sRNATarBase


NAR Molecular Biology Database Collection entry number 1832
Jiang Wang1, Tao Liu1, Bo Zhao1, Qixuan Lu1, Zheng Wang1, Yuan Cao2, Wuju Li1
1Beijing Institute of Basic Medical Sciences, Taiping Road 27, Haidian district, Beijing 100850, China 2Department of Laboratory Medicine, The 90th General Hospital of Jinan, Shifan Road 25, Jinan, Shandong, 250031, China

Database Description

Bacterial sRNAs are a class of small regulatory RNAs of about 40 – 500 nt in length, and play a variety of important roles in many biological processes through binding to their target mRNAs or proteins. With the application of high-throughput sequencing in sRNA discovery, more and more sRNAs are found. However, only targets of a little part of sRNAs have been elucidated. To facilitate sRNA functional studies such as developing sRNA target prediction models, we updated the database sRNATarBase to version 3.0, which was developed in 2010. The new version contains 611 sRNAtarget entries collected from 158 papers manually, 21276 predicted targets from sRNATarget, and 10486 predicted targets from sTarPicker. Among the 611 entries, there are 334 validated interactions and 247 binding regions. We also presented the detailed information for binding regions of sRNAtarget mRNA interactions and related mutation experiments, as well as the following new features, including NCBI sequence viewer, sRNA regulatory network, target prediction-based GO and pathway annotations, and error report system. Thus, the new version provides comprehensive annotation of validated sRNA-target interactions, which is a useful resource for sRNA functional studies.

Acknowledgements

This work was supported by grants from National Key Basic Research and Development Program (2010CB912801) and National Natural Science Foundation of China (31271404, 31071157, 31100960, 31471244).


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