico Abascal, Daniel Cerdán-Vélez, Laura Martínez Gómez, Jesús Vázquez, and Michael L Tress. Evidence for widespread translation of 5′ untranslated regions. Nucleic Acids Research, 52:8112-8126, Jul 2024. URL: https://doi.org/10.1093/nar/gkae571, doi:10.1093/nar/gkae571. This article has 9 citations and is from a highest quality peer-reviewed journal.

13. (rodriguez2024evidenceforwidespread pages 3-4): Jose Manuel Rodriguez, Federico Abascal, Daniel Cerdán-Vélez, Laura Martínez Gómez, Jesús Vázquez, and Michael L Tress. Evidence for widespread translation of 5′ untranslated regions. Nucleic Acids Research, 52:8112-8126, Jul 2024. URL: https://doi.org/10.1093/nar/gkae571, doi:10.1093/nar/gkae571. This article has 9 citations and is from a highest quality peer-reviewed journal.

14. (yang2024widespreadstablenoncanonical pages 4-4): Haiwang Yang, Qianru Li, Emily K. Stroup, Sheng Wang, and Zhe Ji. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and orf features. Nature Communications, Mar 2024. URL: https://doi.org/10.1038/s41467-024-46240-9, doi:10.1038/s41467-024-46240-9. This article has 72 citations and is from a highest quality peer-reviewed journal.

15. (yang2024widespreadstablenoncanonical pages 1-2): Haiwang Yang, Qianru Li, Emily K. Stroup, Sheng Wang, and Zhe Ji. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and orf features. Nature Communications, Mar 2024. URL: https://doi.org/10.1038/s41467-024-46240-9, doi:10.1038/s41467-024-46240-9. This article has 72 citations and is from a highest quality peer-reviewed journal.

16. (yang2024widespreadstablenoncanonical pages 5-6): Haiwang Yang, Qianru Li, Emily K. Stroup, Sheng Wang, and Zhe Ji. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and orf features. Nature Communications, Mar 2024. URL: https://doi.org/10.1038/s41467-024-46240-9, doi:10.1038/s41467-024-46240-9. This article has 72 citations and is from a highest quality peer-reviewed journal.

17. (yang2024widespreadstablenoncanonical pages 12-13): Haiwang Yang, Qianru Li, Emily K. Stroup, Sheng Wang, and Zhe Ji. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and orf features. Nature Communications, Mar 2024. URL: https://doi.org/10.1038/s41467-024-46240-9, doi:10.1038/s41467-024-46240-9. This article has 72 citations and is from a highest quality peer-reviewed journal.

18. (dasgupta2024upstreamopenreading pages 10-11): Anwesha Dasgupta and John R. Prensner. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer, May 2024. URL: https://doi.org/10.1093/narcan/zcae023, doi:10.1093/narcan/zcae023. This article has 18 citations and is from a peer-reviewed journal.

19. (souza2024rp3ribosomeprofilingassisted pages 3-5): Eduardo Vieira de Souza, Angie L. Bookout, Christopher A. Barnes, Brendan Miller, Pablo Machado, Luiz A. Basso, Cristiano V. Bizarro, and Alan Saghatelian. Rp3: ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery. Nature Communications, Aug 2024. URL: https://doi.org/10.1038/s41467-024-50301-4, doi:10.1038/s41467-024-50301-4. This article has 18 citations and is from a highest quality peer-reviewed journal.

20. (souza2024rp3ribosomeprofilingassisted pages 2-3): Eduardo Vieira de Souza, Angie L. Bookout, Christopher A. Barnes, Brendan Miller, Pablo Machado, Luiz A. Basso, Cristiano V. Bizarro, and Alan Saghatelian. Rp3: ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery. Nature Communications, Aug 2024. URL: https://doi.org/10.1038/s41467-024-50301-4, doi:10.1038/s41467-024-50301-4. This article has 18 citations and is from a highest quality peer-reviewed journal.

21. (souza2024rp3ribosomeprofilingassisted pages 5-7): Eduardo Vieira de Souza, Angie L. Bookout, Christopher A. Barnes, Brendan Miller, Pablo Machado, Luiz A. Basso, Cristiano V. Bizarro, and Alan Saghatelian. Rp3: ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery. Nature Communications, Aug 2024. URL: https://doi.org/10.1038/s41467-024-50301-4, doi:10.1038/s41467-024-50301-4. This article has 18 citations and is from a highest quality peer-reviewed journal.

