Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
28 hits were found for AUUGGAUACAGAAAGAGAC (19 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_152506 | C21orf129 | 1553 | 1571 | u | U | U | G | G | A | U | A | C | A | G | A | c | A | u | A | G | A | C | 62 | 3 | 11 | false | <90% | 2033 | |||
| NM_000375 | UROS | 529 | 547 | c | c | U | G | G | A | U | A | C | A | G | A | A | g | G | A | G | A | a | 62 | 4 | 11 | c | false | <90% | 1279 | ||
| NM_003637 | ITGA10 | 1552 | 1570 | A | U | U | G | G | A | U | A | C | A | G | A | u | A | G | g | G | A | u | 58 | 3 | 12 | false | <90% | 5189 | |||
| NM_000927 | ABCB1 | 4033 | 4051 | u | c | U | G | G | A | U | A | C | A | G | A | A | A | G | u | G | A | a | 55 | 4 | 13 | c | false | <90% | 4872 | ||
| NM_183238 | ZNF605 | 3665 | 3683 | A | U | U | a | G | A | U | A | C | A | G | A | A | A | a | A | G | A | a | 33 | 3 | 10 | c | false | <90% | 6238 | ||
| NM_002740 | PRKCI | 1128 | 1146 | A | U | U | G | G | g | U | A | C | A | G | A | c | A | G | A | G | A | a | 21 | 3 | 6 | false | <90% | 4884 | |||
| NM_016323 | HERC5 | 1271 | 1289 | u | c | U | G | G | A | U | A | a | A | G | A | A | A | G | A | G | A | a | 21 | 4 | 9 | bc | false | <90% | 3525 | ||
| NM_006342 | TACC3 | 395 | 413 | u | c | U | G | G | A | c | A | C | A | G | A | A | A | G | A | G | A | a | 15 | 4 | 11 | bc | false | <90% | 2788 | ||
| NM_004487 | GOLGB1 | 1053 | 1071 | u | g | U | G | G | A | a | A | C | A | G | A | A | A | G | A | G | A | g | 15 | 4 | 11 | bc | false | <90% | 11185 | ||
| NM_031886 | KCNA7 | 2991 | 3009 | A | a | a | G | G | A | U | A | g | A | G | A | A | A | G | A | G | A | C | 8 | 3 | 10 | bc | false | <90% | 4372 | ||
| NM_014920 | ICK | 3441 | 3459 | u | U | U | G | G | A | g | A | C | A | G | A | A | A | a | A | G | A | C | 6 | 3 | 7 | c | false | <90% | 6095 | ||
| NM_016513 | ICK | 3574 | 3592 | u | U | U | G | G | A | g | A | C | A | G | A | A | A | a | A | G | A | C | 6 | 3 | 7 | c | false | <90% | 6228 | ||
| NM_016396 | CTDSPL2 | 1960 | 1978 | A | a | g | G | G | u | U | A | C | A | G | A | A | A | G | A | G | A | C | 5 | 3 | 13 | bc | false | <90% | 4875 | ||
| NM_018451 | CENPJ | 2989 | 3007 | A | U | U | G | G | A | a | A | C | A | G | A | A | A | u | A | G | A | a | 4 | 3 | 7 | c | false | <90% | 5187 | ||
| NM_152369 | SLC44A3 | 787 | 805 | A | U | U | G | G | A | c | A | C | A | G | A | A | A | G | g | G | A | a | 2 | 3 | 8 | c | false | <90% | 2098 | ||
| NM_018850 | ABCB4 | 1762 | 1780 | A | U | U | G | G | A | c | A | C | A | G | A | A | A | G | u | G | A | a | 2 | 3 | 8 | c | false | <90% | 3826 | ||
| NM_000443 | ABCB4 | 1762 | 1780 | A | U | U | G | G | A | c | A | C | A | G | A | A | A | G | u | G | A | a | 2 | 3 | 8 | c | false | <90% | 3967 | ||
| NM_018849 | ABCB4 | 1762 | 1780 | A | U | U | G | G | A | c | A | C | A | G | A | A | A | G | u | G | A | a | 2 | 3 | 8 | c | false | <90% | 3988 | ||
| NM_017752 | TBC1D8B | 5436 | 5454 | A | U | U | G | a | A | U | A | C | u | G | A | A | A | G | A | G | A | u | -39 | 3 | 8 | bc | false | <90% | 5726 | ||
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_030969 | TMEM14B | 702 | 720 | a | U | C | U | C | U | U | U | C | U | G | U | A | U | C | u | A | u | a | 64 | 4 | 14 | c | false | <90% | 935 | ||
| XM_001134429 | MUC5AC | 240 | 258 | c | c | a | U | C | U | U | U | C | U | G | U | A | U | C | C | A | A | g | 62 | 4 | 15 | bc | false | <90% | 3811 | ||
| NM_014982 | PCNX | 1406 | 1424 | G | c | C | U | C | U | U | U | C | U | G | g | A | U | C | C | A | A | a | 49 | 3 | 9 | false | <90% | 12936 | |||
| NM_003035 | STIL | 2753 | 2771 | G | c | C | a | C | U | U | U | C | U | G | U | A | U | C | C | A | A | c | 46 | 3 | 14 | bc | false | <90% | 5016 | ||
| NM_001048166 | STIL | 2753 | 2771 | G | c | C | a | C | U | U | U | C | U | G | U | A | U | C | C | A | A | c | 46 | 3 | 14 | bc | false | <90% | 5019 | ||
| NM_021912 | GABRB3 | 3655 | 3673 | a | U | C | U | u | U | U | U | C | U | G | U | A | U | C | C | A | g | U | 43 | 3 | 12 | c | false | <90% | 5725 | ||
| NM_000814 | GABRB3 | 3741 | 3759 | a | U | C | U | u | U | U | U | C | U | G | U | A | U | C | C | A | g | U | 43 | 3 | 12 | c | false | <90% | 5811 | ||
| NM_002594 | PCSK2 | 192 | 210 | G | U | C | U | C | U | U | U | C | U | c | U | A | U | a | C | A | A | a | 9 | 3 | 10 | c | false | <90% | 4745 | ||
| NM_031301 | APH1B | 264 | 282 | G | U | C | U | C | U | g | U | C | U | a | U | A | U | C | C | A | A | g | -32 | 3 | 7 | c | false | <90% | 939 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1699
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