Automatic recommendation
Not OK - siRNA is not specific
22 hits were found for UGAUAUGUUGAAUGUUAAU (18 guide strand hits and 4 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_022783 | DEPDC6 | 2102 | 2120 | g | a | A | U | A | U | G | U | U | G | A | A | U | G | U | U | A | A | a | 81 | 3 | 16 | abc | false | <90% | 2187 | ||
| NM_003472 | DEK | 2683 | 2701 | a | u | A | U | A | U | G | U | U | G | A | A | U | G | U | U | A | A | c | 81 | 3 | 16 | abc | false | <90% | 2879 | ||
| NM_000586 | IL2 | 724 | 742 | U | a | u | U | A | U | G | U | U | G | A | A | U | G | U | U | A | A | a | 64 | 3 | 15 | bc | false | <90% | 822 | ||
| NM_001040428 | SPATA7 | 1358 | 1376 | U | G | A | U | A | U | G | U | U | G | A | A | U | G | U | a | u | u | U | 47 | 3 | 15 | c | false | <90% | 1915 | ||
| NM_018418 | SPATA7 | 1454 | 1472 | U | G | A | U | A | U | G | U | U | G | A | A | U | G | U | a | u | u | U | 47 | 3 | 15 | c | false | <90% | 2011 | ||
| NM_015040 | PIP5K3 | 9662 | 9680 | U | G | A | c | A | U | G | U | U | G | A | A | U | u | U | U | A | A | a | 38 | 3 | 9 | c | false | <90% | 9901 | ||
| NM_001033 | RRM1 | 1936 | 1954 | U | G | A | U | A | U | G | U | g | G | A | A | U | G | U | U | A | c | U | 37 | 2 | 8 | c | false | <90% | 3117 | ||
| NM_024666 | FLJ11506 | 1652 | 1670 | g | G | A | U | A | U | G | U | U | G | u | A | U | G | U | U | A | g | a | 29 | 4 | 9 | c | false | <90% | 2774 | ||
| NM_001103 | ACTN2 | 4074 | 4092 | U | G | A | U | c | U | G | U | U | G | A | A | U | G | U | U | c | A | U | 25 | 2 | 11 | c | false | <90% | 4181 | ||
| NM_003895 | SYNJ1 | 6218 | 6236 | g | a | A | U | A | U | G | U | a | G | A | A | U | G | U | U | A | A | a | 21 | 4 | 9 | bc | false | <90% | 6997 | ||
| NM_203446 | SYNJ1 | 6260 | 6278 | g | a | A | U | A | U | G | U | a | G | A | A | U | G | U | U | A | A | a | 21 | 4 | 9 | bc | false | <90% | 7039 | ||
| NM_005865 | PRSS16 | 1789 | 1807 | U | G | g | U | A | U | u | U | U | G | A | A | U | G | U | U | A | A | a | 9 | 3 | 11 | bc | false | <90% | 2722 | ||
| NM_018117 | BRWD2 | 4537 | 4555 | U | G | A | U | A | U | u | U | U | G | A | A | U | u | U | U | A | A | c | 9 | 3 | 6 | c | false | <90% | 4724 | ||
| NM_018227 | UBE1L2 | 4044 | 4062 | U | G | A | a | A | U | G | U | a | G | A | A | U | G | U | U | A | A | a | -1 | 3 | 9 | bc | false | <90% | 5385 | ||
| NM_181836 | TMED7 | 1690 | 1708 | U | G | A | U | A | U | G | U | U | u | A | A | U | u | U | U | A | A | a | -7 | 3 | 9 | c | false | <90% | 3587 | ||
| NM_024511 | C4orf15 | 4902 | 4920 | U | G | A | U | A | c | u | U | U | G | A | A | U | G | U | U | A | A | U | -29 | 2 | 12 | bc | false | <90% | 5620 | ||
| NM_018252 | C1orf75 | 1712 | 1730 | U | G | A | U | u | U | G | U | U | a | A | A | U | G | U | U | A | A | a | -39 | 3 | 8 | bc | false | <90% | 2475 | ||
| NM_006577 | B3GNT2 | 2513 | 2531 | U | G | A | U | A | U | u | U | U | a | A | A | U | G | U | U | A | A | g | -54 | 3 | 8 | bc | false | <90% | 2788 | ||
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_212479 | ZMYND11 | 1180 | 1198 | g | a | a | A | A | C | A | U | U | C | A | A | g | A | U | A | U | C | A | 56 | 4 | 9 | false | <90% | 2129 | |||
| NM_006624 | ZMYND11 | 1180 | 1198 | g | a | a | A | A | C | A | U | U | C | A | A | g | A | U | A | U | C | A | 56 | 4 | 9 | false | <90% | 4204 | |||
| NM_000092 | COL4A4 | 9102 | 9120 | u | U | U | A | A | u | A | U | U | C | A | A | C | A | U | A | U | u | u | 27 | 4 | 11 | c | false | <90% | 10341 | ||
| NR_002723 | GABPAP | 60735 | 60753 | A | U | U | A | A | C | A | U | U | u | A | A | C | A | U | A | a | u | g | -13 | 4 | 9 | c | false | <90% | 194142 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1648
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