ArticleNucleic acids research2016
sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Bacterial small RNAs and extracellular vesicles in inflammatory and osteoimmune diseases: regulatory mechanisms and host-microbe communication.Archives of microbiology · 2026Review
- FungiSNC: An integrated database for fungi small non-coding RNAs based on high-throughput sequencing.Journal of advanced research · 2026Article
- GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions.BMC bioinformatics · 2025Article
- Plant miRNAs influence soil bacterial growth and amino acid uptake, restructuring community composition.ISME communications · 2025Article
- Article
- TargetRNA3: predicting prokaryotic RNA regulatory targets with machine learning.Genome biology · 2023Article
- RNA interaction format: a general data format for RNA interactions.Bioinformatics (Oxford, England) · 2023Article
- sInterBase: a comprehensive database of Escherichia coli sRNA-mRNA interactions.Bioinformatics (Oxford, England) · 2023Article
- CsrA Shows Selective Regulation of sRNA-mRNA Networks.bioRxiv : the preprint server for biology · 2023Article
- CsrA selectively modulates sRNA-mRNA regulator outcomes.Frontiers in molecular biosciences · 2023Article
- Review
- sRNARFTarget: a fast machine-learning-based approach for transcriptome-wide sRNA target prediction.RNA biology · 2022Article
- RNA Sequencing Unveils Very Small RNAs With Potential Regulatory Functions in Bacteria.Frontiers in molecular biosciences · 2022Article
- Recent Research Advances in Small Regulatory RNAs in Streptococcus.Current microbiology · 2021Review
- An Integrated Database of Small RNAs and Their Interplay With Transcriptional Gene Regulatory Networks in Corynebacteria.Frontiers in microbiology · 2021Article
- Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation.eLife · 2020Article
- RNAInter in 2020: RNA interactome repository with increased coverage and annotation.Nucleic acids research · 2020Article
- Stochastic Analysis Demonstrates the Dual Role of Hfq in ChaperoningFrontiers in molecular biosciences · 2020Article
- Characterization of novel small RNAs (sRNAs) contributing to the desiccation response ofRNA biology · 2019Article
- Article
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7 authors.
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Abstract
Bacterial sRNAs are a class of small regulatory RNAs of about 40-500 nt in length; they play multiple biological roles through binding to their target mRNAs or proteins. Therefore, elucidating sRNA targets is very important. However, only targets of a few sRNAs have been described. To facilitate sRNA functional studies such as developing sRNA target prediction models, we updated the sRNATarBase database, which was initially developed in 2010. The new version (recently moved to http://ccb1.bmi.ac.cn/srnatarbase/) contains 771 sRNA-target entries manually collected from 213 papers, and 23 290 and 11 750 predicted targets from sRNATarget and sTarPicker, respectively. Among the 771 entries, 475 and 17 were involved in validated sRNA-mRNA and sRNA-protein interactions, respectively, while 279 had no reported interactions. We also presented detailed information for 316 binding regions of sRNA-target mRNA interactions and related mutation experiments, as well as new features, including NCBI sequence viewer, sRNA regulatory network, target prediction-based GO and pathway annotations, and error report system. The new version provides a comprehensive annotation of validated sRNA-target interactions, and will be a useful resource for bacterial sRNA studies.
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