Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
10 hits were found for UGAGACAGACGUGAUGCUC (4 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_001458 | FLNC | 257 | 275 | U | G | A | G | A | C | A | G | A | C | G | a | G | A | U | G | C | c | g | 58 | 3 | 11 | false | <90% | 9146 | |||
| NM_014371 | AKAP8L | 414 | 432 | g | G | A | G | A | C | A | G | A | C | a | U | G | A | U | G | C | a | a | 29 | 4 | 9 | c | false | <90% | 2136 | ||
| NM_001086 | AADAC | 487 | 505 | g | c | A | G | A | C | A | G | A | C | u | U | G | A | U | G | C | U | g | 20 | 4 | 8 | c | false | <90% | 1725 | ||
| NM_176820 | NLRP9 | 3361 | 3379 | U | G | A | c | A | C | A | G | A | a | G | U | G | A | U | G | C | U | a | -24 | 3 | 8 | bc | false | <90% | 3484 | ||
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_021072 | HCN1 | 4009 | 4027 | c | A | G | C | A | U | C | A | C | G | U | C | U | G | U | u | U | g | g | 64 | 4 | 14 | c | false | <90% | 5386 | ||
| NM_001009877 | BRD9 | 2050 | 2068 | G | A | G | C | A | U | C | A | C | G | U | g | U | G | g | C | U | C | c | 36 | 3 | 11 | false | <90% | 2395 | |||
| NM_023924 | BRD9 | 2519 | 2537 | G | A | G | C | A | U | C | A | C | G | U | g | U | G | g | C | U | C | c | 36 | 3 | 11 | false | <90% | 2843 | |||
| NR_002723 | GABPAP | 12502 | 12520 | G | u | G | C | A | U | C | A | u | G | U | C | U | G | U | C | U | C | u | 23 | 3 | 9 | bc | false | <90% | 194142 | ||
| NM_181521 | CMTM4 | 2476 | 2494 | G | A | G | C | A | c | C | A | C | G | U | C | U | G | c | C | U | C | A | 12 | 2 | 8 | c | false | <90% | 8133 | ||
| NM_001037984 | MGC15523 | 3783 | 3801 | c | A | G | C | A | g | C | A | g | G | U | C | U | G | U | C | U | C | A | -25 | 3 | 10 | bc | false | <90% | 4303 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2564
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