Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
21 hits were found for GAGGAAUGCUUGUGAGAAA (13 guide strand hits and 8 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_032842 | FLJ14803 | 1742 | 1760 | c | A | G | G | A | A | U | G | C | U | U | G | g | G | A | G | A | g | u | 79 | 4 | 11 | false | <90% | 3560 | |||
| NM_014859 | KIAA0672 | 1389 | 1407 | a | u | G | G | A | A | U | G | C | U | U | G | U | G | A | a | A | A | g | 55 | 4 | 13 | c | false | <90% | 4227 | ||
| NM_020121 | UGCGL2 | 2582 | 2600 | u | A | a | G | A | A | U | G | C | U | U | u | U | G | A | G | A | A | A | 44 | 3 | 8 | false | <90% | 4848 | |||
| NM_012338 | TSPAN12 | 2331 | 2349 | G | A | a | a | A | A | U | G | C | U | U | G | U | G | A | G | A | A | u | 38 | 3 | 14 | bc | false | <90% | 2579 | ||
| NM_153810 | C10orf46 | 6399 | 6417 | c | A | G | G | A | A | U | G | C | U | U | a | U | G | A | a | A | A | A | 38 | 3 | 10 | false | <90% | 6758 | |||
| NM_001690 | ATP6V1A | 2474 | 2492 | c | A | G | G | A | A | U | G | u | U | U | G | U | G | A | G | A | A | A | 37 | 2 | 10 | bc | false | <90% | 4567 | ||
| NM_018177 | N4BP2 | 570 | 588 | a | c | a | G | A | A | U | G | C | U | U | u | U | G | A | G | A | A | A | 33 | 4 | 8 | false | <90% | 6616 | |||
| NM_001004745 | OR5T1 | 941 | 959 | a | A | a | G | A | u | U | G | C | U | U | G | U | G | A | G | A | A | A | 15 | 3 | 13 | bc | false | <90% | 981 | ||
| XR_015579 | LOC731716 | 694 | 712 | a | A | G | G | A | A | U | G | C | U | g | c | U | G | A | G | A | A | A | 2 | 3 | 9 | false | <90% | 1787 | |||
| NM_003690 | PRKRA | 650 | 668 | a | A | G | G | A | A | U | G | C | U | g | c | U | G | A | G | A | A | A | 2 | 3 | 9 | false | <90% | 1835 | |||
| NM_004376 | COX15 | 1030 | 1048 | G | A | G | G | A | A | U | G | u | U | U | u | U | G | A | G | A | A | u | 1 | 3 | 8 | false | <90% | 2884 | |||
| NM_078470 | COX15 | 1030 | 1048 | G | A | G | G | A | A | U | G | u | U | U | u | U | G | A | G | A | A | u | 1 | 3 | 8 | false | <90% | 4081 | |||
| NM_002611 | PDK2 | 227 | 245 | c | A | G | c | A | A | U | G | C | c | U | G | U | G | A | G | A | A | A | -21 | 3 | 9 | bc | false | <90% | 2319 | ||
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_004972 | JAK2 | 2302 | 2320 | U | U | U | C | U | C | A | C | A | A | G | C | A | U | U | u | g | g | u | 42 | 4 | 15 | c | false | <90% | 5097 | ||
| NM_005832 | KCNMB2 | 1980 | 1998 | c | U | U | C | U | g | A | C | A | A | G | C | A | U | U | C | C | c | u | 27 | 4 | 11 | c | false | <90% | 2499 | ||
| NM_181361 | KCNMB2 | 2024 | 2042 | c | U | U | C | U | g | A | C | A | A | G | C | A | U | U | C | C | c | u | 27 | 4 | 11 | c | false | <90% | 2543 | ||
| NM_133510 | RAD51L1 | 295 | 313 | U | U | U | C | U | C | A | C | c | A | G | C | A | U | U | C | u | U | a | 11 | 3 | 8 | c | false | <90% | 1566 | ||
| NM_002877 | RAD51L1 | 295 | 313 | U | U | U | C | U | C | A | C | c | A | G | C | A | U | U | C | u | U | a | 11 | 3 | 8 | c | false | <90% | 1875 | ||
| NM_133509 | RAD51L1 | 295 | 313 | U | U | U | C | U | C | A | C | c | A | G | C | A | U | U | C | u | U | a | 11 | 3 | 8 | c | false | <90% | 2513 | ||
| NM_001018003 | SORBS3 | 1424 | 1442 | c | g | a | C | U | C | A | C | A | g | G | C | A | U | U | C | C | U | C | -15 | 4 | 9 | bc | false | <90% | 2027 | ||
| NM_005775 | SORBS3 | 2543 | 2561 | c | g | a | C | U | C | A | C | A | g | G | C | A | U | U | C | C | U | C | -15 | 4 | 9 | bc | false | <90% | 3145 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2141
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