Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
19 hits were found for UUUCCUGGCUAGUGGAUUU (7 guide strand hits and 12 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_002293 | LAMC1 | 7310 | 7328 | U | U | U | C | C | U | G | G | C | U | A | G | U | u | c | A | U | U | U | 55 | 2 | 13 | c | false | <90% | 7889 | ||
| NM_080764 | SUHW2 | 646 | 664 | c | U | U | C | C | U | G | G | C | U | g | G | U | G | G | A | U | g | a | 29 | 4 | 9 | c | false | <90% | 5733 | ||
| NM_018643 | TREM1 | 688 | 706 | U | c | U | C | C | U | G | G | C | U | g | G | U | G | G | A | U | U | c | 22 | 3 | 8 | c | false | <90% | 948 | ||
| NM_021943 | ZFAND3 | 1023 | 1041 | g | a | g | C | a | U | G | G | C | U | A | G | U | G | G | A | U | U | U | 15 | 4 | 14 | bc | false | <90% | 3005 | ||
| NM_001006605 | FAM69A | 119 | 137 | U | U | U | C | C | U | G | G | u | U | A | G | U | G | G | u | U | U | U | 13 | 2 | 8 | c | false | <90% | 670 | ||
| NM_003264 | TLR2 | 2257 | 2275 | a | U | U | C | C | U | G | G | C | a | A | G | U | G | G | A | U | c | a | 7 | 4 | 8 | c | false | <90% | 3417 | ||
| NM_014801 | PCNXL2 | 2678 | 2696 | U | U | c | C | C | U | G | G | C | a | A | G | U | G | G | A | U | U | a | -7 | 3 | 8 | bc | false | <90% | 6817 | ||
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 | |||||||||||||
| XM_001129965 | LOC728224 | 798 | 816 | u | A | A | U | C | C | A | C | U | A | G | C | u | A | a | G | A | A | A | 62 | 3 | 11 | false | <90% | 1104 | |||
| XM_001130340 | KRTAP4-8 | 828 | 846 | u | A | A | U | C | C | A | C | U | A | G | C | u | A | a | G | A | A | A | 62 | 3 | 11 | false | <90% | 1134 | |||
| XM_927495 | KRTAP4-8 | 828 | 846 | u | A | A | U | C | C | A | C | U | A | G | C | u | A | a | G | A | A | A | 62 | 3 | 11 | false | <90% | 1134 | |||
| XM_926590 | LOC653240 | 873 | 891 | u | A | A | U | C | C | A | C | U | A | G | C | u | A | a | G | A | A | A | 62 | 3 | 11 | false | <90% | 1180 | |||
| NM_033059 | KRTAP4-14 | 873 | 891 | u | A | A | U | C | C | A | C | U | A | G | C | u | A | a | G | A | A | A | 62 | 3 | 11 | false | <90% | 1219 | |||
| NM_014991 | WDFY3 | 4730 | 4748 | u | A | A | c | C | C | A | C | U | A | G | C | C | A | G | c | A | A | A | 35 | 3 | 11 | c | false | <90% | 14315 | ||
| NR_002723 | GABPAP | 36820 | 36838 | A | A | A | U | C | C | A | C | c | A | G | C | C | u | G | G | A | A | A | 20 | 2 | 8 | c | false | <90% | 194142 | ||
| NM_002718 | PPP2R3A | 2069 | 2087 | A | A | u | U | C | C | A | g | U | A | G | C | C | A | G | G | A | A | g | 13 | 3 | 10 | bc | false | <90% | 6762 | ||
| NM_002598 | PDCD2 | 372 | 390 | g | A | A | U | C | a | A | C | U | A | c | C | C | A | G | G | A | A | A | -26 | 3 | 8 | c | false | <90% | 1311 | ||
| NM_144781 | PDCD2 | 372 | 390 | g | A | A | U | C | a | A | C | U | A | c | C | C | A | G | G | A | A | A | -26 | 3 | 8 | c | false | <90% | 2066 | ||
| NM_022771 | TBC1D15 | 1194 | 1212 | A | A | A | U | C | C | A | u | c | A | G | C | C | A | G | G | A | A | c | -27 | 3 | 9 | bc | false | <90% | 3228 | ||
| NM_032168 | WDR75 | 466 | 484 | A | A | A | U | C | C | u | C | a | A | G | C | C | A | G | G | A | A | g | -31 | 3 | 9 | bc | false | <90% | 2777 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4776
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