Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for CCUUGUGGUACUGCCUGAU (9 guide strand hits and 9 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_020853 | KIAA1467 | 803 | 821 | a | g | U | U | G | U | G | G | U | A | C | U | G | C | C | a | G | A | c | 55 | 4 | 13 | c | false | <90% | 4725 | ||
| NM_014631 | SH3PXD2A | 3376 | 3394 | g | C | U | g | G | U | G | G | U | A | C | U | G | C | C | a | G | A | U | 35 | 3 | 11 | c | false | <90% | 11264 | ||
| XR_015877 | LOC728850 | 1555 | 1573 | C | C | U | U | G | a | G | G | U | A | C | U | c | C | C | U | G | A | g | 21 | 3 | 6 | false | <90% | 1925 | |||
| XR_015112 | LOC727736 | 1623 | 1641 | C | C | U | U | G | a | G | G | U | A | C | U | c | C | C | U | G | A | g | 21 | 3 | 6 | false | <90% | 1993 | |||
| NM_003025 | SH3GL1 | 1342 | 1360 | C | C | U | U | G | a | G | G | U | A | C | U | c | C | C | U | G | A | g | 21 | 3 | 6 | false | <90% | 2460 | |||
| XR_017405 | LOC285412 | 1986 | 2004 | g | C | U | U | c | U | G | G | U | A | g | U | G | C | C | U | G | A | U | -14 | 3 | 8 | c | false | <90% | 2279 | ||
| XR_019409 | LOC285412 | 1987 | 2005 | g | C | U | U | c | U | G | G | U | A | g | U | G | C | C | U | G | A | U | -14 | 3 | 8 | c | false | <90% | 2287 | ||
| NM_138282 | ATP6V1G2 | 59 | 77 | C | C | U | U | u | g | G | G | U | A | C | U | G | C | C | U | G | A | g | -19 | 3 | 12 | bc | false | <90% | 1440 | ||
| NM_130463 | ATP6V1G2 | 59 | 77 | C | C | U | U | u | g | G | G | U | A | C | U | G | C | C | U | G | A | g | -19 | 3 | 12 | bc | false | <90% | 1594 | ||
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_194302 | CCDC108 | 4670 | 4688 | A | U | g | A | G | G | C | A | G | U | A | u | C | A | C | A | A | G | G | 46 | 2 | 8 | false | <90% | 5975 | |||
| NM_017859 | UCKL1 | 800 | 818 | A | U | C | A | a | G | C | A | G | U | A | C | a | A | C | A | A | G | u | 33 | 3 | 7 | false | <90% | 1833 | |||
| NM_000448 | RAG1 | 1567 | 1585 | u | g | C | A | G | u | C | A | G | U | A | C | C | A | C | A | A | G | a | 18 | 4 | 12 | bc | false | <90% | 6557 | ||
| NM_000283 | PDE6B | 807 | 825 | g | a | g | A | G | G | C | A | G | U | u | C | C | A | C | A | A | G | G | 5 | 4 | 8 | c | false | <90% | 3283 | ||
| XR_019200 | LOC391744 | 154 | 172 | A | U | C | A | G | G | a | A | G | U | A | C | C | A | u | A | A | G | u | 4 | 3 | 7 | c | false | <90% | 443 | ||
| NR_003377 | LOC728939 | 3392 | 3410 | A | U | C | A | G | G | a | A | G | U | A | C | C | A | g | A | A | G | u | 4 | 3 | 7 | c | false | <90% | 18232 | ||
| NM_003173 | SUV39H1 | 303 | 321 | c | U | C | A | a | G | C | A | G | U | u | C | C | A | C | A | A | G | G | -14 | 3 | 8 | c | false | <90% | 2745 | ||
| NM_014714 | IFT140 | 3302 | 3320 | g | U | C | A | u | G | C | u | G | U | A | C | C | A | C | A | A | G | G | -15 | 3 | 11 | bc | false | <90% | 4966 | ||
| NM_031271 | TEX15 | 8258 | 8276 | A | U | C | A | G | c | C | A | u | U | A | C | C | A | C | A | A | G | c | -28 | 3 | 9 | bc | false | <90% | 10155 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2618
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