Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for GUUGUCAAUAUGCUAAAAC (9 guide strand hits and 8 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_207490 | FLJ45721 | 571 | 589 | G | U | U | G | U | C | A | A | c | A | U | G | C | U | A | A | u | A | a | 11 | 3 | 8 | c | false | <90% | 2509 | ||
| NM_207662 | ZC3H14 | 1629 | 1647 | G | U | U | G | U | C | A | u | U | A | U | u | C | U | A | A | A | A | a | 0 | 3 | 7 | false | <90% | 3018 | |||
| NM_207661 | ZC3H14 | 2274 | 2292 | G | U | U | G | U | C | A | u | U | A | U | u | C | U | A | A | A | A | a | 0 | 3 | 7 | false | <90% | 3663 | |||
| NM_207660 | ZC3H14 | 2287 | 2305 | G | U | U | G | U | C | A | u | U | A | U | u | C | U | A | A | A | A | a | 0 | 3 | 7 | false | <90% | 3676 | |||
| NM_024824 | ZC3H14 | 2750 | 2768 | G | U | U | G | U | C | A | u | U | A | U | u | C | U | A | A | A | A | a | 0 | 3 | 7 | false | <90% | 4139 | |||
| XM_926158 | LOC642443 | 353 | 371 | u | U | U | G | U | C | u | A | U | A | U | c | C | U | A | A | A | A | C | -2 | 3 | 7 | false | <90% | 2331 | |||
| XM_936495 | LOC647346 | 353 | 371 | u | U | U | G | U | C | u | A | U | A | U | c | C | U | A | A | A | A | C | -2 | 3 | 7 | false | <90% | 2625 | |||
| NM_172240 | WDR51B | 2299 | 2317 | G | U | U | u | U | C | A | g | U | A | U | G | C | U | A | A | A | A | a | -3 | 3 | 10 | bc | false | <90% | 2984 | ||
| NM_024783 | AGBL2 | 1064 | 1082 | a | U | U | G | U | C | A | A | c | u | U | G | C | U | A | A | A | A | C | -44 | 3 | 9 | bc | false | <90% | 3411 | ||
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_001025356 | TMEM16F | 5500 | 5518 | a | U | U | U | U | A | G | C | A | U | A | U | U | G | A | a | A | c | a | 64 | 4 | 14 | c | false | <90% | 5987 | ||
| NM_020774 | MIB1 | 6055 | 6073 | a | U | U | U | U | A | G | C | A | U | A | U | U | G | A | a | A | u | g | 64 | 4 | 14 | c | false | <90% | 9308 | ||
| NM_153220 | MGC35440 | 782 | 800 | G | U | U | U | c | A | G | C | A | U | A | U | U | G | A | C | c | A | g | 20 | 3 | 11 | c | false | <90% | 2298 | ||
| XM_929706 | LOC653781 | 3749 | 3767 | a | g | c | U | U | A | G | C | A | U | g | U | U | G | A | C | A | A | C | 5 | 4 | 8 | c | false | <90% | 3826 | ||
| XM_001130062 | LOC728378 | 3912 | 3930 | a | g | c | U | U | A | G | C | A | U | g | U | U | G | A | C | A | A | C | 5 | 4 | 8 | c | false | <90% | 3989 | ||
| XM_928585 | LOC653269 | 3912 | 3930 | a | g | c | U | U | A | G | C | A | U | g | U | U | G | A | C | A | A | C | 5 | 4 | 8 | c | false | <90% | 3989 | ||
| NM_022965 | FGFR3 | 3051 | 3069 | u | U | U | U | U | A | a | C | u | U | A | U | U | G | A | C | A | A | C | -28 | 3 | 10 | bc | false | <90% | 3757 | ||
| NM_000142 | FGFR3 | 3387 | 3405 | u | U | U | U | U | A | a | C | u | U | A | U | U | G | A | C | A | A | C | -28 | 3 | 10 | bc | false | <90% | 4093 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1802
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