Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for GCAAGAGCCUCCAUAGUAA (3 guide strand hits and 10 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_145756 | ZNF396 | 1161 | 1179 | a | C | A | A | G | A | G | C | C | U | C | C | A | U | A | c | U | A | u | 66 | 3 | 14 | c | false | <90% | 2792 | ||
| NM_001037813 | ZNF284 | 1094 | 1112 | G | u | A | A | G | A | G | C | u | U | C | C | A | U | A | G | U | A | g | 23 | 3 | 9 | bc | false | <90% | 2222 | ||
| NM_004760 | STK17A | 3519 | 3537 | u | g | A | A | G | A | G | C | C | U | u | C | A | U | A | G | U | A | u | 20 | 4 | 8 | c | false | <90% | 3949 | ||
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 | |||||||||||||
| XM_929946 | PCLO | 9318 | 9336 | U | U | A | C | U | A | U | G | G | A | G | u | C | U | C | U | U | a | C | 63 | 2 | 11 | false | <90% | 15033 | |||
| XM_940805 | PCLO | 9321 | 9339 | U | U | A | C | U | A | U | G | G | A | G | u | C | U | C | U | U | a | C | 63 | 2 | 11 | false | <90% | 15036 | |||
| XM_935710 | PCLO | 9351 | 9369 | U | U | A | C | U | A | U | G | G | A | G | u | C | U | C | U | U | a | C | 63 | 2 | 11 | false | <90% | 15066 | |||
| XM_930966 | LOC642637 | 335 | 353 | U | c | A | C | U | A | U | G | G | A | G | G | C | U | C | U | a | G | a | 60 | 3 | 14 | ac | false | <90% | 603 | ||
| XM_943406 | LOC642637 | 335 | 353 | U | c | A | C | U | A | U | G | G | A | G | G | C | U | C | U | a | G | a | 60 | 3 | 14 | ac | false | <90% | 603 | ||
| NM_138413 | C10orf65 | 1233 | 1251 | c | U | A | C | U | A | U | G | G | A | G | G | C | c | C | c | U | G | C | 52 | 3 | 12 | c | false | <90% | 2480 | ||
| XR_018791 | LOC650560 | 1960 | 1978 | U | g | g | C | U | A | U | G | G | A | G | G | C | U | u | U | U | G | C | 44 | 3 | 11 | c | false | <90% | 2049 | ||
| NM_001410 | MEGF8 | 217 | 235 | c | c | u | C | U | A | U | G | G | A | G | G | C | U | C | c | U | G | C | 40 | 4 | 12 | c | false | <90% | 10966 | ||
| NM_133487 | RAD51 | 399 | 417 | a | U | A | C | U | g | U | G | G | A | G | G | C | U | g | U | U | G | C | 9 | 3 | 8 | c | false | <90% | 1963 | ||
| NM_002875 | RAD51 | 399 | 417 | a | U | A | C | U | g | U | G | G | A | G | G | C | U | g | U | U | G | C | 9 | 3 | 8 | c | false | <90% | 2254 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1827
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