Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
24 hits were found for UGACUCCCUCAACACUGGG (16 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_004526 | MCM2 | 1326 | 1344 | U | G | g | C | U | C | C | C | U | C | A | A | C | A | C | U | G | c | c | 72 | 3 | 14 | c | false | <90% | 3453 | ||
| NM_001077628 | APH1A | 1295 | 1313 | g | u | A | C | U | C | C | C | U | C | A | A | g | A | C | U | G | G | a | 71 | 4 | 10 | false | <90% | 1875 | |||
| NM_016022 | APH1A | 1633 | 1651 | g | u | A | C | U | C | C | C | U | C | A | A | g | A | C | U | G | G | a | 71 | 4 | 10 | false | <90% | 2213 | |||
| XR_017362 | LOC653786 | 73 | 91 | a | G | A | C | U | C | C | C | U | C | A | g | C | A | C | U | G | G | a | 59 | 3 | 10 | false | <90% | 1476 | |||
| NM_170664 | OTOA | 1301 | 1319 | g | G | A | C | U | C | C | C | U | C | A | g | C | A | C | U | G | G | a | 59 | 3 | 10 | false | <90% | 2703 | |||
| NM_144672 | OTOA | 2207 | 2225 | g | G | A | C | U | C | C | C | U | C | A | g | C | A | C | U | G | G | a | 59 | 3 | 10 | false | <90% | 3624 | |||
| NM_001001919 | OR13C4 | 230 | 248 | c | c | A | u | U | C | C | C | U | C | A | A | C | A | C | U | G | G | u | 44 | 4 | 14 | bc | false | <90% | 957 | ||
| NM_173354 | SNF1LK | 3689 | 3707 | U | c | g | C | U | C | C | C | U | C | A | g | C | A | C | U | G | G | G | 35 | 3 | 8 | false | <90% | 4706 | |||
| NM_207343 | RNF214 | 1193 | 1211 | c | a | A | C | U | C | C | C | c | C | A | A | C | A | C | U | G | G | a | 21 | 4 | 9 | bc | false | <90% | 2694 | ||
| NM_001077239 | RNF214 | 1194 | 1212 | c | a | A | C | U | C | C | C | c | C | A | A | C | A | C | U | G | G | a | 21 | 4 | 9 | bc | false | <90% | 2695 | ||
| NM_001010915 | PTPLAD2 | 2551 | 2569 | g | c | A | C | U | C | C | u | U | C | A | A | C | A | C | U | G | G | u | 19 | 4 | 10 | bc | false | <90% | 4112 | ||
| XM_001127013 | LOC728260 | 388 | 406 | g | c | u | C | U | C | C | C | U | C | c | A | C | A | C | U | G | G | G | 5 | 4 | 8 | c | false | <90% | 918 | ||
| XM_001131885 | LOC732112 | 388 | 406 | g | c | u | C | U | C | C | C | U | C | c | A | C | A | C | U | G | G | G | 5 | 4 | 8 | c | false | <90% | 918 | ||
| NM_006593 | TBR1 | 1172 | 1190 | g | G | A | u | U | C | C | C | c | C | A | A | C | A | C | U | G | G | G | 1 | 3 | 10 | bc | false | <90% | 3186 | ||
| XM_931227 | LOC90120 | 1631 | 1649 | U | G | A | C | U | C | C | a | g | C | A | A | C | A | C | U | G | G | c | -27 | 3 | 9 | bc | false | <90% | 2799 | ||
| XM_946026 | LOC90120 | 1631 | 1649 | U | G | A | C | U | C | C | a | g | C | A | A | C | A | C | U | G | G | c | -27 | 3 | 9 | bc | false | <90% | 2799 | ||
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_032564 | DGAT2 | 833 | 851 | g | C | C | u | G | U | G | U | U | G | A | G | G | G | A | G | U | a | c | 53 | 4 | 13 | c | false | <90% | 2439 | ||
| NM_004323 | BAG1 | 1807 | 1825 | C | C | C | A | G | U | G | U | U | G | A | c | u | G | A | G | U | C | u | 50 | 3 | 11 | false | <90% | 3885 | |||
| XM_939746 | LOC644285 | 214 | 232 | C | C | C | A | G | U | G | U | U | G | g | G | G | G | A | G | g | g | A | 12 | 3 | 10 | c | false | <90% | 2484 | ||
| XM_929631 | LOC644285 | 214 | 232 | C | C | C | A | G | U | G | U | U | G | g | G | G | G | A | G | g | g | A | 12 | 3 | 10 | c | false | <90% | 2484 | ||
| NM_000395 | CSF2RB | 896 | 914 | C | C | C | A | G | U | G | c | U | G | A | G | G | G | A | G | g | g | g | 6 | 4 | 8 | c | false | <90% | 2996 | ||
| NM_014944 | CLSTN1 | 1041 | 1059 | u | C | C | A | c | U | G | g | U | G | A | G | G | G | A | G | U | C | A | -15 | 3 | 11 | bc | false | <90% | 5179 | ||
| NM_001009566 | CLSTN1 | 1071 | 1089 | u | C | C | A | c | U | G | g | U | G | A | G | G | G | A | G | U | C | A | -15 | 3 | 11 | bc | false | <90% | 5209 | ||
| NM_006946 | SPTBN2 | 6481 | 6499 | C | C | C | A | G | U | G | U | U | a | A | u | G | G | A | G | U | C | u | -21 | 3 | 9 | false | <90% | 7864 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1818
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