Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
22 hits were found for CCAGAGGGCAGUGUGUCGU (9 guide strand hits and 13 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_022369 | STRA6 | 721 | 739 | g | C | A | G | A | G | G | G | C | A | G | a | G | U | G | U | C | c | c | 56 | 4 | 10 | false | <90% | 2820 | |||
| XM_001129008 | LOC728993 | 41 | 59 | C | C | A | G | A | G | G | G | C | A | G | a | G | U | G | U | g | G | a | 37 | 3 | 11 | false | <90% | 837 | |||
| XM_001130786 | LOC729613 | 41 | 59 | C | C | A | G | A | G | G | G | C | A | G | a | G | U | G | U | g | G | a | 37 | 3 | 11 | false | <90% | 837 | |||
| XR_019543 | LOC440991 | 238 | 256 | C | C | A | G | A | G | G | G | C | A | G | U | G | U | a | g | a | G | c | 20 | 4 | 14 | c | false | <90% | 829 | ||
| XR_017665 | LOC440991 | 238 | 256 | C | C | A | G | A | G | G | G | C | A | G | U | G | U | a | g | a | G | c | 20 | 4 | 14 | c | false | <90% | 829 | ||
| NM_001005 | RPS3 | 268 | 286 | C | C | A | G | A | G | G | G | C | A | G | U | G | U | a | g | a | G | c | 20 | 4 | 14 | c | false | <90% | 855 | ||
| XR_018868 | LOC645000 | 403 | 421 | C | C | A | G | A | G | G | G | C | A | G | U | G | U | a | g | a | G | c | 20 | 4 | 14 | c | false | <90% | 976 | ||
| XR_016848 | LOC645000 | 403 | 421 | C | C | A | G | A | G | G | G | C | A | G | U | G | U | a | g | a | G | c | 20 | 4 | 14 | c | false | <90% | 976 | ||
| XM_001131964 | LOC729985 | 5 | 23 | C | C | A | G | A | G | G | G | C | A | c | U | G | U | G | U | u | a | U | 12 | 3 | 10 | c | false | <90% | 258 | ||
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_001001991 | DKFZP586H2123 | 1885 | 1903 | A | C | G | A | C | A | C | A | C | U | G | C | g | C | U | C | U | G | G | 89 | 1 | 12 | false | <90% | 2747 | |||
| NM_015430 | DKFZP586H2123 | 1936 | 1954 | A | C | G | A | C | A | C | A | C | U | G | C | g | C | U | C | U | G | G | 89 | 1 | 12 | false | <90% | 2798 | |||
| NM_024482 | GMEB1 | 1414 | 1432 | u | C | c | A | C | A | C | A | C | U | G | C | C | u | U | C | U | G | G | 58 | 3 | 10 | c | false | <90% | 1944 | ||
| NM_006582 | GMEB1 | 1447 | 1465 | u | C | c | A | C | A | C | A | C | U | G | C | C | u | U | C | U | G | G | 58 | 3 | 10 | c | false | <90% | 1960 | ||
| NM_001044 | SLC6A3 | 3409 | 3427 | A | u | G | g | C | A | C | A | C | U | G | C | C | C | U | C | U | G | c | 46 | 3 | 14 | bc | false | <90% | 3925 | ||
| NM_000554 | CRX | 4391 | 4409 | c | C | c | A | C | A | C | A | C | U | G | g | C | C | U | C | U | G | G | 44 | 3 | 8 | false | <90% | 4461 | |||
| XM_001134429 | MUC5AC | 2690 | 2708 | A | a | c | A | C | A | C | A | C | U | G | C | C | C | U | g | U | G | G | 42 | 3 | 12 | c | false | <90% | 3811 | ||
| XM_001130382 | LOC730855 | 8791 | 8809 | A | a | c | A | C | A | C | A | C | U | G | C | C | C | U | g | U | G | G | 42 | 3 | 12 | c | false | <90% | 9912 | ||
| NM_002401 | MAP3K3 | 3921 | 3939 | A | C | c | c | C | A | C | A | C | U | G | C | C | C | U | C | U | G | a | 38 | 3 | 14 | bc | false | <90% | 4750 | ||
| NM_203351 | MAP3K3 | 4014 | 4032 | A | C | c | c | C | A | C | A | C | U | G | C | C | C | U | C | U | G | a | 38 | 3 | 14 | bc | false | <90% | 4843 | ||
| NM_030626 | LRRC27 | 539 | 557 | c | u | a | A | g | A | C | A | C | U | G | C | C | C | U | C | U | G | G | 15 | 4 | 14 | bc | false | <90% | 6382 | ||
| XR_015558 | LOC731674 | 1666 | 1684 | A | C | c | A | C | A | a | A | C | U | G | C | C | C | U | C | U | G | a | 9 | 3 | 11 | bc | false | <90% | 1849 | ||
| XR_016307 | LOC387745 | 1717 | 1735 | A | C | c | A | C | A | a | A | C | U | G | C | C | C | U | C | U | G | a | 9 | 3 | 11 | bc | false | <90% | 1900 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3125
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)
Motif found in guide strand
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