Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for GAAUGUCCUGGAUCACACA (8 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_018289 | VPS53 | 518 | 536 | G | A | A | U | G | U | C | C | U | G | G | A | g | C | A | C | u | u | c | 58 | 4 | 12 | false | <90% | 2209 | |||
| XR_015445 | LOC730773 | 717 | 735 | c | A | A | U | G | U | C | C | U | G | G | g | U | C | A | C | A | a | g | 56 | 4 | 10 | false | <90% | 866 | |||
| XR_015348 | LOC728179 | 717 | 735 | c | A | A | U | G | U | C | C | U | G | G | g | U | C | A | C | A | a | g | 56 | 4 | 10 | false | <90% | 866 | |||
| NM_032576 | CYorf15B | 2489 | 2507 | a | A | u | U | G | U | C | C | U | G | G | A | U | C | A | u | A | C | A | 52 | 3 | 12 | c | false | <90% | 5533 | ||
| NM_015050 | KIAA0082 | 1188 | 1206 | u | u | u | U | G | U | C | C | U | G | G | A | U | a | A | C | A | C | A | 47 | 4 | 10 | c | false | <90% | 4030 | ||
| NM_020443 | NAV1 | 1136 | 1154 | G | A | A | U | G | U | C | C | U | G | G | A | U | C | u | C | c | g | g | 44 | 4 | 14 | c | false | <90% | 11365 | ||
| NM_153754 | C21orf88 | 109 | 127 | G | c | c | U | G | U | C | C | U | G | G | g | U | C | A | C | A | C | A | 35 | 3 | 8 | false | <90% | 1088 | |||
| NM_014734 | KIAA0247 | 1483 | 1501 | G | A | A | U | G | U | g | C | U | G | G | A | U | C | A | a | A | C | c | 2 | 3 | 8 | c | false | <90% | 5402 | ||
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_015137 | KIAA0143 | 908 | 926 | c | a | U | G | U | G | A | U | C | C | A | G | G | A | g | A | U | U | C | 61 | 3 | 12 | c | false | <90% | 5148 | ||
| NM_173649 | FLJ40172 | 1598 | 1616 | g | G | U | G | U | G | A | U | C | C | A | G | c | A | C | u | U | U | C | 61 | 3 | 11 | false | <90% | 2048 | |||
| NM_016312 | WBP11 | 615 | 633 | a | u | U | u | U | G | A | U | C | C | A | G | G | A | C | A | U | U | C | 49 | 3 | 15 | bc | false | <90% | 2690 | ||
| NM_000583 | GC | 1152 | 1170 | U | G | U | G | U | G | A | U | C | C | A | G | G | A | a | A | c | a | C | 49 | 3 | 14 | c | false | <90% | 1801 | ||
| NM_133373 | PLCD3 | 1113 | 1131 | U | G | U | G | U | G | u | U | C | C | A | G | G | A | C | A | U | g | a | 26 | 3 | 10 | c | false | <90% | 3477 | ||
| NM_030918 | SNX27 | 1624 | 1642 | c | a | U | G | U | G | A | g | C | C | A | G | G | A | C | A | U | U | C | 24 | 3 | 11 | bc | false | <90% | 7085 | ||
| NM_015567 | SLITRK5 | 564 | 582 | a | a | U | G | U | u | A | U | C | C | A | G | G | A | C | A | U | U | g | 18 | 4 | 12 | bc | false | <90% | 4461 | ||
| NM_052900 | CSMD3 | 6079 | 6097 | a | G | U | G | U | G | A | U | C | a | A | G | G | A | u | A | U | U | C | -9 | 3 | 8 | c | false | <90% | 12643 | ||
| NM_198124 | CSMD3 | 6283 | 6301 | a | G | U | G | U | G | A | U | C | a | A | G | G | A | u | A | U | U | C | -9 | 3 | 8 | c | false | <90% | 13042 | ||
| NM_198123 | CSMD3 | 6391 | 6409 | a | G | U | G | U | G | A | U | C | a | A | G | G | A | u | A | U | U | C | -9 | 3 | 8 | c | false | <90% | 13150 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1724
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 sense 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