short Open Reading Frame database

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short Open Reading Frame database

metasource: Fairsharing.org
version: FAIRsharing.org: sorfs.org; short Open Reading Frame database; DOI: https://doi.org/10.25504/FAIRsharing.x7pwnw; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

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sorfs.org

metasource: Fairsharing.org
version: FAIRsharing.org: sorfs.org; short Open Reading Frame database; DOI: https://doi.org/10.25504/FAIRsharing.x7pwnw; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

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sORFs

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:22.005651

metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:22.005651

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Other names: sorfs.org, sORFs

sORFs.org is a database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are provided, a default one enabling quick lookup of sORFs and a BioMart interface providing advanced query and export possibilities. At present, sORFs.org harbors 263 354 sORFs that demonstrate ribosome occupancy, originating from three different cell lines: HCT116 (human), E14_mESC (mouse) and S2 (fruit fly).

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Publications:

Publications

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sORFs.org: a repository of small ORFs identified by ribosome profiling
PMID: 26527729

metasource: Fairsharing.org
version: FAIRsharing.org: sorfs.org; short Open Reading Frame database; DOI: https://doi.org/10.25504/FAIRsharing.x7pwnw; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:22.005651

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http://dx.doi.org/10.1093/nar/gkv1175

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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http://dx.doi.org/10.1093/nar/gkx1130

metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:22.005651

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• sORFs.org: a repository of small ORFs identified by ribosome profiling PubMed citations: 50.

  50 articles citing: sORFs.org: a repository of small ORFs identified by ribosome profiling

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  An Rtn4/Nogo-A-interacting micropeptide modulates synaptic plasticity with age. PMID:35771867

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  Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures. PMID:35300685

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  Small Open Reading Frames, How to Find Them and Determine Their Function. PMID:35154250

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  Identification of Non-Canonical Translation Products in C. elegans Using Tandem Mass Spectrometry. PMID:34759956

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  Small Protein Enrichment Improves Proteomics Detection of sORF Encoded Polypeptides. PMID:34721520

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  Ion Mobility Coupled to a Time-of-Flight Mass Analyzer Combined With Fragment Intensity Predictions Improves Identification of Classical Bioactive Peptides and Small Open Reading Frame-Encoded Peptides. PMID:34604223

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  MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses. PMID:34156446

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  Improved Identification of Small Open Reading Frames Encoded Peptides by Top-Down Proteomic Approaches and De Novo Sequencing. PMID:34067398

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  Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics. PMID:33823297

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  Circular RNAs in Human Cancer. PMID:33537235

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  LncRNA-Encoded Peptide: Functions and Predicting Methods. PMID:33520729

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  The role of micropeptides in biology. PMID:33507325

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  Small Open Reading Frames: How Important Are They for Molecular Evolution? PMID:33193682

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  LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients. PMID:33112702

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  Elucidation of the Signatures of Proteasome-Catalyzed Peptide Splicing. PMID:33072102

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  A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation. PMID:32744504

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  Characterising the loss-of-function impact of 5' untranslated region variants in 15,708 individuals. PMID:32461616

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  PsORF: a database of small ORFs in plants. PMID:32333496

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  Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly. PMID:32161263

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  Emerging role of tumor-related functional peptides encoded by lncRNA and circRNA. PMID:32019587

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  Translated Long Non-Coding Ribonucleic Acid ZFAS1 Promotes Cancer Cell Migration by Elevating Reactive Oxygen Species Production in Hepatocellular Carcinoma. PMID:31781169

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  MiPepid: MicroPeptide identification tool using machine learning. PMID:31703551

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  ncRNA-Encoded Peptides or Proteins and Cancer. PMID:31526596

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  Coding or Noncoding, the Converging Concepts of RNAs. PMID:31178900

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  Bacterial sepsis triggers an antiviral response that causes translation shutdown. PMID:30507610

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  Alternative REST Splicing Underappreciated. PMID:30280122

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  PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. PMID:30049792

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  HRPDviewer: human ribosome profiling data viewer. PMID:30010738

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  The small peptide world in long noncoding RNAs. PMID:30010717

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  Public proteomics data: How the field has evolved from sceptical inquiry to the promise of in silico proteomics. PMID:29900110

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  Approaches to identify and characterize microProteins and their potential uses in biotechnology. PMID:29670998

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  Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. PMID:29626081

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  A comprehensive catalog of predicted functional upstream open reading frames in humans. PMID:29562350

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  De novo annotation and characterization of the translatome with ribosome profiling data. PMID:29538776

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  A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting. PMID:29433444

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  An update on sORFs.org: a repository of small ORFs identified by ribosome profiling. PMID:29140531

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  The functions and unique features of long intergenic non-coding RNA. PMID:29138516

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  Probably less than one-tenth of the genes produce only the wild type protein without at least one additional protein isoform in some human cancer cell lines. PMID:29137297

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  REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes. PMID:28977509

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  Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs. PMID:28825667

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  Mining for Micropeptides. PMID:28528987

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  An atlas of human long non-coding RNAs with accurate 5' ends. PMID:28241135

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  Insights into the mechanisms of eukaryotic translation gained with ribosome profiling. PMID:27923997

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  The orphan G protein-coupled receptor GPR139 is activated by the peptides: Adrenocorticotropic hormone (ACTH), α-, and β-melanocyte stimulating hormone (α-MSH, and β-MSH), and the conserved core motif HFRW. PMID:27916541

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  Drought stress differentially regulates the expression of small open reading frames (sORFs) in Arabidopsis roots and shoots. PMID:27471796

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  Nowhere to hide: unconventional translation yields cryptic peptides for immune surveillance. PMID:27319338

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  Incredible RNA: Dual Functions of Coding and Noncoding. PMID:27137091

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  Ribosome Footprint Profiling of Translation throughout the Genome. PMID:27015305

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  Translation from the 5' untranslated region shapes the integrated stress response. PMID:26823435

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  The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. PMID:26740669
• http://dx.doi.org/10.1093/nar/gkv1175
• http://dx.doi.org/10.1093/nar/gkx1130

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genome map

metasource: Fairsharing.org
version: FAIRsharing.org: sorfs.org; short Open Reading Frame database; DOI: https://doi.org/10.25504/FAIRsharing.x7pwnw; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

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ribosomal rna

metasource: Fairsharing.org
version: FAIRsharing.org: sorfs.org; short Open Reading Frame database; DOI: https://doi.org/10.25504/FAIRsharing.x7pwnw; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

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protein sequence databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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protein domain databases; protein classification

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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small molecules

metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:22.005651

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gene transcripts

metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:22.005651

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functional, regulatory and non-coding rna

metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:22.005651

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genome map ribosomal rna protein sequence protein domains and classification small molecule gene transcripts functional, regulatory and non-coding rna