Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for UCAUCUCUUGUUCAUGUCC (8 guide strand hits and 14 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_018372 | C1orf103 | 1160 | 1178 | c | C | A | U | C | U | C | U | U | G | U | U | C | c | U | G | U | u | a | 70 | 4 | 12 | c | false | <90% | 3349 | ||
| NM_080682 | VCAM1 | 1703 | 1721 | U | C | A | U | C | U | C | U | U | G | U | a | C | A | U | G | U | g | g | 58 | 3 | 11 | false | <90% | 2843 | |||
| NM_001078 | VCAM1 | 1979 | 1997 | U | C | A | U | C | U | C | U | U | G | U | a | C | A | U | G | U | g | g | 58 | 3 | 11 | false | <90% | 3119 | |||
| NM_000384 | APOB | 10917 | 10935 | U | C | A | g | C | U | C | U | U | G | U | U | C | A | g | G | U | C | C | 38 | 2 | 10 | c | false | <90% | 14121 | ||
| XR_016039 | LOC731950 | 5594 | 5612 | U | C | A | U | u | U | C | U | U | G | U | U | a | A | U | G | U | C | u | 33 | 3 | 7 | false | <90% | 5853 | |||
| NM_138390 | TMEM169 | 3012 | 3030 | U | C | u | U | u | U | C | U | U | G | U | U | C | A | U | G | U | C | u | 23 | 3 | 13 | bc | false | <90% | 3307 | ||
| NM_005981 | TSPAN31 | 426 | 444 | U | a | A | U | C | U | C | U | U | G | c | U | C | A | U | G | U | C | u | 22 | 3 | 8 | c | false | <90% | 1749 | ||
| NM_020128 | MDM1 | 1142 | 1160 | U | C | u | U | C | U | C | U | g | G | U | U | C | A | U | G | U | C | C | 20 | 2 | 10 | bc | false | <90% | 2092 | ||
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_031310 | PLVAP | 494 | 512 | G | G | A | C | A | U | G | A | A | C | A | A | G | A | G | c | U | G | c | 68 | 2 | 15 | c | false | <90% | 2317 | ||
| NM_001006615 | WDR31 | 421 | 439 | G | G | A | C | A | U | G | A | A | C | A | u | G | A | G | A | U | c | A | 63 | 2 | 11 | false | <90% | 2322 | |||
| NM_145241 | WDR31 | 551 | 569 | G | G | A | C | A | U | G | A | A | C | A | u | G | A | G | A | U | c | A | 63 | 2 | 11 | false | <90% | 2452 | |||
| NM_001012361 | WDR31 | 554 | 572 | G | G | A | C | A | U | G | A | A | C | A | u | G | A | G | A | U | c | A | 63 | 2 | 11 | false | <90% | 2455 | |||
| NM_032342 | C9orf125 | 302 | 320 | a | G | A | C | A | U | G | A | A | C | A | A | a | A | G | u | U | G | A | 61 | 3 | 11 | false | <90% | 2110 | |||
| NM_152510 | HORMAD2 | 1737 | 1755 | u | G | A | g | A | U | G | A | A | C | A | A | u | A | G | A | U | G | A | 50 | 3 | 8 | false | <90% | 1909 | |||
| XM_496269 | DKFZp686J0529 | 943 | 961 | G | G | A | C | A | U | G | A | A | C | A | A | G | A | G | g | g | a | c | 42 | 4 | 15 | c | false | <90% | 2236 | ||
| NM_152620 | TRIM60 | 758 | 776 | c | a | g | a | A | U | G | A | A | C | A | A | G | A | G | A | U | G | A | 30 | 4 | 15 | bc | false | <90% | 1842 | ||
| NM_014862 | ARNT2 | 3605 | 3623 | a | G | A | C | A | a | G | A | A | C | A | A | G | A | G | c | U | G | A | 8 | 3 | 9 | c | false | <90% | 6576 | ||
| XR_018333 | LOC441687 | 1638 | 1656 | G | G | A | C | A | a | G | A | A | C | A | A | G | A | G | A | a | u | u | 5 | 4 | 10 | c | false | <90% | 2047 | ||
| XR_017135 | LOC441687 | 1638 | 1656 | G | G | A | C | A | a | G | A | A | C | A | A | G | A | G | A | a | u | u | 5 | 4 | 10 | c | false | <90% | 2047 | ||
| NM_018318 | CCDC91 | 1184 | 1202 | u | G | A | a | A | a | G | A | A | C | A | A | G | A | G | A | U | G | A | -2 | 3 | 13 | bc | false | <90% | 2352 | ||
| NM_016343 | CENPF | 1082 | 1100 | G | G | A | C | A | U | G | A | A | a | A | A | G | A | a | A | U | G | A | -7 | 2 | 9 | c | false | <90% | 10316 | ||
| NM_147191 | MMP21 | 1203 | 1221 | G | G | A | C | A | U | G | g | A | a | A | A | G | A | G | A | U | G | A | -44 | 2 | 9 | bc | false | <90% | 1919 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2489
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