Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
9 hits were found for AGAGCUGAAACAACUAUAC (7 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_003463 | PTP4A1 | 2911 | 2929 | A | G | A | G | C | U | G | A | A | A | C | A | u | C | U | A | a | A | u | 61 | 3 | 12 | false | <90% | 5099 | |||
| NM_024629 | MLF1IP | 1066 | 1084 | A | c | A | G | C | U | G | A | A | A | C | A | A | C | U | A | c | A | a | 60 | 3 | 14 | ac | false | <90% | 2547 | ||
| NM_174900 | ZFP42 | 228 | 246 | u | G | A | G | C | U | G | A | A | A | C | A | A | a | U | g | U | A | C | 52 | 3 | 12 | c | false | <90% | 2646 | ||
| NM_001008536 | TCHHL1 | 158 | 176 | A | G | A | G | C | U | G | A | A | A | C | A | A | C | U | c | a | u | C | 47 | 3 | 15 | c | false | <90% | 3603 | ||
| NM_002126 | HLF | 3955 | 3973 | g | u | A | G | C | U | G | A | A | A | a | A | A | C | U | A | U | A | u | 20 | 4 | 8 | c | false | <90% | 5607 | ||
| XM_943356 | LOC643680 | 410 | 428 | A | G | A | G | u | U | G | A | A | A | C | c | A | C | U | A | U | A | a | 9 | 3 | 6 | false | <90% | 584 | |||
| XM_931901 | LOC643680 | 410 | 428 | A | G | A | G | u | U | G | A | A | A | C | c | A | C | U | A | U | A | a | 9 | 3 | 6 | false | <90% | 584 | |||
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_002766 | PRPSAP1 | 1448 | 1466 | a | U | u | U | A | G | U | U | G | U | U | U | C | A | G | C | U | C | c | 73 | 3 | 15 | bc | false | <90% | 1728 | ||
| NR_003135 | CEP170L | 6656 | 6674 | u | U | A | U | A | G | U | U | G | U | U | c | C | A | G | C | U | u | U | 61 | 3 | 10 | false | <90% | 90477 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3354
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