Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for CACUUCCGAAACUACUGUU (4 guide strand hits and 7 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_001125827 | LOC727820 | 1694 | 1712 | C | A | C | U | U | C | C | G | A | A | A | C | c | A | C | U | u | g | g | 58 | 4 | 12 | false | <90% | 8160 | |||
| NM_018223 | CHFR | 2250 | 2268 | a | u | u | U | U | C | C | G | A | A | A | C | U | A | C | a | G | U | U | 40 | 4 | 12 | c | false | <90% | 3138 | ||
| NM_031914 | SYT16 | 2791 | 2809 | g | A | g | U | U | C | a | G | A | A | A | C | U | A | C | U | G | U | U | 12 | 3 | 12 | bc | false | <90% | 3137 | ||
| NM_020940 | KIAA1600 | 1856 | 1874 | C | A | g | U | U | C | C | G | A | g | A | C | U | A | C | U | G | U | g | -7 | 3 | 8 | bc | false | <90% | 5334 | ||
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_181836 | TMED7 | 1514 | 1532 | A | A | C | A | G | U | A | G | U | U | U | C | a | G | u | A | G | U | G | 64 | 2 | 12 | false | <90% | 3587 | |||
| NM_153013 | C5orf33 | 2003 | 2021 | c | A | C | A | G | U | A | G | U | U | U | u | G | G | A | A | u | U | G | 40 | 3 | 10 | false | <90% | 3659 | |||
| NM_207304 | MBNL2 | 735 | 753 | A | A | C | A | G | U | A | G | U | U | U | u | G | G | A | A | u | c | a | 35 | 4 | 11 | false | <90% | 4600 | |||
| NM_144778 | MBNL2 | 735 | 753 | A | A | C | A | G | U | A | G | U | U | U | u | G | G | A | A | u | c | a | 35 | 4 | 11 | false | <90% | 4731 | |||
| NM_004598 | SPOCK1 | 2954 | 2972 | A | A | C | A | G | U | A | G | U | c | U | C | u | G | A | A | G | U | u | 1 | 3 | 9 | false | <90% | 4841 | |||
| XM_930678 | LOC642441 | 6452 | 6470 | c | c | a | A | G | U | g | G | U | U | U | C | G | G | A | A | G | U | G | 0 | 4 | 12 | bc | false | <90% | 8151 | ||
| XM_001134398 | LOC730256 | 6455 | 6473 | c | c | a | A | G | U | g | G | U | U | U | C | G | G | A | A | G | U | G | 0 | 4 | 12 | bc | false | <90% | 8176 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2418
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