| URL: | http://www.shenglilabs.com/LncPep |
| Full name: | the lncRNA coding peptides database |
| Description: | LncPep provides annotations for lncRNAs, peptides and supporting evidence. LncPep totally covers 10,580,228 peptides translated from 883,804 lncRNAs across 39 different species. It provides 7 evidence including Mass Spectrometry, ribosome profiling, Pfam, translation initiation site, N6-methyladenosine modification of RNA sites, CPC2, and CPAT for users to explore and evaluated the predicted peptides. |
| Year founded: | 2021 |
| Last update: | |
| Version: | v1.0 |
| Accessibility: |
Accessible
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| Country/Region: | China |
| Data type: | |
| Data object: | |
| Database category: | |
| Major species: | |
| Keywords: |
| University/Institution: | Shanghai Jiao Tong University |
| Address: | Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China |
| City: | Shanghai |
| Province/State: | |
| Country/Region: | China |
| Contact name (PI/Team): | Shengli Li |
| Contact email (PI/Helpdesk): | shengli.li@shsmu.edu.cn |
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LncPep: A Resource of Translational Evidences for lncRNAs. [PMID: 35141219]
Long noncoding RNAs (lncRNAs) are a type of transcript that is >200 nucleotides long with no protein-coding capacity. Accumulating studies have suggested that lncRNAs contain open reading frames (ORFs) that encode peptides. Although several noncoding RNA-encoded peptide-related databases have been developed, most of them display only a small number of experimentally validated peptides, and resources focused on lncRNA-encoded peptides are still lacking. We used six types of evidence, coding potential assessment tool (CPAT), coding potential calculator v2.0 (CPC2), N6-methyladenosine modification of RNA sites (m6A), Pfam, ribosome profiling (Ribo-seq), and translation initiation sites (TISs), to evaluate the coding potential of 883,804 lncRNAs across 39 species. We constructed a comprehensive database of lncRNA-encoded peptides, LncPep (http://www.shenglilabs.com/LncPep/). LncPep provides three major functional modules: 1) user-friendly searching/browsing interface, 2) prediction and BLAST modules for exploring novel lncRNAs and peptides, and 3) annotations for lncRNAs, peptides and supporting evidence. Taken together, LncPep is a user-friendly and convenient platform for discovering and investigating peptides encoded by lncRNAs. |