Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
16 hits were found for CUGAACACUUCACUGCAAG (7 guide strand hits and 9 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_052909 | KIAA1909 | 1096 | 1114 | u | g | G | A | A | C | A | C | U | U | C | g | C | U | G | C | A | A | a | 47 | 4 | 9 | false | <90% | 11507 | |||
| NM_033188 | KRTAP4-5 | 664 | 682 | a | U | G | A | A | C | A | C | U | U | C | c | C | U | G | C | c | A | G | 40 | 3 | 10 | false | <90% | 927 | |||
| XM_371461 | KIAA1671 | 5696 | 5714 | C | U | G | A | g | C | A | C | U | U | C | A | C | U | G | C | u | g | u | 17 | 4 | 11 | c | false | <90% | 8164 | ||
| XM_938689 | KIAA1671 | 5696 | 5714 | C | U | G | A | g | C | A | C | U | U | C | A | C | U | G | C | u | g | u | 17 | 4 | 11 | c | false | <90% | 8164 | ||
| XM_001131269 | GRB14 | 12 | 30 | a | U | G | A | c | C | A | C | U | U | C | c | C | U | G | C | A | A | G | 12 | 3 | 7 | false | <90% | 2264 | |||
| NM_004490 | GRB14 | 542 | 560 | a | U | G | A | c | C | A | C | U | U | C | c | C | U | G | C | A | A | G | 12 | 3 | 7 | false | <90% | 2402 | |||
| NM_033274 | ADAM19 | 4398 | 4416 | u | U | G | A | A | a | A | C | c | U | C | A | C | U | G | C | A | A | G | -25 | 3 | 10 | bc | false | <90% | 6466 | ||
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_001083585 | RABEP1 | 4495 | 4513 | C | U | U | G | C | A | G | U | G | A | A | G | U | G | U | U | C | u | G | 97 | 1 | 17 | ac | false | <90% | 5322 | ||
| NM_004703 | RABEP1 | 4594 | 4612 | C | U | U | G | C | A | G | U | G | A | A | G | U | G | U | U | C | u | G | 97 | 1 | 17 | ac | false | <90% | 5421 | ||
| NM_022751 | FAM59A | 1564 | 1582 | g | c | a | G | C | A | G | U | G | A | A | G | U | c | U | U | C | A | G | 47 | 4 | 10 | c | false | <90% | 3055 | ||
| NM_000113 | TOR1A | 1660 | 1678 | g | g | g | G | C | A | G | U | G | A | A | G | U | G | U | U | u | A | G | 43 | 4 | 13 | c | false | <90% | 2117 | ||
| NM_130436 | DYRK1A | 33 | 51 | u | U | U | c | C | A | G | U | G | A | A | G | U | G | U | U | u | A | G | 37 | 3 | 12 | c | false | <90% | 6580 | ||
| NM_014742 | TM9SF4 | 2694 | 2712 | C | U | U | G | C | A | G | U | G | A | A | c | U | G | U | U | u | u | u | 35 | 4 | 11 | false | <90% | 3752 | |||
| NR_002923 | BCORL2 | 1945 | 1963 | C | U | U | G | C | A | G | U | G | A | u | G | U | G | U | U | u | g | a | 7 | 4 | 10 | c | false | <90% | 3460 | ||
| NM_005385 | NKTR | 2584 | 2602 | u | g | a | G | C | A | G | U | c | A | A | G | U | G | U | U | C | A | G | 6 | 4 | 10 | bc | false | <90% | 7312 | ||
| NM_018072 | HEATR1 | 354 | 372 | C | U | U | G | g | A | G | c | G | A | A | G | U | G | U | U | C | A | G | -13 | 2 | 11 | bc | false | <90% | 6791 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2217
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