Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GGACAGAGCCCAUUACAAU (15 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_182506 | MAGEB10 | 610 | 628 | u | G | A | a | A | G | A | G | C | C | C | A | U | U | A | C | A | A | a | 56 | 3 | 14 | bc | false | <90% | 1567 | ||
| NM_173199 | NR4A3 | 1861 | 1879 | c | c | A | a | A | G | A | G | C | C | C | A | U | U | A | C | A | A | c | 44 | 4 | 14 | bc | false | <90% | 2588 | ||
| NM_173200 | NR4A3 | 1209 | 1227 | c | c | A | a | A | G | A | G | C | C | C | A | U | U | A | C | A | A | c | 44 | 4 | 14 | bc | false | <90% | 4983 | ||
| NM_006981 | NR4A3 | 1861 | 1879 | c | c | A | a | A | G | A | G | C | C | C | A | U | U | A | C | A | A | c | 44 | 4 | 14 | bc | false | <90% | 5635 | ||
| NM_173198 | NR4A3 | 2608 | 2626 | c | c | A | a | A | G | A | G | C | C | C | A | U | U | A | C | A | A | c | 44 | 4 | 14 | bc | false | <90% | 6382 | ||
| XM_001130425 | LOC645864 | 377 | 395 | G | G | A | a | A | G | A | G | C | C | C | A | U | U | A | C | g | A | g | 34 | 3 | 12 | c | false | <90% | 1011 | ||
| XM_942566 | LOC645864 | 377 | 395 | G | G | A | a | A | G | A | G | C | C | C | A | U | U | A | C | g | A | g | 34 | 3 | 12 | c | false | <90% | 1011 | ||
| NM_176081 | TRDMT1 | 2860 | 2878 | a | G | A | C | A | G | A | G | C | C | u | A | U | U | A | C | A | A | g | 31 | 3 | 9 | c | false | <90% | 7143 | ||
| NM_176083 | TRDMT1 | 2926 | 2944 | a | G | A | C | A | G | A | G | C | C | u | A | U | U | A | C | A | A | g | 31 | 3 | 9 | c | false | <90% | 7209 | ||
| NM_004412 | TRDMT1 | 2998 | 3016 | a | G | A | C | A | G | A | G | C | C | u | A | U | U | A | C | A | A | g | 31 | 3 | 9 | c | false | <90% | 7281 | ||
| NM_016574 | DRD2 | 252 | 270 | G | G | A | C | A | G | A | c | C | C | C | A | c | U | A | C | A | A | c | 22 | 3 | 7 | false | <90% | 2556 | |||
| NM_000795 | DRD2 | 252 | 270 | G | G | A | C | A | G | A | c | C | C | C | A | c | U | A | C | A | A | c | 22 | 3 | 7 | false | <90% | 2643 | |||
| XR_018457 | LOC442153 | 277 | 295 | a | c | u | C | A | G | u | G | C | C | C | A | U | U | A | C | A | A | U | 0 | 4 | 12 | bc | false | <90% | 1592 | ||
| XR_016425 | LOC442153 | 277 | 295 | a | c | u | C | A | G | u | G | C | C | C | A | U | U | A | C | A | A | U | 0 | 4 | 12 | bc | false | <90% | 1592 | ||
| XR_018355 | LOC134357 | 839 | 857 | u | G | A | C | c | c | A | G | C | C | C | A | U | U | A | C | A | A | U | -16 | 3 | 13 | bc | false | <90% | 1052 | ||
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_021080 | DAB1 | 1577 | 1595 | g | U | U | G | c | A | A | U | G | G | G | C | g | C | U | G | U | C | C | 36 | 3 | 7 | false | <90% | 2580 | |||
| NM_012096 | APPL1 | 2590 | 2608 | A | U | U | G | U | A | A | U | u | G | G | C | U | g | U | G | U | C | C | 20 | 2 | 8 | c | false | <90% | 6061 | ||
| XR_017972 | LOC283174 | 1628 | 1646 | u | g | g | G | a | A | A | U | G | G | G | C | U | C | U | G | U | C | C | 15 | 4 | 14 | bc | false | <90% | 3887 | ||
| XR_017873 | LOC283174 | 1629 | 1647 | u | g | g | G | a | A | A | U | G | G | G | C | U | C | U | G | U | C | C | 15 | 4 | 14 | bc | false | <90% | 3888 | ||
| NR_002774 | HTR7P | 1316 | 1334 | g | U | U | G | U | g | A | U | c | G | G | C | U | C | U | G | U | C | C | -25 | 3 | 10 | bc | false | <90% | 2774 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2602
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