Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for UCUCAAUCUCGGGAAUCUC (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 | |||||||||||||
| NM_005618 | DLL1 | 70 | 88 | g | C | U | C | A | A | U | C | U | C | u | G | G | A | c | U | C | U | C | 11 | 3 | 9 | c | false | <90% | 3366 | ||
| NM_001025930 | TTLL3 | 543 | 561 | U | C | U | C | A | A | U | C | U | C | c | G | G | A | A | U | u | U | g | 10 | 3 | 10 | c | false | <90% | 3415 | ||
| NM_015644 | TTLL3 | 538 | 556 | U | C | U | C | A | A | U | C | U | C | c | G | G | A | A | U | u | U | g | 10 | 3 | 10 | c | false | <90% | 3454 | ||
| NM_175861 | TMTC1 | 1803 | 1821 | U | u | U | C | A | A | U | C | U | g | G | G | G | A | A | U | C | U | C | 5 | 2 | 9 | bc | false | <90% | 8821 | ||
| XM_939699 | C20orf82 | 2360 | 2378 | g | g | U | C | A | A | U | C | U | g | G | G | G | A | A | U | C | U | u | -1 | 4 | 8 | bc | false | <90% | 2587 | ||
| XM_097736 | C20orf82 | 2360 | 2378 | g | g | U | C | A | A | U | C | U | g | G | G | G | A | A | U | C | U | u | -1 | 4 | 8 | bc | false | <90% | 2587 | ||
| NM_001356 | DDX3X | 174 | 192 | U | C | U | C | A | g | U | u | U | C | G | G | G | A | A | U | C | U | g | -30 | 3 | 10 | bc | false | <90% | 5433 | ||
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_138769 | RHOT2 | 478 | 496 | c | A | G | u | U | U | C | C | C | G | A | G | A | U | U | G | A | G | A | 61 | 2 | 15 | bc | false | <90% | 2509 | ||
| XR_017344 | LOC283343 | 654 | 672 | G | A | c | A | U | U | C | u | C | G | A | G | A | U | U | G | A | G | u | 13 | 3 | 10 | bc | false | <90% | 1231 | ||
| XR_019211 | LOC283343 | 654 | 672 | G | A | c | A | U | U | C | u | C | G | A | G | A | U | U | G | A | G | u | 13 | 3 | 10 | bc | false | <90% | 1231 | ||
| NM_001011885 | BTBD1 | 2330 | 2348 | a | u | G | A | U | U | C | C | C | a | A | G | A | U | U | G | A | G | A | 3 | 3 | 9 | bc | false | <90% | 3220 | ||
| NM_025238 | BTBD1 | 2418 | 2436 | a | u | G | A | U | U | C | C | C | a | A | G | A | U | U | G | A | G | A | 3 | 3 | 9 | bc | false | <90% | 3308 | ||
| NM_139017 | IL31RA | 1489 | 1507 | G | A | G | A | U | U | C | C | C | a | A | G | A | g | U | G | A | G | A | -2 | 2 | 9 | c | false | <90% | 2393 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1914
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