Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for GACAUAGAUUGUUGGUGCA (10 guide strand hits and 6 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_003692 | TMEFF1 | 2114 | 2132 | u | u | C | A | U | A | G | A | U | U | G | U | U | G | G | U | G | u | u | 78 | 4 | 15 | ac | false | <90% | 2299 | ||
| NM_001004059 | OR4S2 | 567 | 585 | a | A | C | A | U | A | c | A | U | U | G | U | U | G | G | U | G | u | u | 24 | 4 | 10 | c | false | <90% | 936 | ||
| NM_012448 | STAT5B | 3123 | 3141 | u | A | C | A | a | A | G | A | U | U | G | U | U | G | G | g | G | C | A | 20 | 3 | 10 | c | false | <90% | 5171 | ||
| NM_032228 | MLSTD2 | 774 | 792 | G | c | C | A | U | c | G | A | U | U | G | U | U | G | G | U | G | C | c | 20 | 3 | 12 | bc | false | <90% | 5224 | ||
| NM_001011657 | ZMAT1 | 1618 | 1636 | G | A | C | A | U | A | G | A | a | U | G | U | U | G | G | a | G | C | A | 13 | 2 | 8 | c | false | <90% | 3448 | ||
| NM_032441 | ZMAT1 | 4292 | 4310 | G | A | C | A | U | A | G | A | a | U | G | U | U | G | G | a | G | C | A | 13 | 2 | 8 | c | false | <90% | 6122 | ||
| NM_020935 | USP37 | 4010 | 4028 | G | A | a | A | U | g | G | A | U | U | G | U | U | G | G | U | G | C | u | 12 | 3 | 12 | bc | false | <90% | 8015 | ||
| NM_014342 | MTCH2 | 840 | 858 | u | g | g | A | U | A | G | A | c | U | G | U | U | G | G | U | G | C | A | 6 | 4 | 10 | bc | false | <90% | 2524 | ||
| XM_374912 | XRRA1 | 7041 | 7059 | G | A | C | A | U | A | a | A | U | U | G | U | U | G | G | U | a | g | g | 2 | 4 | 9 | c | false | <90% | 7270 | ||
| XM_945928 | XRRA1 | 7041 | 7059 | G | A | C | A | U | A | a | A | U | U | G | U | U | G | G | U | a | g | g | 2 | 4 | 9 | c | false | <90% | 7270 | ||
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_006289 | TLN1 | 7299 | 7317 | g | c | C | A | C | C | A | A | C | A | A | U | C | U | g | U | G | U | g | 56 | 4 | 12 | c | false | <90% | 8187 | ||
| XM_495886 | RNF169 | 4206 | 4224 | c | c | u | A | C | C | A | A | C | A | A | U | u | U | A | U | G | U | C | 56 | 4 | 9 | false | <90% | 8900 | |||
| XM_940188 | RNF169 | 4206 | 4224 | c | c | u | A | C | C | A | A | C | A | A | U | u | U | A | U | G | U | C | 56 | 4 | 9 | false | <90% | 8900 | |||
| XM_936538 | FAT3 | 918 | 936 | U | G | C | c | C | C | A | A | C | A | A | U | C | c | A | U | G | U | a | 38 | 3 | 9 | c | false | <90% | 19162 | ||
| XM_926199 | FAT3 | 918 | 936 | U | G | C | c | C | C | A | A | C | A | A | U | C | c | A | U | G | U | a | 38 | 3 | 9 | c | false | <90% | 19163 | ||
| NM_022840 | METTL4 | 2384 | 2402 | U | G | C | A | C | u | A | A | C | A | u | U | C | U | A | U | G | U | u | -29 | 3 | 7 | c | false | <90% | 3691 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1087
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