Automatic recommendation
Not OK - siRNA is not specific
19 hits were found for CAGCAAUUCAUUGAGUAUG (18 guide strand hits and 1 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_080546 | SLC44A1 | 3219 | 3237 | u | g | G | C | A | A | U | U | C | A | U | U | G | A | G | U | A | U | c | 81 | 3 | 16 | abc | false | <90% | 4540 | ||
| NM_001032288 | UBE2V1 | 1871 | 1889 | a | A | G | C | A | A | U | U | C | A | U | U | G | u | G | U | A | c | u | 70 | 4 | 12 | c | false | <90% | 2138 | ||
| NM_022442 | UBE2V1 | 1917 | 1935 | a | A | G | C | A | A | U | U | C | A | U | U | G | u | G | U | A | c | u | 70 | 4 | 12 | c | false | <90% | 2194 | ||
| NM_003349 | Kua-UEV | 2117 | 2135 | a | A | G | C | A | A | U | U | C | A | U | U | G | u | G | U | A | c | u | 70 | 4 | 12 | c | false | <90% | 2388 | ||
| NM_199144 | UBE2V1 | 2200 | 2218 | a | A | G | C | A | A | U | U | C | A | U | U | G | u | G | U | A | c | u | 70 | 4 | 12 | c | false | <90% | 2477 | ||
| NM_021988 | UBE2V1 | 2277 | 2295 | a | A | G | C | A | A | U | U | C | A | U | U | G | u | G | U | A | c | u | 70 | 4 | 12 | c | false | <90% | 2554 | ||
| NM_199203 | Kua-UEV | 2581 | 2599 | a | A | G | C | A | A | U | U | C | A | U | U | G | u | G | U | A | c | u | 70 | 4 | 12 | c | false | <90% | 2852 | ||
| NM_000706 | AVPR1A | 3336 | 3354 | a | A | u | C | A | A | U | U | C | A | U | U | G | u | G | U | A | U | G | 58 | 3 | 10 | c | false | <90% | 4154 | ||
| NM_001040439 | MAPK8IP3 | 436 | 454 | g | A | G | a | A | A | U | U | C | A | U | U | G | A | G | U | u | U | G | 37 | 3 | 12 | c | false | <90% | 5635 | ||
| NM_015133 | MAPK8IP3 | 436 | 454 | g | A | G | a | A | A | U | U | C | A | U | U | G | A | G | U | u | U | G | 37 | 3 | 12 | c | false | <90% | 5653 | ||
| NM_199414 | PRC1 | 1433 | 1451 | C | A | G | a | A | A | U | U | C | A | U | g | G | A | G | U | A | U | G | 29 | 2 | 7 | false | <90% | 3011 | |||
| NM_199413 | PRC1 | 1433 | 1451 | C | A | G | a | A | A | U | U | C | A | U | g | G | A | G | U | A | U | G | 29 | 2 | 7 | false | <90% | 3091 | |||
| NM_003981 | PRC1 | 1433 | 1451 | C | A | G | a | A | A | U | U | C | A | U | g | G | A | G | U | A | U | G | 29 | 2 | 7 | false | <90% | 3128 | |||
| XM_001127470 | PABPC5 | 1426 | 1444 | a | g | G | C | A | A | U | U | g | A | U | U | G | A | G | U | A | U | a | 21 | 4 | 9 | bc | false | <90% | 3005 | ||
| NM_080832 | PABPC5 | 1865 | 1883 | a | g | G | C | A | A | U | U | g | A | U | U | G | A | G | U | A | U | a | 21 | 4 | 9 | bc | false | <90% | 3521 | ||
| NM_001034 | RRM2 | 1155 | 1173 | a | A | G | C | A | A | U | a | C | A | U | U | G | A | G | U | u | U | G | 12 | 3 | 8 | c | false | <90% | 2500 | ||
| NM_024969 | FAM130A2 | 1676 | 1694 | g | A | G | C | A | A | U | U | C | g | U | U | G | A | c | U | A | U | G | -9 | 3 | 8 | c | false | <90% | 2965 | ||
| NM_152467 | KLHL10 | 375 | 393 | a | A | G | C | u | A | a | U | C | A | U | U | G | A | G | U | A | U | G | -19 | 3 | 12 | bc | false | <90% | 1969 | ||
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_207499 | FLJ41841 | 3179 | 3197 | u | u | U | A | a | U | C | A | A | U | G | A | A | U | U | G | C | U | u | 30 | 4 | 13 | bc | false | <90% | 3230 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1970
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