Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for UGUUGCCCAAGGUCUUACA (10 guide strand hits and 3 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_002229 | RPL23AP13 | 1047 | 1065 | g | c | U | U | G | C | C | C | A | A | G | G | g | C | U | U | A | C | u | 71 | 4 | 10 | false | <90% | 2302 | |||
| NM_198900 | FMNL3 | 7601 | 7619 | a | c | U | U | G | C | C | C | A | A | G | G | U | C | U | c | A | C | A | 60 | 3 | 13 | c | false | <90% | 11039 | ||
| NM_175736 | FMNL3 | 7754 | 7772 | a | c | U | U | G | C | C | C | A | A | G | G | U | C | U | c | A | C | A | 60 | 3 | 13 | c | false | <90% | 11192 | ||
| NM_001010976 | LOC149950 | 180 | 198 | c | c | U | U | G | C | C | C | A | A | G | G | U | C | U | c | A | C | c | 55 | 4 | 13 | c | false | <90% | 846 | ||
| NM_021961 | TEAD1 | 4538 | 4556 | U | G | U | U | G | C | C | C | A | A | G | a | U | g | U | U | A | C | A | 46 | 2 | 11 | false | <90% | 8850 | |||
| NM_053276 | VIT | 1220 | 1238 | U | G | U | U | G | C | C | C | A | A | G | c | U | C | U | U | g | a | c | 35 | 4 | 11 | false | <90% | 2745 | |||
| NM_001043318 | C14orf43 | 5937 | 5955 | U | G | U | U | u | C | C | C | A | A | G | G | U | C | U | U | u | u | c | 17 | 4 | 11 | c | false | <90% | 7656 | ||
| NM_194278 | C14orf43 | 6381 | 6399 | U | G | U | U | u | C | C | C | A | A | G | G | U | C | U | U | u | u | c | 17 | 4 | 11 | c | false | <90% | 8100 | ||
| XR_017713 | LOC152217 | 1139 | 1157 | a | G | U | U | G | C | C | C | A | A | a | G | U | C | U | U | g | C | A | 13 | 3 | 9 | c | false | <90% | 1413 | ||
| XR_017724 | LOC152217 | 1167 | 1185 | a | G | U | U | G | C | C | C | A | A | a | G | U | C | U | U | g | C | A | 13 | 3 | 9 | c | false | <90% | 1441 | ||
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_001708 | OPN1SW | 416 | 434 | U | G | U | A | A | G | c | C | C | U | U | c | G | G | C | A | A | C | u | -5 | 3 | 6 | false | <90% | 1101 | |||
| NM_001684 | ATP2B4 | 2241 | 2259 | U | G | U | g | A | G | A | C | C | a | U | G | G | G | C | A | A | C | g | -24 | 3 | 8 | bc | false | <90% | 8733 | ||
| NM_001001396 | ATP2B4 | 2241 | 2259 | U | G | U | g | A | G | A | C | C | a | U | G | G | G | C | A | A | C | g | -24 | 3 | 8 | bc | false | <90% | 8911 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2703
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