Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for GGGAGCUAGUUGAAAUUAA (11 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 | |||||||||||||
| NM_014709 | USP34 | 2424 | 2442 | a | G | G | A | G | C | U | A | G | U | U | c | A | g | A | U | U | A | A | 44 | 3 | 10 | false | <90% | 11326 | |||
| NM_005665 | EVI5 | 1281 | 1299 | a | a | G | A | G | C | a | A | G | U | U | G | A | A | A | U | U | A | A | 20 | 3 | 12 | bc | false | <90% | 7403 | ||
| NM_014309 | RBM9 | 4691 | 4709 | G | G | G | A | G | C | U | A | G | U | g | G | A | A | A | U | c | u | A | 12 | 3 | 10 | c | false | <90% | 6948 | ||
| NM_001082579 | RBM9 | 4697 | 4715 | G | G | G | A | G | C | U | A | G | U | g | G | A | A | A | U | c | u | A | 12 | 3 | 10 | c | false | <90% | 6954 | ||
| NM_001082577 | RBM9 | 4700 | 4718 | G | G | G | A | G | C | U | A | G | U | g | G | A | A | A | U | c | u | A | 12 | 3 | 10 | c | false | <90% | 6957 | ||
| NM_001082578 | RBM9 | 4700 | 4718 | G | G | G | A | G | C | U | A | G | U | g | G | A | A | A | U | c | u | A | 12 | 3 | 10 | c | false | <90% | 6957 | ||
| NM_001082576 | RBM9 | 4728 | 4746 | G | G | G | A | G | C | U | A | G | U | g | G | A | A | A | U | c | u | A | 12 | 3 | 10 | c | false | <90% | 6985 | ||
| NM_001031695 | RBM9 | 4740 | 4758 | G | G | G | A | G | C | U | A | G | U | g | G | A | A | A | U | c | u | A | 12 | 3 | 10 | c | false | <90% | 6997 | ||
| NM_007350 | PHLDA1 | 1761 | 1779 | G | c | c | A | G | C | U | g | G | U | U | G | A | A | A | U | U | A | A | 6 | 3 | 11 | bc | false | <90% | 5913 | ||
| NM_004193 | GBF1 | 2312 | 2330 | G | G | G | A | a | C | U | A | a | U | U | G | A | A | A | U | U | A | A | -11 | 2 | 10 | bc | false | <90% | 6376 | ||
| NM_019605 | SERTAD4 | 1712 | 1730 | G | G | G | A | G | C | U | A | G | a | U | G | A | A | A | U | g | g | c | -13 | 4 | 9 | c | false | <90% | 2038 | ||
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_014679 | CEP57 | 2627 | 2645 | a | U | A | A | U | U | U | C | A | A | C | U | A | G | a | U | C | a | a | 65 | 4 | 13 | c | false | <90% | 3158 | ||
| NM_006479 | RAD51AP1 | 1952 | 1970 | a | g | A | A | U | U | U | C | A | A | C | U | A | G | C | U | u | C | u | 58 | 4 | 14 | ac | false | <90% | 2142 | ||
| NM_001001732 | C10orf130 | 1583 | 1601 | U | U | A | u | U | U | U | C | A | A | C | a | A | G | C | U | C | C | C | 29 | 2 | 7 | false | <90% | 1890 | |||
| NM_017610 | RNF111 | 4176 | 4194 | U | U | A | A | U | U | U | C | A | A | u | U | A | G | C | U | a | g | a | 7 | 4 | 10 | c | false | <90% | 5556 | ||
| NM_014231 | VAMP1 | 1316 | 1334 | a | U | A | A | U | U | U | a | A | c | C | U | A | G | C | U | C | C | C | -46 | 3 | 9 | bc | false | <90% | 2748 | ||
| NM_199245 | VAMP1 | 1719 | 1737 | a | U | A | A | U | U | U | a | A | c | C | U | A | G | C | U | C | C | C | -46 | 3 | 9 | bc | false | <90% | 3151 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2475
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