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:
OR
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
Human - Homo sapiens
Mouse - Mus musculus
Rat - Rattus norvegicus
Cattle - Bos taurus
Pig - Sus scrofa
Dog - Canis familiaris
Frog - Xenopus laevis
Chicken - Gallus gallus
Fruitfly - Drosophila melanogaster
Worm - Caenorhabditis elegans
Zebrafish - Danio rerio
Mosquito - Anopheles gambiae
No 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:
20%
25%
30%
35%
40%
45%
50%
55%
60%
65%
70%
75%
80%
85%
90%
Maximum G/C percentage:
20%
25%
30%
35%
40%
45%
50%
55%
60%
65%
70%
75%
80%
85%
90%
Step 5: Select vector and strand orientation and click "RNAi Design" to design shRNA.
Vector:
pENTR™/H1/T0
pENTR™/U6
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:
Sense-loop-antisense
Antisense-loop-sense
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.
