Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
36 hits were found for CAGAGAAAUUGCUGAUAUA (24 guide strand hits and 12 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_020961 | KIAA1627 | 239 | 257 | g | A | G | A | G | A | A | A | U | U | G | C | U | G | A | a | A | c | A | 69 | 3 | 14 | c | false | <90% | 2138 | ||
| NM_024753 | TTC21B | 2269 | 2287 | u | A | G | A | G | A | A | A | U | U | G | C | U | G | A | a | A | g | A | 69 | 3 | 14 | c | false | <90% | 4916 | ||
| NM_002887 | RARS | 443 | 461 | a | A | G | A | G | A | A | A | U | U | G | C | U | G | A | a | A | a | c | 64 | 4 | 14 | c | false | <90% | 2154 | ||
| NM_001966 | EHHADH | 2054 | 2072 | u | A | G | A | G | A | A | A | U | U | G | C | a | G | A | a | A | U | A | 61 | 3 | 11 | false | <90% | 3821 | |||
| NM_000049 | ASPA | 866 | 884 | u | g | G | A | G | A | A | A | U | U | G | C | U | G | c | U | A | U | c | 56 | 4 | 12 | c | false | <90% | 1435 | ||
| NM_198506 | FLJ44691 | 2167 | 2185 | C | A | G | A | G | A | A | A | U | U | G | C | U | G | c | U | u | U | g | 46 | 3 | 14 | c | false | <90% | 3781 | ||
| NM_020141 | C1orf119 | 1482 | 1500 | g | A | G | A | G | A | A | g | U | U | G | C | U | G | A | U | A | U | u | 30 | 3 | 10 | bc | false | <90% | 2768 | ||
| XM_001125757 | LOC727778 | 2998 | 3016 | g | A | G | A | G | A | A | g | U | U | G | C | U | G | A | U | A | U | u | 30 | 3 | 10 | bc | false | <90% | 4271 | ||
| XM_001125727 | LOC727778 | 3059 | 3077 | g | A | G | A | G | A | A | g | U | U | G | C | U | G | A | U | A | U | u | 30 | 3 | 10 | bc | false | <90% | 4332 | ||
| NM_052867 | NALCN | 567 | 585 | g | u | u | u | G | A | A | A | U | U | G | C | U | G | A | U | A | U | A | 30 | 4 | 15 | bc | false | <90% | 6923 | ||
| NM_012233 | RAB3GAP1 | 1087 | 1105 | C | A | a | A | G | A | A | A | c | U | G | C | U | G | A | U | A | U | A | 20 | 2 | 10 | bc | false | <90% | 4179 | ||
| NM_018897 | DNAH7 | 3738 | 3756 | C | A | G | A | c | A | A | A | U | U | G | a | U | G | A | U | A | U | u | 9 | 3 | 6 | false | <90% | 12395 | |||
| NM_012262 | HS2ST1 | 5190 | 5208 | C | A | G | A | G | A | A | g | U | U | G | C | U | G | u | U | A | U | g | 8 | 3 | 7 | c | false | <90% | 6708 | ||
| XM_936559 | LOC647500 | 269 | 287 | C | A | G | A | G | A | A | A | U | U | c | C | U | G | A | c | A | U | c | 7 | 3 | 10 | c | false | <90% | 1110 | ||
| XM_001128547 | LOC647500 | 116 | 134 | C | A | G | A | G | A | A | A | U | U | c | C | U | G | A | c | A | U | c | 7 | 3 | 10 | c | false | <90% | 1280 | ||
| XM_001129593 | LOC729182 | 269 | 287 | C | A | G | A | G | A | A | A | U | U | c | C | U | G | A | c | A | U | c | 7 | 3 | 10 | c | false | <90% | 2298 | ||
| NM_172232 | ABCA5 | 3140 | 3158 | u | c | a | A | G | A | A | A | U | U | a | C | U | G | A | U | A | U | A | 5 | 4 | 8 | c | false | <90% | 5939 | ||
| NM_018672 | ABCA5 | 4245 | 4263 | u | c | a | A | G | A | A | A | U | U | a | C | U | G | A | U | A | U | A | 5 | 4 | 8 | c | false | <90% | 7044 | ||
