Automatic recommendation
Not OK - siRNA is not specific
18 hits were found for GCACAGGAAGACACCCUAU (14 guide strand hits and 4 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_002727 | RFPL1S | 4052 | 4070 | a | C | A | C | A | G | G | A | A | G | A | C | c | C | C | C | U | c | U | 84 | 3 | 11 | false | <90% | 5112 | |||
| NM_016235 | GPRC5B | 1298 | 1316 | a | C | A | C | A | G | G | A | A | G | A | C | A | C | C | u | U | u | g | 64 | 4 | 14 | c | false | <90% | 2870 | ||
| NM_015226 | KIAA0350 | 4287 | 4305 | u | C | A | a | A | G | G | A | A | G | A | C | A | C | C | C | U | c | U | 58 | 3 | 13 | c | false | <90% | 6786 | ||
| XR_018055 | LOC442291 | 1243 | 1261 | G | a | A | C | A | G | G | A | A | G | A | C | A | C | C | C | c | c | a | 57 | 4 | 14 | ac | false | <90% | 1278 | ||
| XR_017369 | LOC442663 | 1243 | 1261 | G | a | A | C | A | G | G | A | A | G | A | C | A | C | C | C | c | c | a | 57 | 4 | 14 | ac | false | <90% | 1278 | ||
| XR_018573 | LOC442663 | 1243 | 1261 | G | a | A | C | A | G | G | A | A | G | A | C | A | C | C | C | c | c | a | 57 | 4 | 14 | ac | false | <90% | 1278 | ||
| NM_182914 | SYNE2 | 312 | 330 | G | a | A | C | A | G | G | A | A | G | A | C | A | C | C | C | a | g | a | 57 | 4 | 14 | ac | false | <90% | 21882 | ||
| NM_015180 | SYNE2 | 312 | 330 | G | a | A | C | A | G | G | A | A | G | A | C | A | C | C | C | a | g | a | 57 | 4 | 14 | ac | false | <90% | 21816 | ||
| NM_017791 | C14orf58 | 2257 | 2275 | u | C | A | C | A | G | G | A | A | G | A | a | A | g | C | C | U | A | U | 44 | 3 | 10 | false | <90% | 3614 | |||
| NM_020820 | PREX1 | 6178 | 6196 | G | C | A | C | A | G | G | A | A | G | c | C | A | C | C | C | U | g | c | 31 | 3 | 10 | c | false | <90% | 6633 | ||
| NM_006841 | SLC38A3 | 2152 | 2170 | u | C | A | C | A | G | G | A | u | G | A | C | A | C | C | C | U | c | c | 30 | 4 | 8 | c | false | <90% | 2559 | ||
| NM_173832 | ZFP41 | 601 | 619 | u | C | A | g | A | G | G | A | A | G | A | a | A | C | C | C | U | A | U | 27 | 3 | 7 | false | <90% | 4786 | |||
| NM_172215 | CAMKK2 | 2717 | 2735 | G | C | c | C | A | a | G | A | A | G | A | C | A | C | C | C | U | A | c | 12 | 3 | 12 | bc | false | <90% | 2852 | ||
| NM_172214 | CAMKK2 | 2846 | 2864 | G | C | c | C | A | a | G | A | A | G | A | C | A | C | C | C | U | A | c | 12 | 3 | 12 | bc | false | <90% | 2981 | ||
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_018897 | DNAH7 | 7273 | 7291 | g | c | A | G | G | G | U | G | U | C | U | U | C | C | U | G | U | u | u | 78 | 4 | 15 | ac | false | <90% | 12395 | ||
| NM_181537 | KRT27 | 1403 | 1421 | A | g | A | G | G | G | U | G | U | C | U | U | C | C | U | G | a | a | C | 62 | 3 | 14 | ac | false | <90% | 1635 | ||
| NM_013267 | GLS2 | 860 | 878 | g | U | g | G | G | G | U | G | U | C | U | c | C | C | U | G | U | G | C | 44 | 3 | 8 | false | <90% | 2636 | |||
| NM_020689 | SLC24A3 | 2050 | 2068 | g | U | A | u | G | G | U | G | U | g | U | U | C | C | U | G | U | G | C | -21 | 3 | 9 | bc | false | <90% | 3905 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2314
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