Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for UGUUCAGGCUAGAGAGGCA (7 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 | |||||||||||||
| XM_001133018 | LOC730373 | 42 | 60 | a | G | a | U | C | A | G | G | C | U | A | a | A | G | A | G | G | C | A | 44 | 3 | 8 | false | <90% | 246 | |||
| XM_001132878 | LOC730195 | 42 | 60 | a | G | a | U | C | A | G | G | C | U | A | a | A | G | A | G | G | C | A | 44 | 3 | 8 | false | <90% | 246 | |||
| XM_001129909 | LOC731512 | 42 | 60 | a | G | a | U | C | A | G | G | C | U | A | a | A | G | A | G | G | C | A | 44 | 3 | 8 | false | <90% | 246 | |||
| NM_024576 | OGFRL1 | 1542 | 1560 | a | G | U | U | u | A | G | G | C | U | A | G | A | G | A | G | G | a | A | 43 | 3 | 12 | c | false | <90% | 1755 | ||
| XM_001132212 | HS3ST4 | 1366 | 1384 | a | a | a | U | g | A | G | G | C | U | A | G | A | G | A | G | G | C | A | 15 | 4 | 14 | bc | false | <90% | 2808 | ||
| NM_006040 | HS3ST4 | 1758 | 1776 | a | a | a | U | g | A | G | G | C | U | A | G | A | G | A | G | G | C | A | 15 | 4 | 14 | bc | false | <90% | 3203 | ||
| NM_024643 | C14orf140 | 1372 | 1390 | c | G | U | U | C | A | G | G | C | U | g | G | A | G | A | G | a | C | A | 13 | 3 | 9 | c | false | <90% | 2093 | ||
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_175852 | TXLNA | 2406 | 2424 | U | G | C | C | U | C | U | C | U | A | G | C | C | U | G | c | A | C | A | 73 | 1 | 15 | c | false | <90% | 4843 | ||
| NM_005242 | F2RL1 | 1146 | 1164 | U | G | C | C | U | C | U | C | U | A | c | C | C | U | u | A | A | C | A | 14 | 2 | 10 | c | false | <90% | 2876 | ||
| NM_000783 | CYP26A1 | 395 | 413 | U | G | C | C | U | C | U | C | U | A | a | C | C | U | G | c | A | C | g | 7 | 3 | 10 | c | false | <90% | 2099 | ||
| NM_057157 | CYP26A1 | 542 | 560 | U | G | C | C | U | C | U | C | U | A | a | C | C | U | G | c | A | C | g | 7 | 3 | 10 | c | false | <90% | 2246 | ||
| NR_001545 | TTTY15 | 1115 | 1133 | U | G | C | C | U | u | U | C | U | A | G | a | C | U | G | A | A | C | c | -2 | 3 | 6 | false | <90% | 5262 | |||
| NM_153815 | RASGRF1 | 496 | 514 | U | G | C | C | U | C | U | C | U | g | c | C | C | U | G | A | A | C | u | -49 | 3 | 9 | c | false | <90% | 2843 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2683
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