Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for GUUCUCUAAACGAACUUUA (7 guide strand hits and 4 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_019051 | MRPL50 | 603 | 621 | G | U | U | C | U | C | U | A | A | A | C | c | c | A | C | U | U | U | u | 50 | 3 | 11 | false | <90% | 1027 | |||
| NM_016588 | NRN1 | 594 | 612 | G | U | U | C | U | C | U | A | A | A | C | u | A | A | C | U | a | U | u | 37 | 3 | 11 | false | <90% | 2072 | |||
| NM_021064 | HIST1H2AG | 498 | 516 | c | U | U | C | U | C | U | A | A | A | a | G | A | A | C | U | U | a | A | 34 | 3 | 9 | c | false | <90% | 2267 | ||
| NM_032169 | ACAD11 | 1439 | 1457 | a | c | U | C | U | C | c | A | A | A | C | G | A | A | C | U | U | U | c | 15 | 4 | 11 | bc | false | <90% | 3556 | ||
| NM_024675 | PALB2 | 1180 | 1198 | G | U | U | C | U | C | U | A | A | A | u | G | A | A | C | U | c | a | c | 7 | 4 | 10 | c | false | <90% | 4069 | ||
| NM_152270 | SLFN11 | 3083 | 3101 | G | U | U | u | U | C | U | A | A | A | g | G | A | A | C | U | U | U | A | 1 | 2 | 8 | c | false | <90% | 4915 | ||
| NM_144682 | SLFN13 | 3132 | 3150 | G | U | U | u | U | C | U | A | A | A | g | G | A | A | C | U | U | U | A | 1 | 2 | 8 | c | false | <90% | 8431 | ||
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_001042604 | XRN1 | 2503 | 2521 | U | g | A | A | G | U | U | C | G | U | c | U | A | G | A | G | A | A | a | 22 | 3 | 8 | c | false | <90% | 10053 | ||
| NM_019001 | XRN1 | 2503 | 2521 | U | g | A | A | G | U | U | C | G | U | c | U | A | G | A | G | A | A | a | 22 | 3 | 8 | c | false | <90% | 10092 | ||
| NM_199436 | SPAST | 3268 | 3286 | a | A | A | A | G | U | U | u | G | U | U | U | A | c | A | G | A | A | C | 16 | 3 | 6 | c | false | <90% | 5125 | ||
| NM_014946 | SPAST | 3364 | 3382 | a | A | A | A | G | U | U | u | G | U | U | U | A | c | A | G | A | A | C | 16 | 3 | 6 | c | false | <90% | 5221 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2709
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