Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for GAAUGUGUGUACUGCAAGC (12 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_031276 | TEX11 | 642 | 660 | c | u | A | U | G | U | G | U | G | U | A | C | U | G | C | A | A | u | g | 78 | 4 | 15 | ac | false | <90% | 3029 | ||
| NM_001003811 | TEX11 | 764 | 782 | c | u | A | U | G | U | G | U | G | U | A | C | U | G | C | A | A | u | g | 78 | 4 | 15 | ac | false | <90% | 3151 | ||
| XM_941554 | CCDC85A | 3273 | 3291 | G | A | A | U | G | U | G | U | G | U | A | C | U | G | g | A | A | a | u | 67 | 3 | 14 | c | false | <90% | 3983 | ||
| NM_001080433 | CCDC85A | 3273 | 3291 | G | A | A | U | G | U | G | U | G | U | A | C | U | G | g | A | A | a | u | 67 | 3 | 14 | c | false | <90% | 3983 | ||
| NM_001532 | SLC29A2 | 2183 | 2201 | G | c | A | U | G | U | G | U | G | U | A | C | U | G | C | A | c | u | u | 57 | 4 | 14 | ac | false | <90% | 2529 | ||
| NM_001040167 | LFNG | 1289 | 1307 | G | u | g | U | G | U | G | U | G | U | A | C | U | G | C | A | u | G | C | 45 | 3 | 13 | c | false | <90% | 2384 | ||
| NM_002885 | RAP1GAP | 958 | 976 | G | A | A | U | c | U | G | U | G | U | A | C | U | G | C | A | A | c | u | 40 | 3 | 12 | c | false | <90% | 3270 | ||
| NM_003262 | TLOC1 | 4272 | 4290 | G | A | A | U | a | U | G | U | G | U | A | C | a | G | C | A | A | G | u | 33 | 3 | 7 | false | <90% | 6541 | |||
| NM_006321 | ARIH2 | 2255 | 2273 | a | A | A | U | G | U | c | U | G | U | A | C | U | G | C | A | A | G | a | 26 | 3 | 11 | bc | false | <90% | 4081 | ||
| NM_000296 | PKD1 | 7314 | 7332 | G | A | g | U | G | U | G | U | G | U | c | C | U | G | C | A | A | G | g | 14 | 3 | 7 | c | false | <90% | 14135 | ||
| NM_001009944 | PKD1 | 7314 | 7332 | G | A | g | U | G | U | G | U | G | U | c | C | U | G | C | A | A | G | g | 14 | 3 | 7 | c | false | <90% | 14138 | ||
| NM_000693 | ALDH1A3 | 1970 | 1988 | c | c | c | U | G | U | G | U | G | U | u | C | U | G | C | A | A | G | C | 5 | 4 | 8 | c | false | <90% | 3442 | ||
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_017769 | KIAA1333 | 1902 | 1920 | u | u | U | U | a | C | A | G | U | A | C | A | C | A | C | A | U | U | a | 30 | 4 | 13 | bc | false | <90% | 5534 | ||
| NM_080684 | PTPN13 | 517 | 535 | G | C | U | U | G | C | A | G | U | g | C | c | C | A | C | A | U | U | a | -21 | 3 | 9 | false | <90% | 7546 | |||
| NM_006264 | PTPN13 | 517 | 535 | G | C | U | U | G | C | A | G | U | g | C | c | C | A | C | A | U | U | a | -21 | 3 | 9 | false | <90% | 8062 | |||
| NM_080683 | PTPN13 | 517 | 535 | G | C | U | U | G | C | A | G | U | g | C | c | C | A | C | A | U | U | a | -21 | 3 | 9 | false | <90% | 8119 | |||
| NM_080685 | PTPN13 | 517 | 535 | G | C | U | U | G | C | A | G | U | g | C | c | C | A | C | A | U | U | a | -21 | 3 | 9 | false | <90% | 8133 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2946
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