Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
25 hits were found for AAUGCUACAUUCUUCAUCU (8 guide strand hits and 17 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 | |||||||||||||
| NR_003263 | SDHAP3 | 13378 | 13396 | A | A | U | G | g | U | A | C | A | U | U | C | c | U | C | A | U | C | U | 38 | 2 | 7 | false | <90% | 21323 | |||
| NM_031264 | MUPCDH | 994 | 1012 | A | A | U | G | g | U | A | C | A | U | U | C | a | U | C | A | U | C | c | 33 | 3 | 7 | false | <90% | 2837 | |||
| NM_021924 | MUPCDH | 994 | 1012 | A | A | U | G | g | U | A | C | A | U | U | C | a | U | C | A | U | C | c | 33 | 3 | 7 | false | <90% | 3419 | |||
| NM_015263 | DMXL2 | 3087 | 3105 | c | A | U | G | C | c | A | C | A | U | U | C | U | U | C | A | U | C | a | 29 | 3 | 12 | bc | false | <90% | 10580 | ||
| NM_152430 | OR51E1 | 228 | 246 | A | g | U | G | C | U | A | C | A | U | a | C | U | U | C | A | U | C | c | 22 | 3 | 8 | c | false | <90% | 1350 | ||
| NM_021977 | SLC22A3 | 5449 | 5467 | A | A | U | G | C | U | A | C | A | a | U | C | U | U | C | A | U | a | a | 9 | 3 | 9 | c | false | <90% | 5624 | ||
| NM_005646 | TARBP1 | 1592 | 1610 | A | A | U | G | C | U | A | C | c | U | U | C | U | U | C | A | a | a | c | 8 | 4 | 8 | c | false | <90% | 5130 | ||
| NM_019014 | POLR1B | 3295 | 3313 | g | A | U | G | C | U | A | C | A | c | c | C | U | U | C | A | U | C | U | -46 | 3 | 8 | c | false | <90% | 5968 | ||
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_144695 | C1orf58 | 562 | 580 | u | G | A | U | G | A | A | G | A | A | U | G | c | A | G | C | A | g | a | 79 | 4 | 11 | false | <90% | 1686 | |||
| NM_001616 | ACVR2A | 1940 | 1958 | A | c | A | U | G | A | A | G | A | A | U | G | U | A | G | C | c | c | U | 62 | 3 | 14 | ac | false | <90% | 5244 | ||
| NM_006724 | MAP3K4 | 4807 | 4825 | A | G | A | U | G | A | A | G | A | A | U | G | a | A | G | C | c | U | a | 61 | 3 | 12 | false | <90% | 5351 | |||
| NM_005922 | MAP3K4 | 4957 | 4975 | A | G | A | U | G | A | A | G | A | A | U | G | a | A | G | C | c | U | a | 61 | 3 | 12 | false | <90% | 5501 | |||
| NM_145860 | PDCD10 | 171 | 189 | A | G | A | U | G | A | A | G | A | A | U | G | a | A | G | C | u | g | a | 58 | 4 | 12 | false | <90% | 1212 | |||
| NM_145859 | PDCD10 | 265 | 283 | A | G | A | U | G | A | A | G | A | A | U | G | a | A | G | C | u | g | a | 58 | 4 | 12 | false | <90% | 1313 | |||
| NM_007217 | PDCD10 | 416 | 434 | A | G | A | U | G | A | A | G | A | A | U | G | a | A | G | C | u | g | a | 58 | 4 | 12 | false | <90% | 1454 | |||
| NM_024302 | MMP28 | 1977 | 1995 | c | c | u | U | G | A | A | G | A | A | U | G | c | A | G | C | A | U | U | 56 | 4 | 9 | false | <90% | 2480 | |||
| NM_003879 | CFLAR | 1619 | 1637 | c | G | A | U | G | A | A | G | A | A | U | G | U | g | G | a | A | U | U | 52 | 3 | 12 | c | false | <90% | 2243 | ||
| NM_001029964 | TTLL13 | 1704 | 1722 | A | G | A | U | G | A | A | G | A | A | U | G | U | g | G | C | c | U | g | 51 | 3 | 13 | c | false | <90% | 1793 | ||
| NM_153757 | NAP1L5 | 1443 | 1461 | A | G | A | U | G | u | A | G | A | A | U | G | U | A | G | C | A | a | a | 29 | 3 | 11 | c | false | <90% | 1912 | ||
| NM_020920 | CHD8 | 953 | 971 | A | G | A | U | G | A | A | G | A | A | a | G | c | A | G | C | A | U | U | 28 | 2 | 10 | false | <90% | 7525 | |||
| NM_203408 | FAM47A | 2108 | 2126 | A | G | A | U | G | A | A | G | u | A | U | G | g | A | G | C | A | U | g | 24 | 3 | 8 | false | <90% | 2556 | |||
| NM_006870 | DSTN | 281 | 299 | u | G | A | U | G | A | A | G | u | A | U | G | U | c | G | C | A | U | U | 18 | 3 | 7 | c | false | <90% | 1614 | ||
| NM_001011546 | DSTN | 413 | 431 | u | G | A | U | G | A | A | G | u | A | U | G | U | c | G | C | A | U | U | 18 | 3 | 7 | c | false | <90% | 1746 | ||
| NM_176821 | NLRP10 | 1757 | 1775 | A | G | A | U | G | A | A | c | A | A | U | G | U | A | u | C | A | U | U | 13 | 2 | 7 | c | false | <90% | 2020 | ||
| NM_152565 | ATP6V0D2 | 855 | 873 | A | G | A | U | G | A | A | G | A | A | c | G | U | A | G | C | g | g | a | 7 | 4 | 10 | c | false | <90% | 2370 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1936
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