Automatic recommendation
Not OK - siRNA is not specific
16 hits were found for AGCUGAAAUUGAUCCAAUG (10 guide strand hits and 6 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_003149 | GPR98 | 15001 | 15019 | u | G | C | U | G | A | A | A | U | U | G | A | a | C | C | A | A | U | G | 87 | 2 | 11 | false | <90% | 19250 | |||
| NM_032119 | GPR98 | 15084 | 15102 | u | G | C | U | G | A | A | A | U | U | G | A | a | C | C | A | A | U | G | 87 | 2 | 11 | false | <90% | 19333 | |||
| NM_207490 | FLJ45721 | 2397 | 2415 | g | G | C | U | G | A | A | A | U | U | G | A | U | C | a | A | A | g | G | 70 | 3 | 13 | c | false | <90% | 2509 | ||
| NM_018724 | IL20 | 1047 | 1065 | A | u | u | U | G | A | A | A | U | U | G | A | a | C | C | A | A | U | G | 58 | 3 | 9 | false | <90% | 1252 | |||
| NM_178313 | SPTBN1 | 6217 | 6235 | A | G | C | U | G | A | A | A | U | U | G | A | U | g | C | A | c | g | u | 49 | 4 | 13 | c | false | <90% | 9091 | ||
| NM_003128 | SPTBN1 | 6120 | 6138 | A | G | C | U | G | A | A | A | U | U | G | A | U | g | C | A | c | g | u | 49 | 4 | 13 | c | false | <90% | 10238 | ||
| NM_001013717 | LOC441108 | 835 | 853 | u | G | C | U | G | A | g | A | U | U | G | A | U | C | C | A | A | U | c | 26 | 3 | 11 | bc | false | <90% | 2025 | ||
| NM_015271 | TRIM2 | 1399 | 1417 | A | G | C | U | G | A | A | A | g | U | G | A | U | C | C | g | A | U | c | 8 | 3 | 8 | c | false | <90% | 6734 | ||
| XM_938907 | KIAA1240 | 1499 | 1517 | g | G | C | U | G | A | u | g | U | U | G | A | U | C | C | A | A | U | G | -30 | 3 | 11 | bc | false | <90% | 8103 | ||
| XM_039676 | KIAA1240 | 1499 | 1517 | g | G | C | U | G | A | u | g | U | U | G | A | U | C | C | A | A | U | G | -30 | 3 | 11 | bc | false | <90% | 8103 | ||
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_000333 | ATXN7 | 3435 | 3453 | C | A | c | U | G | G | A | U | C | A | A | g | U | U | C | A | G | C | c | 41 | 3 | 8 | false | <90% | 4416 | |||
| NM_001689 | ATP5G3 | 2279 | 2297 | a | A | U | U | G | G | A | U | g | A | A | U | U | a | C | A | G | C | U | 18 | 3 | 7 | c | false | <90% | 2622 | ||
| NM_001002258 | ATP5G3 | 2355 | 2373 | a | A | U | U | G | G | A | U | g | A | A | U | U | a | C | A | G | C | U | 18 | 3 | 7 | c | false | <90% | 2698 | ||
| NM_016654 | GABPB2 | 1893 | 1911 | u | A | U | U | u | G | u | U | C | A | A | U | U | U | C | A | G | C | U | -19 | 3 | 12 | bc | false | <90% | 2806 | ||
| NM_005254 | GABPB2 | 1929 | 1947 | u | A | U | U | u | G | u | U | C | A | A | U | U | U | C | A | G | C | U | -19 | 3 | 12 | bc | false | <90% | 2842 | ||
| NM_000057 | BLM | 4225 | 4243 | C | A | U | U | G | G | A | U | C | c | A | g | U | U | C | A | G | C | c | -21 | 3 | 9 | false | <90% | 4528 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2708
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