Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for CAGUCAGCGUGGCACACCA (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 | |||||||||||||
| NM_018714 | COG1 | 1502 | 1520 | g | g | G | U | C | A | G | C | G | U | G | G | C | A | a | A | C | C | g | 56 | 4 | 12 | c | false | <90% | 3035 | ||
| NM_001080423 | GRIP2 | 2063 | 2081 | a | A | G | g | C | A | G | C | G | U | G | G | C | A | C | A | C | a | g | 53 | 4 | 13 | c | false | <90% | 3426 | ||
| XM_940982 | GRIP2 | 2330 | 2348 | a | A | G | g | C | A | G | C | G | U | G | G | C | A | C | A | C | a | g | 53 | 4 | 13 | c | false | <90% | 3693 | ||
| NM_183393 | CADPS | 1821 | 1839 | C | A | G | U | C | A | G | a | G | U | G | G | C | A | C | A | a | a | A | 11 | 3 | 8 | c | false | <90% | 5248 | ||
| NM_183394 | CADPS | 1821 | 1839 | C | A | G | U | C | A | G | a | G | U | G | G | C | A | C | A | a | a | A | 11 | 3 | 8 | c | false | <90% | 5372 | ||
| NM_003716 | CADPS | 1821 | 1839 | C | A | G | U | C | A | G | a | G | U | G | G | C | A | C | A | a | a | A | 11 | 3 | 8 | c | false | <90% | 5489 | ||
| NM_052903 | TUBGCP5 | 3215 | 3233 | C | A | G | U | C | A | G | C | c | U | G | G | C | A | C | A | g | u | c | 8 | 4 | 8 | c | false | <90% | 3829 | ||
| NM_005399 | PRKAB2 | 574 | 592 | C | A | G | U | C | A | G | C | u | U | G | G | C | A | C | A | a | u | u | 8 | 4 | 8 | c | false | <90% | 5431 | ||
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_020705 | TBC1D24 | 1809 | 1827 | g | c | c | U | G | U | G | C | C | A | C | G | g | U | G | A | C | U | G | 56 | 4 | 9 | false | <90% | 4344 | |||
| NM_000088 | COL1A1 | 3916 | 3934 | a | G | a | U | G | U | G | C | C | A | C | u | C | U | G | A | C | U | G | 44 | 3 | 8 | false | <90% | 5927 | |||
| NM_025256 | EHMT2 | 1428 | 1446 | U | G | G | a | G | U | G | C | C | A | C | c | C | U | G | A | C | U | u | 24 | 3 | 7 | false | <90% | 3892 | |||
| NM_006709 | EHMT2 | 1530 | 1548 | U | G | G | a | G | U | G | C | C | A | C | c | C | U | G | A | C | U | u | 24 | 3 | 7 | false | <90% | 3994 | |||
| NM_014953 | DIS3 | 3756 | 3774 | U | G | G | U | G | U | G | C | C | A | g | a | C | U | G | A | C | U | a | 0 | 3 | 10 | false | <90% | 7320 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2131
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