Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for UCCAUAUGCUGUAUGUGAU (8 guide strand hits and 5 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 | |||||||||||||
| XR_018218 | LOC642590 | 1240 | 1258 | U | C | C | A | U | A | U | G | C | U | G | U | A | c | a | U | G | A | c | 50 | 3 | 13 | c | false | <90% | 1670 | ||
| XR_016251 | LOC642590 | 1240 | 1258 | U | C | C | A | U | A | U | G | C | U | G | U | A | c | a | U | G | A | c | 50 | 3 | 13 | c | false | <90% | 1670 | ||
| XR_017680 | LOC646347 | 1245 | 1263 | U | C | C | A | U | A | U | G | C | U | G | U | A | c | a | U | G | A | c | 50 | 3 | 13 | c | false | <90% | 1690 | ||
| XR_019455 | LOC649911 | 1245 | 1263 | U | C | C | A | U | A | U | G | C | U | G | U | A | c | a | U | G | A | c | 50 | 3 | 13 | c | false | <90% | 1690 | ||
| NM_004595 | SMS | 1250 | 1268 | U | C | C | A | U | A | U | G | C | U | G | U | A | c | a | U | G | A | c | 50 | 3 | 13 | c | false | <90% | 1717 | ||
| NM_138940 | CD200R1 | 755 | 773 | U | C | C | A | U | A | U | G | C | U | u | U | A | U | G | U | G | A | a | 33 | 2 | 10 | c | false | <90% | 956 | ||
| NM_138939 | CD200R1 | 824 | 842 | U | C | C | A | U | A | U | G | C | U | u | U | A | U | G | U | G | A | a | 33 | 2 | 10 | c | false | <90% | 1025 | ||
| NM_022124 | CDH23 | 3338 | 3356 | U | C | C | A | U | g | U | G | C | U | G | g | A | U | G | U | G | A | a | -2 | 3 | 6 | false | <90% | 11073 | |||
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_153226 | TMEM20 | 1207 | 1225 | u | U | C | A | C | A | U | A | C | A | G | C | A | U | A | c | G | c | A | 69 | 3 | 14 | c | false | <90% | 2396 | ||
| NM_014905 | GLS | 3661 | 3679 | A | U | C | A | C | A | U | A | C | A | G | C | A | a | A | U | u | c | c | 49 | 4 | 13 | c | false | <90% | 4799 | ||
| NM_130768 | ASZ1 | 844 | 862 | u | U | C | A | u | A | U | A | C | A | G | C | A | U | u | U | G | G | A | 21 | 3 | 9 | c | false | <90% | 1831 | ||
| XM_001126495 | LOC728084 | 396 | 414 | c | U | C | A | C | A | a | A | C | A | G | a | A | U | A | U | G | G | A | -2 | 3 | 7 | false | <90% | 514 | |||
| XM_001131377 | LOC731951 | 396 | 414 | c | U | C | A | C | A | a | A | C | A | G | a | A | U | A | U | G | G | A | -2 | 3 | 7 | false | <90% | 514 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1850
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