Welcome to sRNAPrimerDB

sRNAPrimerDB is a comprehensive web primer or probe design tool specifically for small non-coding RNAs (sncRNAs), such as microRNA (miRNA, 20-25 nts), PIWI-interacting RNA (piRNA, 24-32 nts), short interfering RNA (siRNA, 20-25 nts), etc.

sRNAPrimerDB allows users to design several types of primers including generic or specific reverse transcription primers (Linear poly(T) RT primers, Linear S-poly(T) RT primers, stem-loop RT primers, stem-loop poly(A) RT primers, stem-loop poly(T) RT primers, Stem-loop S-poly(T) RT primers), specific PCR forward and reverse primer pairs, double hairpin probe, hybridization oligos for nine methods, such as:

Detailed experimental procedures for each method can be found in the protocol page. In addition, sRNAPrimerDB is also a primers bank, which contains tens of thousands of primer pairs for detecting miRNAs and piRNAs. Primers for sncRNAs that have been experimentally validated are encouraged to submit an online application form by visiting our web site at or www.srnaprimerdb.com.

If you make use of the data presented here, please cite the following article in addition to the primary data sources:

Shengsong Xie, Qin Zhu, Wubin Qu, Zhong Xu, Xiangdong Liu, Xinyun Li, Shijun Li, Wubin Ma, Yiliang Miao, Lisheng Zhang, Xiaoyong Du, Wuzi Dong, Haiwei Li, Changzhi Zhao, Yunlong Wang, Yaping Fang* and Shuhong Zhao*. sRNAPrimerDB: Comprehensive primer design and search web service for small non-coding RNAs. Bioinformatics, 2018, Doi:10.1093/bioinformatics/bty852.

user's manual

Organism Summary


Total 223
Metazoa 115
Viridiplantae 73
Viruses 29
Chromalveolata 5
Mycetozoa 1

Specials Summary


Total 100639
human 23373
mouse 38165
rat 38378
Drosophila melanogaster 723

Primer Summary

Total 531306 2941669
Method A 83243 413387
Method B 58724 411326
Method C 56710 409004
Method D 82309 414237
Method E 82309 398067
Method F 56710 409004
Method G 40585 184724
Method H 47145 201281
Method I 23571 100639

Latest update: 7/2018
Current version: 1.0