Automatic recommendation
Not OK - siRNA is not specific
17 hits were found for UCCCCAACCUCCAAUCACU (7 guide strand hits and 10 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_015980 | HMP19 | 2133 | 2151 | c | C | C | C | C | A | A | C | C | U | C | C | A | A | U | C | A | C | c | 93 | 2 | 17 | abc | false | <90% | 2356 | ||
| NM_170770 | RNF39 | 1052 | 1070 | U | C | C | C | C | A | A | C | C | U | C | C | u | A | U | g | A | C | U | 63 | 2 | 12 | false | <90% | 1353 | |||
| NM_170769 | RNF39 | 1688 | 1706 | U | C | C | C | C | A | A | C | C | U | C | C | u | A | U | g | A | C | U | 63 | 2 | 12 | false | <90% | 1989 | |||
| NM_025236 | RNF39 | 1886 | 1904 | U | C | C | C | C | A | A | C | C | U | C | C | u | A | U | g | A | C | U | 63 | 2 | 12 | false | <90% | 2187 | |||
| NM_152325 | C13orf26 | 541 | 559 | U | C | C | C | C | A | A | C | C | U | C | C | A | g | a | C | A | C | U | 55 | 2 | 13 | c | false | <90% | 1113 | ||
| NM_031207 | HYI | 604 | 622 | g | a | C | C | C | A | A | C | C | U | C | C | A | A | U | u | A | C | a | 55 | 4 | 13 | c | false | <90% | 999 | ||
| XM_001131461 | LOC729831 | 1249 | 1267 | c | C | C | C | C | A | A | a | C | U | C | C | A | c | U | C | A | C | U | 16 | 3 | 6 | c | false | <90% | 1335 | ||
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_496575 | FLJ14082 | 1033 | 1051 | g | G | U | G | A | U | U | G | G | A | G | a | c | U | G | G | G | G | A | 53 | 3 | 10 | false | <90% | 3560 | |||
| XM_936846 | FLJ14082 | 1033 | 1051 | g | G | U | G | A | U | U | G | G | A | G | a | c | U | G | G | G | G | A | 53 | 3 | 10 | false | <90% | 3560 | |||
| NM_015284 | KIAA0467 | 9386 | 9404 | u | G | U | a | A | U | U | G | G | A | G | G | U | U | G | G | G | u | c | 53 | 4 | 13 | c | false | <90% | 10217 | ||
| NM_001039654 | ZNF550 | 233 | 251 | A | G | U | G | A | U | U | c | G | A | G | G | U | U | G | G | G | G | A | 37 | 1 | 11 | bc | false | <90% | 1146 | ||
| XR_016243 | LOC642940 | 1174 | 1192 | u | G | U | c | A | U | U | G | G | A | G | u | U | U | G | G | G | G | A | 27 | 3 | 7 | false | <90% | 1272 | |||
| XR_019117 | LOC642940 | 1180 | 1198 | u | G | U | c | A | U | U | G | G | A | G | u | U | U | G | G | G | G | A | 27 | 3 | 7 | false | <90% | 1278 | |||
| NM_015353 | KCTD2 | 1467 | 1485 | u | G | U | G | g | U | U | G | G | A | G | G | U | U | G | G | u | G | A | 23 | 3 | 11 | c | false | <90% | 3714 | ||
| NM_173547 | TRIM65 | 1707 | 1725 | A | G | a | G | A | U | g | G | G | A | G | G | U | U | G | G | G | G | g | 9 | 3 | 11 | bc | false | <90% | 3429 | ||
| NR_002594 | IMAA | 1231 | 1249 | A | G | U | G | A | a | U | G | G | A | G | G | U | U | c | G | G | G | u | 7 | 3 | 8 | c | false | <90% | 2552 | ||
| NM_015553 | PIP3-E | 5287 | 5305 | A | G | U | G | A | U | U | a | G | A | G | G | U | U | G | G | u | c | c | 6 | 4 | 8 | c | false | <90% | 6687 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2851
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