Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for UCAAUCUCGGGAACCUCAA (9 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 | |||||||||||||
| NM_001006604 | LOC387646 | 534 | 552 | U | C | A | A | U | C | U | C | c | G | G | A | A | C | C | U | a | u | u | 8 | 4 | 8 | c | false | <90% | 3262 | ||
| NM_001006607 | LRRC37A2 | 1443 | 1461 | U | C | A | A | U | C | U | C | c | G | G | A | A | C | C | U | a | u | u | 8 | 4 | 8 | c | false | <90% | 5175 | ||
| NM_014834 | LRRC37A | 1443 | 1461 | U | C | A | A | U | C | U | C | c | G | G | A | A | C | C | U | a | u | u | 8 | 4 | 8 | c | false | <90% | 5177 | ||
| NM_199340 | LRRC37A3 | 1971 | 1989 | U | C | A | A | U | C | U | C | c | G | G | A | A | C | C | U | a | u | u | 8 | 4 | 8 | c | false | <90% | 5665 | ||
| NM_001003790 | ERLIN2 | 62 | 80 | U | C | A | c | U | u | U | C | G | G | G | A | A | C | C | U | C | A | g | -5 | 3 | 12 | bc | false | <90% | 1744 | ||
| NM_080630 | COL11A1 | 1071 | 1089 | U | C | A | A | g | C | U | C | a | G | G | A | A | C | C | U | C | A | g | -16 | 3 | 9 | bc | false | <90% | 7174 | ||
| NM_001854 | COL11A1 | 1071 | 1089 | U | C | A | A | g | C | U | C | a | G | G | A | A | C | C | U | C | A | g | -16 | 3 | 9 | bc | false | <90% | 7291 | ||
| NM_080629 | COL11A1 | 1071 | 1089 | U | C | A | A | g | C | U | C | a | G | G | A | A | C | C | U | C | A | g | -16 | 3 | 9 | bc | false | <90% | 7327 | ||
| NM_001004341 | FLJ16478 | 1325 | 1343 | c | C | A | A | U | C | U | g | G | a | G | A | A | C | C | U | C | A | A | -46 | 3 | 9 | bc | false | <90% | 1976 | ||
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_001129803 | NBPF3 | 62 | 80 | g | U | G | A | G | G | a | U | C | C | C | G | A | G | A | c | U | G | A | 5 | 3 | 8 | c | false | <90% | 1797 | ||
| NM_032264 | NBPF3 | 55 | 73 | g | U | G | A | G | G | a | U | C | C | C | G | A | G | A | c | U | G | A | 5 | 3 | 8 | c | false | <90% | 3783 | ||
| NM_138769 | RHOT2 | 478 | 496 | g | c | c | A | G | u | U | U | C | C | C | G | A | G | A | U | U | G | A | 3 | 4 | 13 | bc | false | <90% | 2509 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1502
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