Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for CCUGUUUAUAACAGACAAA (7 guide strand hits and 7 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_138788 | TMEM45B | 1468 | 1486 | a | C | U | G | U | U | U | A | U | A | A | g | u | G | A | C | A | A | A | 53 | 3 | 10 | false | <90% | 2207 | |||
| NM_199452 | ZNF365 | 1809 | 1827 | C | C | U | G | c | U | U | A | U | A | A | C | A | G | c | C | A | A | g | 18 | 3 | 9 | c | false | <90% | 2695 | ||
| NM_199451 | ZNF365 | 2490 | 2508 | C | C | U | G | c | U | U | A | U | A | A | C | A | G | c | C | A | A | g | 18 | 3 | 9 | c | false | <90% | 3376 | ||
| NM_182511 | CBLN2 | 1014 | 1032 | a | a | a | G | U | g | U | A | U | A | A | C | A | G | A | C | A | A | A | 3 | 4 | 13 | bc | false | <90% | 2750 | ||
| NM_030911 | CDADC1 | 2211 | 2229 | C | C | U | G | U | U | U | A | U | c | A | C | A | G | A | C | u | u | u | -13 | 4 | 9 | c | false | <90% | 3364 | ||
| XR_018050 | LOC442517 | 3 | 21 | g | C | U | G | U | U | U | c | U | A | g | C | A | G | A | C | A | A | A | -25 | 3 | 8 | c | false | <90% | 2142 | ||
| NM_138444 | KCTD12 | 4849 | 4867 | u | C | U | G | U | U | a | A | U | A | u | C | A | G | A | C | A | A | A | -29 | 3 | 8 | c | false | <90% | 6216 | ||
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_004543 | NEB | 4072 | 4090 | g | a | c | G | U | C | U | G | U | U | A | U | A | A | A | C | g | G | G | 43 | 4 | 13 | c | false | <90% | 20632 | ||
| NM_032828 | ZNF587 | 2474 | 2492 | U | U | U | G | U | C | U | G | U | U | A | U | A | A | A | u | g | a | a | 42 | 4 | 15 | c | false | <90% | 6845 | ||
| NM_018440 | PAG1 | 7165 | 7183 | a | a | g | G | U | C | U | G | U | U | A | U | A | A | A | u | A | G | G | 40 | 4 | 12 | c | false | <90% | 10759 | ||
| NM_015291 | DNAJC16 | 5576 | 5594 | U | U | U | u | U | C | U | G | U | U | A | U | A | A | A | a | A | G | a | 32 | 3 | 11 | c | false | <90% | 6035 | ||
| NM_130469 | JDP2 | 1525 | 1543 | U | U | U | G | U | u | U | G | U | U | A | U | g | A | A | C | A | G | a | 21 | 3 | 6 | false | <90% | 1724 | |||
| NM_024007 | EBF1 | 2368 | 2386 | U | U | U | G | U | C | U | u | U | U | A | U | A | A | A | C | c | G | u | 9 | 3 | 8 | c | false | <90% | 2762 | ||
| NM_005207 | CRKL | 2296 | 2314 | c | U | U | G | U | g | U | G | U | U | c | U | A | A | A | C | A | G | G | -26 | 3 | 8 | c | false | <90% | 5235 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3685
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