Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for CUGGUUCGGCUGUACAUGG (6 guide strand hits and 6 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_032431 | SYVN1 | 761 | 779 | a | a | G | G | U | U | C | u | G | C | U | G | U | A | C | A | U | G | G | 24 | 3 | 11 | bc | false | <90% | 3071 | ||
| NM_172230 | SYVN1 | 761 | 779 | a | a | G | G | U | U | C | u | G | C | U | G | U | A | C | A | U | G | G | 24 | 3 | 11 | bc | false | <90% | 3074 | ||
| NM_025139 | ARMC9 | 1229 | 1247 | g | U | G | G | U | g | C | G | G | C | a | G | U | A | C | A | U | G | G | -26 | 3 | 8 | c | false | <90% | 2178 | ||
| NM_005157 | ABL1 | 1015 | 1033 | g | U | G | G | U | g | C | u | G | C | U | G | U | A | C | A | U | G | G | -27 | 3 | 11 | bc | false | <90% | 5384 | ||
| NM_007313 | ABL1 | 1508 | 1526 | g | U | G | G | U | g | C | u | G | C | U | G | U | A | C | A | U | G | G | -27 | 3 | 11 | bc | false | <90% | 5881 | ||
| NM_001077400 | FER1L5 | 770 | 788 | u | U | G | G | U | g | C | G | G | g | U | G | U | A | C | A | U | G | G | -48 | 3 | 9 | bc | false | <90% | 2536 | ||
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_001077523 | AP3D1 | 3414 | 3432 | C | C | A | U | G | U | A | C | A | G | C | C | G | c | u | C | C | A | u | 50 | 3 | 13 | c | false | <90% | 4741 | ||
| NM_003938 | AP3D1 | 3537 | 3555 | C | C | A | U | G | U | A | C | A | G | C | C | G | c | u | C | C | A | u | 50 | 3 | 13 | c | false | <90% | 4863 | ||
| NM_199175 | C21orf123 | 757 | 775 | C | C | A | U | G | U | c | C | A | G | C | C | G | c | A | C | C | A | G | 14 | 2 | 6 | c | false | <90% | 2341 | ||
| NM_021045 | ZNF248 | 3319 | 3337 | C | C | A | U | u | U | A | C | A | G | C | u | G | A | A | C | C | A | c | 9 | 3 | 6 | false | <90% | 4883 | |||
| NM_000875 | IGF1R | 2297 | 2315 | C | C | A | U | G | U | c | C | A | G | C | C | G | A | A | g | C | A | G | 7 | 2 | 8 | c | false | <90% | 11242 | ||
| NM_006472 | TXNIP | 1146 | 1164 | g | C | A | U | G | g | c | C | A | G | C | C | G | A | A | C | C | A | G | -31 | 3 | 12 | bc | false | <90% | 2703 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2108
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