Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for AAUGCCUGUCCUUGCAAAU (14 guide strand hits and 1 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_012314 | KIR2DS4 | 316 | 334 | g | A | U | G | C | C | U | G | U | C | C | U | U | G | C | A | g | g | a | 66 | 4 | 15 | ac | false | <90% | 1586 | ||
| NM_006737 | KIR3DL2 | 588 | 606 | g | A | U | G | C | C | U | G | U | C | C | U | U | G | C | A | g | g | a | 66 | 4 | 15 | ac | false | <90% | 1877 | ||
| NM_001759 | CCND2 | 5914 | 5932 | g | g | U | G | C | C | U | G | U | C | C | U | U | G | a | A | A | A | a | 56 | 4 | 12 | c | false | <90% | 6480 | ||
| NM_153292 | NOS2A | 265 | 283 | A | u | g | G | C | C | U | G | U | C | C | U | U | G | g | A | A | A | U | 44 | 3 | 11 | c | false | <90% | 4104 | ||
| NM_000625 | NOS2A | 265 | 283 | A | u | g | G | C | C | U | G | U | C | C | U | U | G | g | A | A | A | U | 44 | 3 | 11 | c | false | <90% | 4221 | ||
| XM_001130075 | LAMA1 | 2071 | 2089 | g | A | U | G | a | C | U | G | U | C | C | U | U | G | C | c | A | A | U | 20 | 3 | 10 | c | false | <90% | 9304 | ||
| NM_005559 | LAMA1 | 2071 | 2089 | g | A | U | G | a | C | U | G | U | C | C | U | U | G | C | c | A | A | U | 20 | 3 | 10 | c | false | <90% | 9530 | ||
| XM_926002 | LOC642505 | 9 | 27 | u | g | U | G | C | C | U | G | U | C | a | U | U | G | C | A | A | A | a | 20 | 4 | 8 | c | false | <90% | 246 | ||
| XM_937952 | LOC648873 | 9 | 27 | u | g | U | G | C | C | U | G | U | C | a | U | U | G | C | A | A | A | a | 20 | 4 | 8 | c | false | <90% | 246 | ||
| NM_004404 | SEPT2 | 665 | 683 | u | g | U | G | C | C | U | G | U | C | a | U | U | G | C | A | A | A | a | 20 | 4 | 8 | c | false | <90% | 3311 | ||
| NM_001008492 | SEPT2 | 750 | 768 | u | g | U | G | C | C | U | G | U | C | a | U | U | G | C | A | A | A | a | 20 | 4 | 8 | c | false | <90% | 3396 | ||
| NM_006155 | SEPT2 | 851 | 869 | u | g | U | G | C | C | U | G | U | C | a | U | U | G | C | A | A | A | a | 20 | 4 | 8 | c | false | <90% | 3497 | ||
| NM_001008491 | SEPT2 | 952 | 970 | u | g | U | G | C | C | U | G | U | C | a | U | U | G | C | A | A | A | a | 20 | 4 | 8 | c | false | <90% | 3598 | ||
| NM_030639 | BHLHB9 | 1456 | 1474 | u | u | U | G | C | u | U | G | U | C | C | U | U | G | C | A | A | A | a | 18 | 4 | 12 | bc | false | <90% | 4004 | ||
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_016279 | CDH9 | 773 | 791 | u | a | U | U | G | C | A | A | G | G | A | C | A | G | c | C | A | U | a | 56 | 4 | 12 | c | false | <90% | 3075 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2457
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