BLOCK-iT™ RNAi Designer

The easiest way to design effective RNAi molecules for great results
See also:
Synthetics for in vivo RNAi
 Target Design Options:  Stealth RNAi™ siRNA miR RNAi shRNA siRNA to Stealth RNAi™ siRNA siRNA to shRNA
Step 1: Enter an accession number or provide a nucleotide sequence
Accession number:
Nucleotide sequence: Enter only A, C, G, T, and U. See the online Help for additional information
Step 2: If you entered an accession number in Step 1, select regions for target design
Open reading frame (ORF)
5' UTR
3' UTR
Step 3: Choose database for Blast
  NOTE: BLAST is used to compare input sequence with sequences in the database to find unique regions against which to design RNAi targets. The databases contain representative gene sequences for that species. Blast databases were updated on March 23, 2013 and the design output reflects the most up-to-date designs.
Step 4: Choose minimum and maximum G/C percentage
Minimum G/C percentage: Maximum G/C percentage:  
Step 5: Select vector and strand orientation and click "RNAi Design" to design shRNA.
Vector:   NOTE:Choose pENTR™/H1/TO for inducible shRNA expression and pENTR™/U6 for constitutive expression. If you want to design shRNA oligo compatible with both vectors, select pENTR™/U6 vector.
Strand orientation:  
Guarantee: The BLOCK-iT™ Designer uses a proprietary algorithm to design shRNA with the latest resesarch data to optimize for promoter requirements and stem-loop structure. The recommended shRNA sequences designed using the BLOCK-iT™ RNAi Designer have an improved probability over random picking of inducing target gene silencing. However, more than one shRNA may need to be tested for a given gene.