Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for CUCUGUGUAUGGAGACACA (5 guide strand hits and 10 sense strand hits.)
Hits to Guide strand
| Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
| NM_052880 | PIK3IP1 | 1161 | 1179 | g | U | C | U | G | U | G | g | A | U | G | G | A | G | A | C | A | g | u | 28 | 4 | 9 | c | false | <90% | 2443 | ||
| NM_002198 | IRF1 | 995 | 1013 | C | U | C | U | G | U | c | U | A | U | G | G | A | G | A | C | u | u | u | 2 | 4 | 9 | c | false | <90% | 2035 | ||
| NM_148955 | SNX1 | 6997 | 7015 | C | U | C | U | G | U | c | U | u | U | G | G | A | G | A | C | A | C | u | -31 | 3 | 9 | bc | false | <90% | 8026 | ||
| NM_152826 | SNX1 | 7048 | 7066 | C | U | C | U | G | U | c | U | u | U | G | G | A | G | A | C | A | C | u | -31 | 3 | 9 | bc | false | <90% | 8077 | ||
| NM_003099 | SNX1 | 7192 | 7210 | C | U | C | U | G | U | c | U | u | U | G | G | A | G | A | C | A | C | u | -31 | 3 | 9 | bc | false | <90% | 8221 | ||
Hits to Sense strand
| Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
| NM_182579 | C1orf157 | 252 | 270 | a | c | a | G | U | C | U | C | C | A | U | A | C | A | C | A | G | A | c | 62 | 4 | 15 | bc | false | <90% | 1510 | ||
| NM_004688 | NMI | 982 | 1000 | U | G | U | u | U | C | U | C | C | A | U | A | C | A | C | A | G | A | a | 58 | 2 | 14 | bc | false | <90% | 1426 | ||
| XR_019332 | LOC649777 | 2349 | 2367 | U | G | U | G | U | C | U | C | C | A | U | g | C | A | C | A | u | g | c | 35 | 4 | 11 | false | <90% | 2829 | |||
| XR_017181 | LOC643778 | 2349 | 2367 | U | G | U | G | U | C | U | C | C | A | U | g | C | A | C | A | u | g | c | 35 | 4 | 11 | false | <90% | 2829 | |||
| XR_016866 | LOC283155 | 2027 | 2045 | U | G | U | G | U | C | U | C | C | A | U | g | C | A | C | A | u | g | c | 35 | 4 | 11 | false | <90% | 3014 | |||
| XR_018777 | LOC283155 | 2027 | 2045 | U | G | U | G | U | C | U | C | C | A | U | g | C | A | C | A | u | g | c | 35 | 4 | 11 | false | <90% | 3015 | |||
| NM_004329 | BMPR1A | 2666 | 2684 | U | G | U | G | U | C | U | C | C | A | U | g | C | A | C | A | u | g | c | 35 | 4 | 11 | false | <90% | 3631 | |||
| NM_078628 | MSL3L1 | 2905 | 2923 | a | G | U | G | U | C | U | C | C | A | g | A | C | A | C | A | G | u | G | 34 | 3 | 9 | c | false | <90% | 3564 | ||
| NM_002336 | LRP6 | 4846 | 4864 | a | c | c | u | U | C | U | C | C | A | U | A | C | A | C | A | G | A | G | 30 | 4 | 15 | bc | false | <90% | 5301 | ||
| NM_001080113 | PP8961 | 2091 | 2109 | U | G | U | G | U | g | U | C | C | A | U | A | C | A | C | A | u | u | a | 5 | 4 | 10 | c | false | <90% | 2596 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4085
View matched accessions
3 prime seed match details
Immunostimulatory motif search results
UGUGU - Judge et al. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol. 2005 Apr;23(4):457-62. (PMID: 15778705)
Motif found in guide strand
Motif found in sense strand
GUCCUUCAA - Hornung et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med. 2005 Mar;11(3):263-70. Epub 2005 Feb 20. (PMID: 15723075)
No Immunostimulatory motif found (GUCCUUCAA).
Settings used for search
Scores were calculated using scoring scheme SS1
Using AVG scoring mode.
Hit scores
| Parameter | Spec. Score cut-off | Colour | Comment |
| Hit to same gene | Colour | Hits to the same accession or genes with 100 percent identity (i.e. likely transcript variants). It is advisable to always check the genes hit. | |
| High scoring hit | ≥80 | Colour | Hits are very likely to cause an off-target effect |
| Medium scoring hit | <80¸≥40 | Colour | Hits with a small chance of causing an off target effect. |
| Low scoring hit | Colour | Hits very unlikely to cause an off-target effect |
The mismatches are colour coded based on the weighting of that position.
| Cut-off | Colour |
| Match | Colour |
| Wobble base pairs (G-U) | Colour |
| Critical bases (none) | Colour |
| 0.6 bits | Colour |
| 0.4 bits | Colour |
| 0.2 bits | Colour |
SpecificityServer is designed to help you identify potential non-specific matches to your siRNA. It incorporates the latest information about non-specific matches (sequence-specific only).
Designed by: Alistair Chalk, Quan Du, Zicai Liang and Erik L.L. Sonnhammer