Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for CAGACAUGGUGCGAAGAGU (9 guide strand hits and 9 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_018066 | ATPBD1B | 1375 | 1393 | C | A | G | A | C | A | U | G | G | U | G | C | c | A | A | G | c | a | g | 58 | 4 | 12 | false | <90% | 1510 | |||
| XR_016968 | LOC400011 | 946 | 964 | a | A | G | A | C | A | U | G | G | U | G | u | G | A | A | G | A | u | a | 56 | 4 | 10 | false | <90% | 3628 | |||
| XR_019334 | LOC400011 | 946 | 964 | a | A | G | A | C | A | U | G | G | U | G | u | G | A | A | G | A | u | a | 56 | 4 | 10 | false | <90% | 3628 | |||
| NM_007192 | SUPT16H | 1287 | 1305 | a | A | G | A | C | A | U | G | G | U | G | u | G | A | A | G | A | u | a | 56 | 4 | 10 | false | <90% | 4696 | |||
| NM_014239 | EIF2B2 | 318 | 336 | g | c | a | A | C | A | U | G | G | U | G | C | G | g | A | G | A | G | U | 47 | 4 | 10 | c | false | <90% | 1539 | ||
| NM_032433 | ZNF333 | 2523 | 2541 | a | u | u | A | C | A | U | G | G | U | G | a | G | A | A | G | A | G | U | 33 | 4 | 8 | false | <90% | 3767 | |||
| NM_018082 | POLR3B | 1176 | 1194 | C | A | G | u | g | A | U | G | G | U | G | C | G | A | A | G | A | G | U | 11 | 2 | 14 | bc | false | <90% | 4237 | ||
| NM_001034955 | SORBS1 | 2974 | 2992 | C | A | G | c | C | A | U | G | G | c | G | C | G | A | A | G | A | G | a | -24 | 3 | 8 | bc | false | <90% | 6803 | ||
| NM_001034954 | SORBS1 | 3397 | 3415 | C | A | G | c | C | A | U | G | G | c | G | C | G | A | A | G | A | G | a | -24 | 3 | 8 | bc | false | <90% | 7226 | ||
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_203495 | COMMD6 | 1154 | 1172 | c | C | U | C | U | U | C | a | C | A | C | C | c | U | G | U | C | U | G | 25 | 3 | 6 | false | <90% | 1683 | |||
| NM_203497 | COMMD6 | 1193 | 1211 | c | C | U | C | U | U | C | a | C | A | C | C | c | U | G | U | C | U | G | 25 | 3 | 6 | false | <90% | 1722 | |||
| NM_014716 | CENTB1 | 1933 | 1951 | u | C | U | C | U | U | C | c | C | A | C | C | A | U | G | g | C | U | G | 9 | 3 | 7 | c | false | <90% | 2498 | ||
| NM_004573 | PLCB2 | 290 | 308 | A | C | g | C | U | U | g | G | C | A | C | C | A | U | G | U | C | U | c | 9 | 3 | 11 | bc | false | <90% | 4694 | ||
| NM_012154 | EIF2C2 | 2592 | 2610 | A | C | U | C | U | g | C | G | C | A | C | C | A | U | G | U | a | c | u | 5 | 4 | 10 | c | false | <90% | 3567 | ||
| NM_012199 | EIF2C1 | 2759 | 2777 | A | C | U | C | U | g | C | G | C | A | C | C | A | U | G | U | a | c | u | 5 | 4 | 10 | c | false | <90% | 7478 | ||
| NM_148919 | PSMB8 | 384 | 402 | c | u | g | C | U | U | g | G | C | A | C | C | A | U | G | U | C | U | G | 0 | 4 | 12 | bc | false | <90% | 1135 | ||
| NM_004159 | PSMB8 | 851 | 869 | c | u | g | C | U | U | g | G | C | A | C | C | A | U | G | U | C | U | G | 0 | 4 | 12 | bc | false | <90% | 1602 | ||
| NR_002723 | GABPAP | 50792 | 50810 | u | C | U | g | U | U | u | G | C | A | C | C | A | U | G | U | C | U | G | -5 | 3 | 12 | bc | false | <90% | 194142 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2229
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