Automatic recommendation
Not OK - siRNA is not specific
13 hits were found for GGUCCAAGAGAGUGAAUAC (9 guide strand hits and 4 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 | |||||||||||||
| NR_003255 | TSIX | 23363 | 23381 | a | G | U | C | C | A | A | G | A | G | A | G | U | G | A | A | U | u | C | 95 | 2 | 16 | ac | false | <90% | 36861 | ||
| NM_182648 | BAZ1A | 4666 | 4684 | u | c | U | C | C | A | A | G | A | G | A | G | U | G | A | A | U | c | C | 83 | 3 | 15 | ac | false | <90% | 5935 | ||
| NM_013448 | BAZ1A | 4762 | 4780 | u | c | U | C | C | A | A | G | A | G | A | G | U | G | A | A | U | c | C | 83 | 3 | 15 | ac | false | <90% | 6031 | ||
| NM_024637 | GAL3ST4 | 1061 | 1079 | G | G | g | C | C | A | A | G | A | G | A | G | g | G | A | A | U | A | u | 65 | 3 | 9 | false | <90% | 2561 | |||
| XR_017488 | LOC646936 | 1364 | 1382 | G | G | a | C | C | A | A | G | A | G | A | G | U | G | A | A | c | A | a | 51 | 3 | 13 | c | false | <90% | 1538 | ||
| XR_019420 | LOC646936 | 1364 | 1382 | G | G | a | C | C | A | A | G | A | G | A | G | U | G | A | A | c | A | a | 51 | 3 | 13 | c | false | <90% | 1538 | ||
| NM_005077 | TLE1 | 683 | 701 | u | c | g | C | C | A | A | G | A | G | A | u | U | G | A | A | U | A | C | 33 | 4 | 8 | false | <90% | 3283 | |||
| NM_000496 | CRYBB2 | 727 | 745 | c | c | U | C | C | c | A | G | A | G | A | G | U | G | A | A | U | A | a | 18 | 4 | 12 | bc | false | <90% | 781 | ||
| NM_002470 | MYH3 | 5879 | 5897 | G | G | U | C | C | A | c | G | A | G | A | G | U | G | A | A | g | A | g | 5 | 3 | 9 | c | false | <90% | 6037 | ||
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 | |||||||||||||
| NR_001564 | XIST | 5544 | 5562 | G | a | A | U | U | C | A | C | U | C | U | C | U | U | G | G | A | C | u | 83 | 2 | 16 | abc | false | <90% | 19271 | ||
| NM_001005496 | OR5D16 | 39 | 57 | a | c | A | U | U | C | A | C | U | C | U | C | U | U | G | G | g | C | u | 58 | 4 | 14 | ac | false | <90% | 987 | ||
| NM_152232 | TAS1R2 | 1287 | 1305 | a | a | c | U | U | C | A | C | U | C | U | C | c | U | G | G | A | C | C | 56 | 4 | 9 | false | <90% | 2521 | |||
| NM_178542 | C17orf65 | 901 | 919 | G | c | u | U | U | C | A | g | U | C | U | C | U | U | G | G | A | C | C | 6 | 3 | 11 | bc | false | <90% | 2252 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 827
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