Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for AAUGUCCUGGAUCACACAG (6 guide strand hits and 9 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_015050 | KIAA0082 | 1189 | 1207 | u | u | U | G | U | C | C | U | G | G | A | U | a | A | C | A | C | A | G | 76 | 3 | 10 | false | <90% | 4030 | |||
| NM_032576 | CYorf15B | 2490 | 2508 | A | u | U | G | U | C | C | U | G | G | A | U | C | A | u | A | C | A | a | 58 | 3 | 12 | c | false | <90% | 5533 | ||
| NM_022064 | RNF123 | 366 | 384 | g | u | g | G | U | C | C | U | G | G | A | c | C | A | C | A | C | A | G | 33 | 4 | 8 | false | <90% | 4272 | |||
| NM_153754 | C21orf88 | 110 | 128 | c | c | U | G | U | C | C | U | G | G | g | U | C | A | C | A | C | A | G | 25 | 3 | 8 | c | false | <90% | 1088 | ||
| XR_015445 | LOC730773 | 718 | 736 | A | A | U | G | U | C | C | U | G | G | g | U | C | A | C | A | a | g | u | 7 | 4 | 10 | c | false | <90% | 866 | ||
| XR_015348 | LOC728179 | 718 | 736 | A | A | U | G | U | C | C | U | G | G | g | U | C | A | C | A | a | g | u | 7 | 4 | 10 | c | false | <90% | 866 | ||
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_006238 | PPARD | 939 | 957 | C | U | u | U | G | U | G | A | U | C | C | A | c | G | A | C | A | U | c | 65 | 3 | 9 | false | <90% | 3734 | |||
| NM_000583 | GC | 1153 | 1171 | g | U | G | U | G | U | G | A | U | C | C | A | G | G | A | a | A | c | a | 64 | 4 | 14 | c | false | <90% | 1801 | ||
| NM_015137 | KIAA0143 | 908 | 926 | C | c | a | U | G | U | G | A | U | C | C | A | G | G | A | g | A | U | U | 42 | 3 | 12 | c | false | <90% | 5148 | ||
| NM_004603 | STX1A | 840 | 858 | C | U | G | U | G | U | G | A | U | C | C | u | G | G | g | C | A | U | c | 36 | 3 | 11 | false | <90% | 2117 | |||
| NM_021933 | IIP45 | 569 | 587 | C | U | G | g | G | U | G | A | U | C | C | A | G | G | A | C | c | c | c | 32 | 4 | 12 | c | false | <90% | 1588 | ||
| NM_133373 | PLCD3 | 1114 | 1132 | g | U | G | U | G | U | G | u | U | C | C | A | G | G | A | C | A | U | g | 30 | 3 | 10 | bc | false | <90% | 3477 | ||
| NM_016312 | WBP11 | 615 | 633 | C | a | u | U | u | U | G | A | U | C | C | A | G | G | A | C | A | U | U | 17 | 3 | 14 | bc | false | <90% | 2690 | ||
| NM_030918 | SNX27 | 1624 | 1642 | u | c | a | U | G | U | G | A | g | C | C | A | G | G | A | C | A | U | U | 6 | 4 | 10 | bc | false | <90% | 7085 | ||
| NM_015567 | SLITRK5 | 565 | 583 | C | a | a | U | G | U | u | A | U | C | C | A | G | G | A | C | A | U | U | 2 | 3 | 12 | bc | false | <90% | 4461 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1619
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 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