Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for CCGUUGUGUGAUUUGUUAA (5 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_004768 | SFRS11 | 1627 | 1645 | C | C | u | U | U | G | U | G | U | G | A | U | U | U | c | U | U | A | A | 55 | 2 | 11 | c | false | <90% | 2775 | ||
| NM_006882 | MDM2 | 650 | 668 | a | C | c | U | U | G | U | G | U | G | A | U | U | U | G | U | c | A | A | 54 | 3 | 13 | c | false | <90% | 1403 | ||
| NM_006881 | MDM2 | 787 | 805 | a | C | c | U | U | G | U | G | U | G | A | U | U | U | G | U | c | A | A | 54 | 3 | 13 | c | false | <90% | 1540 | ||
| NM_006878 | MDM2 | 860 | 878 | a | C | c | U | U | G | U | G | U | G | A | U | U | U | G | U | c | A | A | 54 | 3 | 13 | c | false | <90% | 1613 | ||
| NM_002392 | MDM2 | 1604 | 1622 | a | C | c | U | U | G | U | G | U | G | A | U | U | U | G | U | c | A | A | 54 | 3 | 13 | c | false | <90% | 2357 | ||
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_001134287 | LOC732474 | 473 | 491 | a | a | A | A | C | A | A | A | U | C | A | C | A | a | A | A | C | G | u | 62 | 4 | 11 | c | false | <90% | 1158 | ||
| NM_006916 | RPE | 1435 | 1453 | U | U | A | A | C | A | A | A | U | C | A | C | c | C | A | A | u | c | u | 58 | 4 | 12 | false | <90% | 2130 | |||
| NM_199229 | RPE | 1432 | 1450 | U | U | A | A | C | A | A | A | U | C | A | C | c | C | A | A | u | c | u | 58 | 4 | 12 | false | <90% | 2492 | |||
| NM_002669 | PLRG1 | 1163 | 1181 | U | U | A | A | C | A | A | A | U | C | A | C | A | a | A | A | a | a | u | 49 | 4 | 13 | c | false | <90% | 1797 | ||
| XM_936897 | KIAA1109 | 13067 | 13085 | U | U | A | A | C | A | A | A | U | C | A | a | A | C | A | A | a | G | c | 37 | 3 | 11 | false | <90% | 15440 | |||
| XM_371706 | KIAA1109 | 13202 | 13220 | U | U | A | A | C | A | A | A | U | C | A | a | A | C | A | A | a | G | c | 37 | 3 | 11 | false | <90% | 15575 | |||
| NM_015186 | VPS13A | 7506 | 7524 | U | U | A | A | u | A | A | A | U | C | A | C | A | C | A | A | a | G | a | 20 | 3 | 11 | c | false | <90% | 10052 | ||
| NM_001018038 | VPS13A | 7506 | 7524 | U | U | A | A | u | A | A | A | U | C | A | C | A | C | A | A | a | G | a | 20 | 3 | 11 | c | false | <90% | 10135 | ||
| NM_001018037 | VPS13A | 7389 | 7407 | U | U | A | A | u | A | A | A | U | C | A | C | A | C | A | A | a | G | a | 20 | 3 | 11 | c | false | <90% | 11145 | ||
| NM_033305 | VPS13A | 7506 | 7524 | U | U | A | A | u | A | A | A | U | C | A | C | A | C | A | A | a | G | a | 20 | 3 | 11 | c | false | <90% | 11262 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 377
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)
Motif found in guide strand
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