22. (mohsen2023microproteins—discoverystructureand pages 4-6): Jessica J. Mohsen, Alina A. Martel, and Sarah A. Slavoff. Microproteins—discovery, structure, and function. PROTEOMICS, Aug 2023. URL: https://doi.org/10.1002/pmic.202100211, doi:10.1002/pmic.202100211. This article has 50 citations and is from a peer-reviewed journal.

23. (dasgupta2024upstreamopenreading pages 11-12): Anwesha Dasgupta and John R. Prensner. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer, May 2024. URL: https://doi.org/10.1093/narcan/zcae023, doi:10.1093/narcan/zcae023. This article has 18 citations and is from a peer-reviewed journal.

24. (yang2024widespreadstablenoncanonical pages 6-8): Haiwang Yang, Qianru Li, Emily K. Stroup, Sheng Wang, and Zhe Ji. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and orf features. Nature Communications, Mar 2024. URL: https://doi.org/10.1038/s41467-024-46240-9, doi:10.1038/s41467-024-46240-9. This article has 72 citations and is from a highest quality peer-reviewed journal.

25. (souza2024rp3ribosomeprofilingassisted pages 9-10): Eduardo Vieira de Souza, Angie L. Bookout, Christopher A. Barnes, Brendan Miller, Pablo Machado, Luiz A. Basso, Cristiano V. Bizarro, and Alan Saghatelian. Rp3: ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery. Nature Communications, Aug 2024. URL: https://doi.org/10.1038/s41467-024-50301-4, doi:10.1038/s41467-024-50301-4. This article has 18 citations and is from a highest quality peer-reviewed journal.

26. (souza2024rp3ribosomeprofilingassisted pages 1-2): Eduardo Vieira de Souza, Angie L. Bookout, Christopher A. Barnes, Brendan Miller, Pablo Machado, Luiz A. Basso, Cristiano V. Bizarro, and Alan Saghatelian. Rp3: ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery. Nature Communications, Aug 2024. URL: https://doi.org/10.1038/s41467-024-50301-4, doi:10.1038/s41467-024-50301-4. This article has 18 citations and is from a highest quality peer-reviewed journal.

Artifacts

• Edison artifact artifact-00
  

Citations

1. tidball2023genomewidecrispriscreen pages 8-10
2. dasgupta2024upstreamopenreading pages 1-1
3. rodriguez2024evidenceforwidespread pages 3-4
4. rodriguez2024evidenceforwidespread pages 1-1
5. yang2024widespreadstablenoncanonical pages 4-5
6. dasgupta2024upstreamopenreading pages 10-11
7. dasgupta2024upstreamopenreading pages 11-12
8. dasgupta2024upstreamopenreading pages 3-4
9. yang2024widespreadstablenoncanonical pages 6-8
10. yang2024widespreadstablenoncanonical pages 1-2
11. tidball2023genomewidecrispriscreen pages 12-15
12. tidball2023genomewidecrispriscreen pages 10-12
13. dasgupta2024upstreamopenreading pages 1-3
14. dasgupta2024upstreamopenreading pages 3-3
15. rodriguez2024evidenceforwidespread pages 2-3
16. rodriguez2024evidenceforwidespread pages 5-6
17. yang2024widespreadstablenoncanonical pages 4-4
18. yang2024widespreadstablenoncanonical pages 5-6
19. yang2024widespreadstablenoncanonical pages 12-13
20. https://doi.org/10.1101/2023.12.13.571474
21. https://doi.org/10.1093/narcan/zcae023
22. https://doi.org/10.1093/nar/gkae571
23. https://doi.org/10.1038/s41467-024-46240-9
24. https://doi.org/10.1038/s41467-024-50301-4
25. https://doi.org/10.1002/pmic.202100211
26. https://doi.org/10.1101/2023.12.13.571474,
27. https://doi.org/10.1093/narcan/zcae023,
28. https://doi.org/10.1093/nar/gkae571,
29. https://doi.org/10.1038/s41467-024-46240-9,
30. https://doi.org/10.1038/s41467-024-50301-4,
31. https://doi.org/10.1002/pmic.202100211,