Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for AGAGGACUCUUGGACUCUC (9 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_004575 | POU4F2 | 1477 | 1495 | A | G | A | a | G | A | C | U | C | U | U | G | G | c | C | U | C | U | C | 43 | 2 | 9 | c | false | <90% | 3141 | ||
| NM_003439 | ZKSCAN1 | 2213 | 2231 | A | a | g | G | c | A | C | U | C | U | U | G | G | A | C | U | C | U | C | 17 | 3 | 14 | bc | false | <90% | 5494 | ||
| NM_033112 | C6orf153 | 922 | 940 | A | G | A | G | G | g | C | U | C | U | U | G | G | A | C | U | a | U | C | 13 | 2 | 10 | c | false | <90% | 1177 | ||
| NM_006640 | SEPT9 | 440 | 458 | c | c | g | G | G | A | C | U | C | U | g | G | G | A | C | U | C | U | C | 5 | 4 | 8 | c | false | <90% | 4452 | ||
| NM_001005411 | FCGR2C | 279 | 297 | A | G | A | G | G | A | C | U | C | U | g | u | G | A | C | U | C | U | g | 0 | 3 | 10 | false | <90% | 1463 | |||
| NM_201563 | FCGR2C | 279 | 297 | A | G | A | G | G | A | C | U | C | U | g | u | G | A | C | U | C | U | g | 0 | 3 | 10 | false | <90% | 1501 | |||
| NM_001005410 | FCGR2C | 279 | 297 | A | G | A | G | G | A | C | U | C | U | g | u | G | A | C | U | C | U | g | 0 | 3 | 10 | false | <90% | 1515 | |||
| NM_020772 | NUFIP2 | 990 | 1008 | A | G | A | G | G | A | C | U | C | g | U | G | G | A | C | c | C | U | a | -13 | 3 | 9 | c | false | <90% | 4999 | ||
| NM_003262 | TLOC1 | 2346 | 2364 | A | G | A | G | a | A | C | U | a | U | U | G | G | A | C | U | C | U | a | -16 | 3 | 9 | bc | false | <90% | 6541 | ||
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_006691 | XLKD1 | 1113 | 1131 | a | A | G | A | G | U | C | C | A | A | G | A | G | U | C | C | a | a | g | 66 | 4 | 15 | ac | false | <90% | 2436 | ||
| NM_006035 | CDC42BPB | 3475 | 3493 | a | g | c | A | G | U | C | C | A | A | G | A | G | g | C | C | U | C | U | 47 | 4 | 10 | c | false | <90% | 6701 | ||
| NM_006534 | NCOA3 | 1902 | 1920 | a | g | G | A | u | U | C | C | A | A | G | A | G | U | C | C | U | C | U | 35 | 3 | 14 | bc | false | <90% | 7923 | ||
| NM_181659 | NCOA3 | 1902 | 1920 | a | g | G | A | u | U | C | C | A | A | G | A | G | U | C | C | U | C | U | 35 | 3 | 14 | bc | false | <90% | 7935 | ||
| NM_016201 | AMOTL2 | 3755 | 3773 | a | A | G | A | G | U | C | a | A | A | u | A | G | U | C | C | U | C | U | -25 | 3 | 8 | c | false | <90% | 4984 | ||
| NM_015026 | MON2 | 3624 | 3642 | c | A | G | A | G | U | u | C | g | A | G | A | G | U | C | C | U | C | U | -28 | 3 | 10 | bc | false | <90% | 10379 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2008
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