Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
13 hits were found for AGAGGGUCAAUCCAUUCUU (5 guide strand hits and 8 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_003135 | CEP170L | 90157 | 90175 | A | c | A | G | G | G | U | C | A | A | U | C | C | A | U | U | u | g | a | 57 | 4 | 14 | ac | false | <90% | 90477 | ||
| NM_001042405 | CEP170 | 6490 | 6508 | A | c | A | G | G | G | U | C | A | A | U | C | C | A | U | U | u | g | a | 57 | 4 | 14 | ac | false | <90% | 6832 | ||
| NM_001042404 | CEP170 | 6568 | 6586 | A | c | A | G | G | G | U | C | A | A | U | C | C | A | U | U | u | g | a | 57 | 4 | 14 | ac | false | <90% | 6910 | ||
| NM_014812 | CEP170 | 6862 | 6880 | A | c | A | G | G | G | U | C | A | A | U | C | C | A | U | U | u | g | a | 57 | 4 | 14 | ac | false | <90% | 7204 | ||
| NM_001004452 | OR1J4 | 261 | 279 | u | c | A | G | G | a | U | C | A | A | U | C | C | A | U | U | C | U | U | 23 | 3 | 13 | bc | false | <90% | 942 | ||
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_012210 | TRIM32 | 2745 | 2763 | c | A | G | A | A | U | G | G | A | U | U | G | A | C | C | C | U | a | g | 90 | 3 | 16 | ac | false | <90% | 3160 | ||
| NM_018202 | TMEM57 | 2679 | 2697 | A | A | a | A | A | U | G | G | A | U | U | G | c | C | C | C | U | C | c | 65 | 3 | 9 | false | <90% | 3158 | |||
| NM_139035 | SMARCA1 | 2261 | 2279 | u | g | G | A | A | U | G | G | A | U | U | G | A | a | C | C | U | C | c | 62 | 4 | 11 | c | false | <90% | 4004 | ||
| NM_003069 | SMARCA1 | 2324 | 2342 | u | g | G | A | A | U | G | G | A | U | U | G | A | a | C | C | U | C | c | 62 | 4 | 11 | c | false | <90% | 4067 | ||
| NM_014979 | SV2C | 2063 | 2081 | u | A | c | A | A | U | G | G | A | U | U | G | A | C | C | a | U | C | U | 52 | 3 | 12 | c | false | <90% | 2362 | ||
| NM_153252 | BRWD3 | 3022 | 3040 | A | A | G | A | A | U | G | G | u | U | U | G | c | C | C | C | U | C | a | 24 | 3 | 8 | false | <90% | 6085 | |||
| NM_207122 | EXT2 | 1614 | 1632 | A | A | G | A | A | U | G | G | A | a | U | G | A | C | C | C | U | C | c | 12 | 2 | 9 | bc | false | <90% | 3651 | ||
| NM_000401 | EXT2 | 1767 | 1785 | A | A | G | A | A | U | G | G | A | a | U | G | A | C | C | C | U | C | c | 12 | 2 | 9 | bc | false | <90% | 3804 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1876
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