Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for GGAAAUCUACUCAAGAUGA (16 guide strand hits and 2 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_147180 | PPP3R2 | 3159 | 3177 | a | u | A | A | A | U | C | U | A | C | U | C | A | A | G | A | U | a | g | 78 | 4 | 15 | ac | false | <90% | 3401 | ||
| NM_003668 | MAPKAPK5 | 381 | 399 | a | G | A | A | A | U | C | U | A | C | U | C | A | A | G | A | a | c | g | 66 | 4 | 15 | ac | false | <90% | 2060 | ||
| NM_139078 | MAPKAPK5 | 381 | 399 | a | G | A | A | A | U | C | U | A | C | U | C | A | A | G | A | a | c | g | 66 | 4 | 15 | ac | false | <90% | 2066 | ||
| NM_152490 | B3GALNT2 | 366 | 384 | G | G | A | A | A | U | C | U | A | C | U | C | A | c | u | A | U | G | A | 55 | 2 | 13 | c | false | <90% | 2022 | ||
| NM_030906 | STK33 | 2302 | 2320 | G | G | A | A | A | U | C | a | A | C | U | C | A | A | G | A | U | G | u | 32 | 2 | 10 | bc | false | <90% | 2707 | ||
| NM_016195 | MPHOSPH1 | 1559 | 1577 | u | c | A | A | A | U | C | U | u | C | U | C | A | A | G | A | U | G | u | 21 | 4 | 9 | bc | false | <90% | 6319 | ||
| NR_002723 | GABPAP | 137502 | 137520 | a | a | A | A | A | U | u | U | A | C | U | C | A | A | G | A | U | G | A | 20 | 3 | 12 | bc | false | <90% | 194142 | ||
| NM_199139 | XAF1 | 2329 | 2347 | a | a | A | A | A | U | C | a | A | C | U | C | A | A | G | A | U | G | g | 19 | 4 | 10 | bc | false | <90% | 3581 | ||
| NM_017523 | XAF1 | 2386 | 2404 | a | a | A | A | A | U | C | a | A | C | U | C | A | A | G | A | U | G | g | 19 | 4 | 10 | bc | false | <90% | 3638 | ||
| NM_144684 | ZNF480 | 3564 | 3582 | a | a | A | A | A | U | C | a | A | C | U | C | A | A | G | A | U | G | g | 19 | 4 | 10 | bc | false | <90% | 4732 | ||
| NM_003126 | SPTA1 | 5126 | 5144 | G | G | A | A | A | c | C | U | A | C | U | C | A | A | G | A | a | G | c | 8 | 3 | 10 | c | false | <90% | 8017 | ||
| XM_939560 | NBPF7 | 1412 | 1430 | G | u | g | A | A | U | C | U | u | C | U | C | A | A | G | A | U | G | A | 8 | 3 | 10 | bc | false | <90% | 1887 | ||
| NM_001047980 | NBPF7 | 1412 | 1430 | G | u | g | A | A | U | C | U | u | C | U | C | A | A | G | A | U | G | A | 8 | 3 | 10 | bc | false | <90% | 1887 | ||
| XR_015513 | LOC729342 | 671 | 689 | a | G | A | A | A | U | C | U | A | u | U | C | A | A | G | A | U | a | c | 7 | 4 | 8 | c | false | <90% | 1320 | ||
| XR_015144 | LOC730467 | 671 | 689 | a | G | A | A | A | U | C | U | A | u | U | C | A | A | G | A | U | a | c | 7 | 4 | 8 | c | false | <90% | 1320 | ||
| NM_015939 | CGI-09 | 433 | 451 | a | G | A | A | A | c | u | U | A | C | U | C | A | A | G | A | U | G | A | -31 | 3 | 12 | bc | false | <90% | 2311 | ||
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_014763 | MRPL19 | 4135 | 4153 | a | C | A | U | C | U | U | G | A | G | U | A | G | A | a | U | U | g | C | 70 | 3 | 13 | c | false | <90% | 7827 | ||
| NM_000909 | NPY1R | 1783 | 1801 | U | C | A | U | C | U | U | G | A | u | U | A | G | A | U | U | a | g | a | -13 | 4 | 9 | c | false | <90% | 2775 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1902
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