| NM_033505 | SELI | 5448 | 5466 | C | A | G | A | G | A | A | A | g | U | G | g | U | G | A | U | A | U | g | 1 | 3 | 8 | false | <90% | 8143 | |||
| NM_001039591 | USP9X | 6310 | 6328 | g | A | G | A | G | A | A | A | U | c | G | C | U | G | g | U | A | U | A | -9 | 3 | 8 | c | false | <90% | 12353 | ||
| NM_001039590 | USP9X | 6310 | 6328 | g | A | G | A | G | A | A | A | U | c | G | C | U | G | g | U | A | U | A | -9 | 3 | 8 | c | false | <90% | 12401 | ||
| XM_001127087 | FLJ43950 | 327 | 345 | C | A | G | A | G | c | A | A | c | U | G | C | U | G | A | U | A | U | c | -28 | 3 | 9 | bc | false | <90% | 4762 | ||
| XM_294521 | FLJ43950 | 406 | 424 | C | A | G | A | G | c | A | A | c | U | G | C | U | G | A | U | A | U | c | -28 | 3 | 9 | bc | false | <90% | 4789 | ||
| XR_015253 | FLJ43859 | 424 | 442 | C | A | G | A | G | c | A | A | c | U | G | C | U | G | A | U | A | U | c | -28 | 3 | 9 | bc | false | <90% | 4871 | ||
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_080283 | ABCA9 | 1811 | 1829 | a | A | U | A | U | C | A | G | C | A | A | g | U | U | C | a | C | U | G | 38 | 3 | 10 | false | <90% | 6310 | |||
| XM_001125703 | CT45-5 | 295 | 313 | g | u | U | A | c | C | A | G | C | A | A | U | U | U | C | U | C | U | G | 35 | 3 | 14 | bc | false | <90% | 546 | ||
| NM_001007551 | CT45-5 | 540 | 558 | g | u | U | A | c | C | A | G | C | A | A | U | U | U | C | U | C | U | G | 35 | 3 | 14 | bc | false | <90% | 1008 | ||
| NM_003235 | TG | 6400 | 6418 | g | c | c | A | c | C | A | G | C | A | A | U | U | U | C | U | C | U | G | 15 | 4 | 14 | bc | false | <90% | 8453 | ||
| NM_003644 | GAS7 | 3811 | 3829 | a | A | U | u | U | C | A | G | a | A | A | U | U | U | C | U | C | U | G | 1 | 3 | 10 | bc | false | <90% | 7773 | ||
| NM_201432 | GAS7 | 4219 | 4237 | a | A | U | u | U | C | A | G | a | A | A | U | U | U | C | U | C | U | G | 1 | 3 | 10 | bc | false | <90% | 8181 | ||
| NM_201433 | GAS7 | 4249 | 4267 | a | A | U | u | U | C | A | G | a | A | A | U | U | U | C | U | C | U | G | 1 | 3 | 10 | bc | false | <90% | 8211 | ||
| NM_033425 | DIXDC1 | 3797 | 3815 | c | A | U | g | U | C | A | c | C | A | A | U | U | U | C | U | C | U | G | 0 | 3 | 11 | bc | false | <90% | 5432 | ||
| NM_001037954 | DIXDC1 | 4264 | 4282 | c | A | U | g | U | C | A | c | C | A | A | U | U | U | C | U | C | U | G | 0 | 3 | 11 | bc | false | <90% | 5899 | ||
| XR_019042 | LOC651130 | 560 | 578 | U | A | U | A | a | C | A | G | g | A | A | U | U | U | C | U | C | U | u | -16 | 3 | 9 | bc | false | <90% | 1975 | ||
| XR_016910 | LOC645294 | 560 | 578 | U | A | U | A | a | C | A | G | g | A | A | U | U | U | C | U | C | U | u | -16 | 3 | 9 | bc | false | <90% | 1975 | ||
| NM_016125 | LOC51136 | 600 | 618 | U | A | U | A | a | C | A | G | g | A | A | U | U | U | C | U | C | U | u | -16 | 3 | 9 | bc | false | <90% | 2031 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3785
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