Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
25 hits were found for GGAUGUGGAUUAUUUGGAA (15 guide strand hits and 10 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_018212 | ENAH | 6729 | 6747 | a | G | c | U | G | U | G | G | A | U | U | A | U | U | U | G | G | u | g | 70 | 4 | 14 | c | false | <90% | 13109 | ||
| NM_001008493 | ENAH | 6792 | 6810 | a | G | c | U | G | U | G | G | A | U | U | A | U | U | U | G | G | u | g | 70 | 4 | 14 | c | false | <90% | 13172 | ||
| NM_139352 | TAF1A | 303 | 321 | a | a | c | U | G | U | G | G | A | U | U | A | U | U | U | G | G | A | A | 67 | 3 | 16 | bc | false | <90% | 1723 | ||
| NM_014835 | OSBPL2 | 980 | 998 | c | c | g | U | G | U | G | G | A | U | U | A | U | U | U | G | G | A | A | 67 | 3 | 16 | bc | false | <90% | 3935 | ||
| NM_144498 | OSBPL2 | 1016 | 1034 | c | c | g | U | G | U | G | G | A | U | U | A | U | U | U | G | G | A | A | 67 | 3 | 16 | bc | false | <90% | 3971 | ||
| NM_004065 | CDR1 | 604 | 622 | a | G | A | U | G | U | G | G | A | U | U | u | U | c | U | G | G | A | A | 44 | 3 | 10 | false | <90% | 1299 | |||
| NM_004065 | CDR1 | 1265 | 1283 | a | G | A | U | G | U | G | G | A | U | U | u | U | c | U | G | G | A | A | 44 | 3 | 10 | false | <90% | 1299 | |||
| NM_001017361 | ECAT1 | 792 | 810 | G | G | A | U | G | U | G | G | A | U | U | u | U | U | U | G | u | u | u | 35 | 4 | 11 | false | <90% | 1063 | |||
| NM_012328 | DNAJB9 | 686 | 704 | G | G | A | g | G | U | G | G | A | U | U | A | U | U | U | G | a | u | g | 32 | 4 | 12 | c | false | <90% | 2371 | ||
| XM_495886 | RNF169 | 4942 | 4960 | u | G | A | U | G | U | G | u | A | U | U | A | U | U | U | G | G | g | g | 28 | 4 | 9 | c | false | <90% | 8900 | ||
| XM_940188 | RNF169 | 4942 | 4960 | u | G | A | U | G | U | G | u | A | U | U | A | U | U | U | G | G | g | g | 28 | 4 | 9 | c | false | <90% | 8900 | ||
| NM_030932 | DIAPH3 | 2087 | 2105 | u | u | u | U | G | U | G | G | A | U | g | A | U | U | U | G | G | A | A | 5 | 4 | 8 | c | false | <90% | 2745 | ||
| NM_001042517 | DIAPH3 | 2916 | 2934 | u | u | u | U | G | U | G | G | A | U | g | A | U | U | U | G | G | A | A | 5 | 4 | 8 | c | false | <90% | 4812 | ||
| NM_004333 | BRAF | 1451 | 1469 | G | G | A | U | c | U | G | G | A | U | c | A | U | U | U | G | G | A | A | -12 | 2 | 8 | c | false | <90% | 2477 | ||
| NM_004766 | COPB2 | 2714 | 2732 | a | G | A | U | u | U | G | G | A | U | a | A | U | U | U | G | G | A | A | -14 | 3 | 8 | c | false | <90% | 3067 | ||
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_024750 | LRRC2 | 1520 | 1538 | U | U | C | C | A | A | A | U | A | A | U | g | C | A | C | A | U | u | u | 58 | 3 | 11 | false | <90% | 1946 | |||
| NM_024512 | LRRC2 | 1522 | 1540 | U | U | C | C | A | A | A | U | A | A | U | g | C | A | C | A | U | u | u | 58 | 3 | 11 | false | <90% | 4860 | |||
| NM_001001661 | ZNF425 | 2795 | 2813 | U | U | C | C | A | A | A | U | A | A | U | C | C | A | u | A | g | a | C | 49 | 3 | 14 | c | false | <90% | 3184 | ||
| XM_374912 | XRRA1 | 6303 | 6321 | c | c | C | C | A | A | A | U | A | A | U | a | C | A | C | A | U | C | a | 47 | 4 | 9 | false | <90% | 7270 | |||
| XM_945928 | XRRA1 | 6303 | 6321 | c | c | C | C | A | A | A | U | A | A | U | a | C | A | C | A | U | C | a | 47 | 4 | 9 | false | <90% | 7270 | |||
| NM_020768 | KCTD16 | 2907 | 2925 | U | U | C | C | A | c | A | U | A | A | U | C | C | A | C | A | U | u | a | 29 | 3 | 11 | c | false | <90% | 5246 | ||
| NM_015335 | THRAP2 | 6915 | 6933 | c | U | g | C | A | A | A | U | A | A | c | C | C | A | C | A | U | C | C | 17 | 3 | 8 | c | false | <90% | 9546 | ||
| NM_207422 | FLJ44635 | 1471 | 1489 | a | g | a | C | A | A | A | U | A | A | a | C | C | A | C | A | U | C | C | 5 | 4 | 8 | c | false | <90% | 2268 | ||
| XR_018985 | LOC645097 | 370 | 388 | U | U | C | C | A | g | A | a | A | A | U | C | C | A | C | A | U | C | u | -30 | 3 | 10 | bc | false | <90% | 738 | ||
| XR_016741 | LOC645097 | 370 | 388 | U | U | C | C | A | g | A | a | A | A | U | C | C | A | C | A | U | C | u | -30 | 3 | 10 | bc | false | <90% | 738 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2222
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