Automatic recommendation
Not OK - siRNA is not specific
13 hits were found for UAUGACUAUGUCAUAUUCA (5 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 | |||||||||||||
| XM_001129340 | LOC284952 | 1336 | 1354 | U | u | U | G | A | C | U | A | U | G | U | C | A | U | A | U | U | u | u | 80 | 3 | 15 | ac | false | <90% | 3218 | ||
| XM_001126137 | LOC284952 | 1336 | 1354 | U | u | U | G | A | C | U | A | U | G | U | C | A | U | A | U | U | u | u | 80 | 3 | 15 | ac | false | <90% | 3218 | ||
| NM_014741 | KIAA0652 | 819 | 837 | c | A | U | G | A | a | U | A | U | G | U | C | A | U | A | U | U | a | u | 27 | 4 | 11 | c | false | <90% | 4043 | ||
| NM_007007 | CPSF6 | 131 | 149 | U | A | U | G | A | C | g | A | U | G | U | C | A | U | A | U | c | u | c | 2 | 4 | 9 | c | false | <90% | 3426 | ||
| NM_178496 | C3orf59 | 1962 | 1980 | U | A | U | u | A | C | U | A | U | u | U | C | A | U | A | U | U | C | u | -24 | 3 | 8 | bc | false | <90% | 3381 | ||
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 | |||||||||||||
| XM_938233 | LOC649163 | 415 | 433 | a | G | A | A | U | A | U | G | A | C | A | U | A | u | U | C | A | a | u | 70 | 4 | 12 | c | false | <90% | 1228 | ||
| XM_497450 | LOC441722 | 415 | 433 | a | G | A | A | U | A | U | G | A | C | A | U | A | u | U | C | A | a | u | 70 | 4 | 12 | c | false | <90% | 1228 | ||
| NM_001001740 | RFWD2 | 1528 | 1546 | U | G | A | A | U | A | U | G | A | C | A | c | u | G | U | C | A | U | c | 50 | 3 | 11 | false | <90% | 2729 | |||
| NM_022457 | RFWD2 | 1600 | 1618 | U | G | A | A | U | A | U | G | A | C | A | c | u | G | U | C | A | U | c | 50 | 3 | 11 | false | <90% | 2801 | |||
| NM_006580 | CLDN16 | 1279 | 1297 | a | G | A | u | U | A | U | G | A | C | A | U | A | G | U | a | A | U | A | 35 | 3 | 11 | c | false | <90% | 1494 | ||
| NM_003802 | MYH13 | 257 | 275 | g | G | A | A | a | A | U | G | A | C | A | a | A | G | U | C | A | U | A | 12 | 3 | 7 | false | <90% | 5992 | |||
| NM_152529 | GPR155 | 3094 | 3112 | U | G | A | A | U | A | U | a | A | u | A | U | A | G | U | C | A | U | c | -49 | 3 | 8 | bc | false | <90% | 7324 | ||
| NM_001033045 | GPR155 | 3243 | 3261 | U | G | A | A | U | A | U | a | A | u | A | U | A | G | U | C | A | U | c | -49 | 3 | 8 | bc | false | <90% | 7473 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1544
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