Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for GUUGGAGAACCAAAUCUCA (16 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_002997 | SDC1 | 1904 | 1922 | c | U | a | G | G | A | G | A | A | C | C | A | A | A | U | C | U | g | g | 70 | 4 | 14 | c | false | <90% | 3217 | ||
| NM_001006946 | SDC1 | 1996 | 2014 | c | U | a | G | G | A | G | A | A | C | C | A | A | A | U | C | U | g | g | 70 | 4 | 14 | c | false | <90% | 3309 | ||
| XM_001126264 | LOC727973 | 823 | 841 | G | a | U | G | G | A | G | A | A | C | C | A | A | u | U | C | U | C | A | 69 | 2 | 11 | c | false | <90% | 1060 | ||
| XM_001131638 | LOC732026 | 825 | 843 | G | a | U | G | G | A | G | A | A | C | C | A | A | u | U | C | U | C | A | 69 | 2 | 11 | c | false | <90% | 1062 | ||
| NM_002644 | PIGR | 1555 | 1573 | G | a | a | G | G | A | G | A | A | C | C | A | A | A | c | C | U | C | A | 44 | 3 | 11 | c | false | <90% | 4266 | ||
| XM_372643 | LOC390738 | 663 | 681 | u | U | U | G | c | A | G | A | A | C | C | A | A | A | U | C | U | u | g | 38 | 4 | 12 | c | false | <90% | 1161 | ||
| XM_936477 | LOC390738 | 663 | 681 | u | U | U | G | c | A | G | A | A | C | C | A | A | A | U | C | U | u | g | 38 | 4 | 12 | c | false | <90% | 1161 | ||
| NM_015683 | ARRDC2 | 1472 | 1490 | G | U | U | G | G | g | G | A | A | C | C | A | A | g | U | C | U | C | A | 17 | 2 | 7 | c | false | <90% | 2518 | ||
| NM_001025604 | ARRDC2 | 1494 | 1512 | G | U | U | G | G | g | G | A | A | C | C | A | A | g | U | C | U | C | A | 17 | 2 | 7 | c | false | <90% | 2539 | ||
| NM_145910 | NEK11 | 486 | 504 | G | U | U | G | G | A | G | A | A | C | u | A | A | A | U | C | c | a | A | 12 | 3 | 10 | c | false | <90% | 2079 | ||
| NM_024800 | NEK11 | 486 | 504 | G | U | U | G | G | A | G | A | A | C | u | A | A | A | U | C | c | a | A | 12 | 3 | 10 | c | false | <90% | 2937 | ||
| NM_001036 | RYR3 | 7825 | 7843 | G | U | U | G | G | A | G | A | A | a | C | A | g | A | U | C | U | C | A | 6 | 2 | 9 | false | <90% | 15563 | |||
| XR_018164 | LOC643766 | 564 | 582 | G | U | U | G | G | A | c | A | A | C | C | A | A | A | U | C | c | a | g | 2 | 4 | 9 | c | false | <90% | 1319 | ||
| XR_016476 | LOC643766 | 564 | 582 | G | U | U | G | G | A | c | A | A | C | C | A | A | A | U | C | c | a | g | 2 | 4 | 9 | c | false | <90% | 1319 | ||
| NM_183416 | KIF1B | 3328 | 3346 | G | U | U | G | G | A | G | A | A | g | C | A | A | u | U | C | U | C | u | -7 | 3 | 9 | c | false | <90% | 5780 | ||
| NM_173570 | ZDHHC23 | 1185 | 1203 | G | U | U | G | G | A | G | A | A | u | C | A | A | A | U | C | a | u | c | -13 | 4 | 9 | c | false | <90% | 3789 | ||
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_014893 | NLGN4Y | 4487 | 4505 | a | G | A | G | A | U | U | U | G | u | c | U | C | U | C | C | A | A | C | -46 | 3 | 8 | c | false | <90% | 5330 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1915
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