Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for CAGUUCUCGAGUUCAUCUU (1 guide strand hits and 17 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_014048 | MKL2 | 1764 | 1782 | C | A | G | U | U | C | U | u | G | A | G | U | U | C | A | U | C | U | c | 32 | 2 | 10 | bc | false | <90% | 8680 | ||
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_203394 | E2F7 | 3699 | 3717 | A | A | G | A | U | G | A | A | C | U | C | u | A | G | A | A | C | U | c | 61 | 2 | 11 | false | <90% | 5742 | |||
| XM_001128206 | FLJ42986 | 122 | 140 | c | A | G | A | U | G | A | A | C | U | g | G | A | G | A | A | C | a | a | 29 | 4 | 9 | c | false | <90% | 1312 | ||
| NM_182945 | NIN | 5177 | 5195 | A | A | G | A | U | G | A | A | C | U | g | G | A | G | A | A | a | a | u | 7 | 4 | 10 | c | false | <90% | 6471 | ||
| NM_182946 | NIN | 5228 | 5246 | A | A | G | A | U | G | A | A | C | U | g | G | A | G | A | A | a | a | u | 7 | 4 | 10 | c | false | <90% | 6522 | ||
| NM_016350 | NIN | 5389 | 5407 | A | A | G | A | U | G | A | A | C | U | g | G | A | G | A | A | a | a | u | 7 | 4 | 10 | c | false | <90% | 6683 | ||
| NM_182944 | NIN | 5177 | 5195 | A | A | G | A | U | G | A | A | C | U | g | G | A | G | A | A | a | a | u | 7 | 4 | 10 | c | false | <90% | 6757 | ||
| NM_020921 | NIN | 5177 | 5195 | A | A | G | A | U | G | A | A | C | U | g | G | A | G | A | A | a | a | u | 7 | 4 | 10 | c | false | <90% | 10259 | ||
| NM_198889 | ANKRD17 | 2988 | 3006 | g | A | G | A | U | u | A | A | C | U | C | u | A | G | A | A | C | U | G | 0 | 3 | 7 | false | <90% | 8637 | |||
| NM_032217 | ANKRD17 | 3741 | 3759 | g | A | G | A | U | u | A | A | C | U | C | u | A | G | A | A | C | U | G | 0 | 3 | 7 | false | <90% | 9390 | |||
| NM_139246 | C9orf97 | 519 | 537 | g | A | G | A | U | G | A | c | C | U | g | G | A | G | A | A | C | U | G | -25 | 3 | 8 | c | false | <90% | 4445 | ||
| NM_001005374 | LRSAM1 | 751 | 769 | A | A | G | A | U | G | g | A | a | U | C | G | A | G | A | A | C | U | c | -31 | 3 | 9 | bc | false | <90% | 2884 | ||
| NM_001005373 | LRSAM1 | 1019 | 1037 | A | A | G | A | U | G | g | A | a | U | C | G | A | G | A | A | C | U | c | -31 | 3 | 9 | bc | false | <90% | 3152 | ||
| NM_138361 | LRSAM1 | 1053 | 1071 | A | A | G | A | U | G | g | A | a | U | C | G | A | G | A | A | C | U | c | -31 | 3 | 9 | bc | false | <90% | 3186 | ||
| XR_017685 | LOC284685 | 1211 | 1229 | A | A | G | A | U | G | A | A | C | a | a | G | A | G | A | A | C | U | G | -44 | 2 | 9 | c | false | <90% | 2197 | ||
| XR_019506 | LOC284685 | 1212 | 1230 | A | A | G | A | U | G | A | A | C | a | a | G | A | G | A | A | C | U | G | -44 | 2 | 9 | c | false | <90% | 2198 | ||
| NM_013986 | EWSR1 | 1253 | 1271 | A | A | G | A | U | G | A | A | C | a | a | G | A | G | A | A | C | U | G | -44 | 2 | 9 | c | false | <90% | 2425 | ||
| NM_005243 | EWSR1 | 1472 | 1490 | A | A | G | A | U | G | A | A | C | a | a | G | A | G | A | A | C | U | G | -44 | 2 | 9 | c | false | <90% | 2644 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3010
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)
No Immunostimulatory motif found (UGUGU).
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