Automatic recommendation
Not OK - siRNA is not specific
10 hits were found for GAGCACUCUUGGACUCUCA (7 guide strand hits and 3 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_003439 | ZKSCAN1 | 2214 | 2232 | a | g | G | C | A | C | U | C | U | U | G | G | A | C | U | C | U | C | g | 81 | 3 | 16 | abc | false | <90% | 5494 | ||
| NM_003756 | EIF3S3 | 418 | 436 | G | g | G | C | A | C | U | C | c | U | G | G | A | C | U | C | U | C | A | 28 | 2 | 10 | bc | false | <90% | 1286 | ||
| NR_002942 | LOC340508 | 1150 | 1168 | G | A | G | C | A | C | U | C | c | U | G | G | g | C | U | C | U | C | c | 24 | 3 | 8 | false | <90% | 2311 | |||
| NM_001079855 | GYG2 | 547 | 565 | c | u | u | C | A | C | U | g | U | U | G | G | A | C | U | C | U | C | A | 4 | 4 | 11 | bc | false | <90% | 3318 | ||
| NM_003918 | GYG2 | 640 | 658 | c | u | u | C | A | C | U | g | U | U | G | G | A | C | U | C | U | C | A | 4 | 4 | 11 | bc | false | <90% | 3411 | ||
| NM_080491 | GAB2 | 3539 | 3557 | G | A | G | C | c | a | U | C | U | U | G | G | A | C | U | C | U | C | c | -19 | 3 | 12 | bc | false | <90% | 6007 | ||
| NM_012296 | GAB2 | 3585 | 3603 | G | A | G | C | c | a | U | C | U | U | G | G | A | C | U | C | U | C | c | -19 | 3 | 12 | bc | false | <90% | 6053 | ||
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_198451 | FOXR2 | 1204 | 1222 | a | G | A | G | A | a | U | C | C | A | A | G | A | G | U | G | C | a | u | 27 | 4 | 11 | c | false | <90% | 1954 | ||
| NM_025207 | FLAD1 | 60 | 78 | U | G | A | G | A | G | U | C | u | A | A | G | A | G | g | G | C | U | C | 15 | 2 | 8 | c | false | <90% | 2218 | ||
| NR_002930 | PTPRV | 2750 | 2768 | U | a | u | G | A | G | g | C | C | A | A | G | A | G | U | G | C | U | C | 2 | 3 | 12 | bc | false | <90% | 4006 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1730
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