Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for ACAGAGCCCAUUACAAUAU (13 guide strand hits and 5 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_173199 | NR4A3 | 1863 | 1881 | A | a | A | G | A | G | C | C | C | A | U | U | A | C | A | A | c | A | g | 60 | 3 | 14 | ac | false | <90% | 2588 | ||
| NM_173200 | NR4A3 | 1211 | 1229 | A | a | A | G | A | G | C | C | C | A | U | U | A | C | A | A | c | A | g | 60 | 3 | 14 | ac | false | <90% | 4983 | ||
| NM_006981 | NR4A3 | 1863 | 1881 | A | a | A | G | A | G | C | C | C | A | U | U | A | C | A | A | c | A | g | 60 | 3 | 14 | ac | false | <90% | 5635 | ||
| NM_173198 | NR4A3 | 2610 | 2628 | A | a | A | G | A | G | C | C | C | A | U | U | A | C | A | A | c | A | g | 60 | 3 | 14 | ac | false | <90% | 6382 | ||
| NM_182506 | MAGEB10 | 612 | 630 | A | a | A | G | A | G | C | C | C | A | U | U | A | C | A | A | a | g | g | 57 | 4 | 14 | ac | false | <90% | 1567 | ||
| XR_018355 | LOC134357 | 841 | 859 | A | C | c | c | A | G | C | C | C | A | U | U | A | C | A | A | U | A | a | 38 | 3 | 14 | bc | false | <90% | 1052 | ||
| XR_018457 | LOC442153 | 279 | 297 | u | C | A | G | u | G | C | C | C | A | U | U | A | C | A | A | U | u | a | 38 | 4 | 12 | c | false | <90% | 1592 | ||
| XR_016425 | LOC442153 | 279 | 297 | u | C | A | G | u | G | C | C | C | A | U | U | A | C | A | A | U | u | a | 38 | 4 | 12 | c | false | <90% | 1592 | ||
| NM_176081 | TRDMT1 | 2862 | 2880 | A | C | A | G | A | G | C | C | u | A | U | U | A | C | A | A | g | u | c | 8 | 4 | 8 | c | false | <90% | 7143 | ||
| NM_176083 | TRDMT1 | 2928 | 2946 | A | C | A | G | A | G | C | C | u | A | U | U | A | C | A | A | g | u | c | 8 | 4 | 8 | c | false | <90% | 7209 | ||
| NM_004412 | TRDMT1 | 3000 | 3018 | A | C | A | G | A | G | C | C | u | A | U | U | A | C | A | A | g | u | c | 8 | 4 | 8 | c | false | <90% | 7281 | ||
| NM_004156 | PPP2CB | 557 | 575 | c | C | A | G | A | a | C | g | C | A | U | U | A | C | A | A | U | A | U | -27 | 3 | 11 | bc | false | <90% | 1807 | ||
| NM_001009552 | PPP2CB | 737 | 755 | c | C | A | G | A | a | C | g | C | A | U | U | A | C | A | A | U | A | U | -27 | 3 | 11 | bc | false | <90% | 1987 | ||
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_001031617 | COX19 | 3607 | 3625 | u | U | A | U | U | G | U | A | A | U | G | G | G | C | U | g | U | a | g | 64 | 4 | 14 | c | false | <90% | 4896 | ||
| NM_001033059 | AMD1 | 1813 | 1831 | u | U | A | U | U | G | U | A | A | U | G | u | G | C | U | C | U | u | U | 61 | 3 | 10 | false | <90% | 3103 | |||
| NM_001634 | AMD1 | 2131 | 2149 | u | U | A | U | U | G | U | A | A | U | G | u | G | C | U | C | U | u | U | 61 | 3 | 10 | false | <90% | 3421 | |||
| NM_003192 | TBCC | 1233 | 1251 | A | g | A | U | U | G | U | A | A | U | G | G | G | C | U | C | c | u | a | 57 | 4 | 14 | ac | false | <90% | 1675 | ||
| NM_004747 | DLG5 | 7006 | 7024 | g | U | A | c | U | G | U | A | c | U | G | G | G | C | U | C | U | G | U | 1 | 3 | 10 | bc | false | <90% | 7493 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2796
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