Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
9 hits were found for CCGAACGUGGUGGGGUUCC (3 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 | |||||||||||||
| XM_001133965 | ASMTL | 580 | 598 | C | u | G | A | A | C | G | U | G | G | U | G | G | G | a | U | U | C | C | 63 | 2 | 12 | c | false | <90% | 1167 | ||
| NM_004192 | ASMTL | 691 | 709 | C | u | G | A | A | C | G | U | G | G | U | G | G | G | a | U | U | C | C | 63 | 2 | 12 | c | false | <90% | 2123 | ||
| NM_007227 | GPR45 | 246 | 264 | a | u | G | A | c | C | G | U | G | G | U | G | G | G | G | U | U | C | C | 35 | 3 | 14 | bc | false | <90% | 1725 | ||
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 | |||||||||||||
| XM_001132718 | LOC732311 | 774 | 792 | G | G | A | A | C | C | C | C | A | C | C | A | g | G | U | U | C | c | u | 81 | 3 | 12 | false | <90% | 891 | |||
| XM_001129139 | LOC729041 | 918 | 936 | G | G | A | A | C | C | C | C | A | C | C | A | g | G | U | U | C | c | u | 81 | 3 | 12 | false | <90% | 1035 | |||
| NM_016307 | PRRX2 | 543 | 561 | G | G | A | A | C | C | g | C | A | C | C | A | C | G | U | U | C | a | a | 26 | 3 | 10 | c | false | <90% | 1327 | ||
| XM_939157 | LOC650070 | 1028 | 1046 | G | G | A | A | C | C | C | C | A | a | C | A | C | G | U | a | C | G | a | -13 | 3 | 9 | c | false | <90% | 1119 | ||
| NM_005685 | GTF2IRD1 | 2580 | 2598 | G | G | A | A | C | C | C | C | A | a | C | A | C | G | U | a | C | G | a | -13 | 3 | 9 | c | false | <90% | 3078 | ||
| NM_016328 | GTF2IRD1 | 2942 | 2960 | G | G | A | A | C | C | C | C | A | a | C | A | C | G | U | a | C | G | a | -13 | 3 | 9 | c | false | <90% | 3446 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 70
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