shRNA Designer

Use this program to design shRNA oligos. The design tool provides targets that have the greatest chance of knocking down your gene.

RefSeq Accession (e.g. NM_002529)

Min GC%

Max GC%

Method 1 (Ui-Tei) Method 2 (Matveeva) CDS Only Strict Parameters Custom Target Parsing

Or input custom nucleotide sequence / targets (one per line):

References:

1. Ui-tei K, Naito Y, Takahashi F, et al. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res. 2004;32(3):936-48.

2. Matveeva OV, Kang Y, Spiridonov AN, et al. Optimization of duplex stability and terminal asymmetry for shRNA design. PLoS ONE. 2010;5(4):e10180.

3. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.

4. Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014 Jan 1;42(1):D764-70.