Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for CCCGCUCAAUGCCUGGAGA (8 guide strand hits and 7 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_003200 | TCF3 | 3932 | 3950 | C | C | a | G | C | U | C | A | A | U | G | C | C | U | G | G | u | a | u | 49 | 4 | 13 | c | false | <90% | 4396 | ||
| NM_001963 | EGF | 4183 | 4201 | C | C | u | a | C | U | C | A | A | U | G | C | C | U | G | G | A | G | A | 43 | 2 | 15 | bc | false | <90% | 4877 | ||
| NM_133375 | DIS3L | 764 | 782 | a | C | C | G | C | U | C | A | A | U | u | C | a | U | G | G | A | G | A | 26 | 3 | 9 | false | <90% | 3685 | |||
| NM_002468 | MYD88 | 1180 | 1198 | a | C | C | u | C | U | C | A | A | U | u | C | C | U | G | G | A | G | A | 0 | 3 | 8 | c | false | <90% | 2826 | ||
| NM_004735 | LRRFIP1 | 186 | 204 | g | C | C | G | C | U | C | A | A | a | G | C | C | g | G | G | A | G | A | -4 | 3 | 8 | c | false | <90% | 3648 | ||
| NM_003260 | TLE2 | 2199 | 2217 | C | C | u | G | C | U | C | A | A | c | G | C | C | U | G | G | A | G | g | -7 | 3 | 8 | bc | false | <90% | 2579 | ||
| NM_130830 | LRRC15 | 2528 | 2546 | g | C | C | G | C | U | C | A | g | U | u | C | C | U | G | G | A | G | A | -23 | 3 | 8 | c | false | <90% | 5938 | ||
| NM_020946 | DENND1A | 3093 | 3111 | C | C | C | c | C | U | C | A | A | g | G | C | C | U | G | G | A | G | c | -24 | 3 | 8 | bc | false | <90% | 5041 | ||
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 | |||||||||||||
| XR_015587 | LOC730833 | 1544 | 1562 | g | C | U | C | C | A | G | G | C | A | U | U | c | A | G | C | G | u | c | 79 | 4 | 11 | false | <90% | 11255 | |||
| NM_002016 | FLG | 1544 | 1562 | g | C | U | C | C | A | G | G | C | A | U | U | c | A | G | C | G | u | c | 79 | 4 | 11 | false | <90% | 12747 | |||
| NM_015157 | PHLDB1 | 1580 | 1598 | c | C | U | C | C | A | G | G | C | A | g | U | G | A | G | C | G | G | G | 36 | 2 | 9 | c | false | <90% | 5695 | ||
| NM_001033551 | TOM1L2 | 4520 | 4538 | U | C | U | C | C | A | G | G | C | A | c | U | G | A | G | C | a | G | G | 15 | 2 | 10 | c | false | <90% | 5675 | ||
| NM_001082968 | TOM1L2 | 4670 | 4688 | U | C | U | C | C | A | G | G | C | A | c | U | G | A | G | C | a | G | G | 15 | 2 | 10 | c | false | <90% | 5825 | ||
| NM_153837 | GPR114 | 2255 | 2273 | U | C | U | C | C | A | G | G | C | A | c | U | G | A | G | g | G | G | a | 7 | 3 | 10 | c | false | <90% | 3848 | ||
| NM_001002254 | DGAT2L4 | 1262 | 1280 | U | C | U | C | C | c | G | G | C | A | U | U | G | A | G | C | c | c | c | 5 | 4 | 10 | c | false | <90% | 2124 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 798
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