Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for GAGCCAUUUGGUUCAUGUG (9 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_005612 | REST | 3587 | 3605 | u | c | G | C | C | A | U | U | U | G | G | U | U | a | A | U | G | U | G | 67 | 3 | 11 | c | false | <90% | 3663 | ||
| NM_001279 | CIDEA | 944 | 962 | G | A | G | C | C | A | U | U | U | G | G | U | c | C | A | U | c | a | u | 58 | 4 | 12 | false | <90% | 996 | |||
| NM_198289 | CIDEA | 1061 | 1079 | G | A | G | C | C | A | U | U | U | G | G | U | c | C | A | U | c | a | u | 58 | 4 | 12 | false | <90% | 1113 | |||
| XR_019466 | LOC649728 | 1255 | 1273 | G | A | G | C | C | A | U | U | U | G | G | U | c | C | A | U | c | a | u | 58 | 4 | 12 | false | <90% | 1307 | |||
| NM_031959 | KRTAP3-2 | 512 | 530 | a | A | a | C | C | A | U | U | U | G | G | U | U | C | c | U | G | U | G | 53 | 3 | 11 | c | false | <90% | 749 | ||
| NM_016201 | AMOTL2 | 4151 | 4169 | a | A | u | a | C | A | U | U | U | G | G | U | U | C | A | U | G | U | G | 41 | 3 | 15 | bc | false | <90% | 4984 | ||
| NM_002451 | MTAP | 2829 | 2847 | G | A | G | C | C | A | U | U | U | G | G | g | U | C | A | a | G | U | a | 35 | 3 | 11 | false | <90% | 4937 | |||
| NR_003135 | CEP170L | 45863 | 45881 | G | A | G | u | C | A | U | U | U | G | G | U | U | C | A | U | a | U | a | 34 | 3 | 12 | c | false | <90% | 90477 | ||
| NM_144582 | TEX261 | 110 | 128 | G | c | G | C | C | A | U | g | U | G | G | U | U | C | A | U | G | U | a | 21 | 3 | 10 | bc | false | <90% | 3381 | ||
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_002941 | ROBO1 | 6104 | 6122 | g | c | C | A | U | G | A | A | C | C | A | A | A | U | G | G | u | U | C | 63 | 3 | 14 | ac | false | <90% | 6629 | ||
| NM_133631 | ROBO1 | 6950 | 6968 | g | c | C | A | U | G | A | A | C | C | A | A | A | U | G | G | u | U | C | 63 | 3 | 14 | ac | false | <90% | 7475 | ||
| NM_004972 | JAK2 | 2083 | 2101 | C | A | u | A | U | G | A | A | C | C | A | A | A | U | G | G | u | g | u | 49 | 4 | 13 | c | false | <90% | 5097 | ||
| NR_000035 | CASP12 | 1091 | 1109 | g | A | C | A | U | G | A | A | a | C | A | A | A | U | G | G | C | U | C | 37 | 2 | 10 | bc | false | <90% | 1306 | ||
| NM_024690 | MUC16 | 32240 | 32258 | g | A | C | A | a | G | A | A | C | C | A | c | A | U | G | G | C | U | C | 12 | 3 | 7 | false | <90% | 43816 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1841
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