Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for CCAAUAGAGUCCACCAGUU (2 guide strand hits and 14 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_003679 | KMO | 3354 | 3372 | u | g | A | A | U | A | G | A | G | U | C | C | A | a | C | A | G | U | a | 62 | 4 | 11 | c | false | <90% | 4992 | ||
| NM_014655 | SLC25A44 | 2747 | 2765 | u | C | A | A | g | A | G | A | G | U | C | C | u | C | C | A | G | U | U | 36 | 3 | 7 | false | <90% | 3486 | |||
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_007356 | LAMB4 | 2198 | 2216 | u | c | C | U | G | G | U | G | G | A | C | U | C | U | c | U | U | G | G | 61 | 3 | 12 | c | false | <90% | 5858 | ||
| NM_003010 | MAP2K4 | 827 | 845 | A | g | C | U | u | G | U | G | G | A | C | U | C | U | A | U | U | G | c | 32 | 3 | 13 | bc | false | <90% | 3752 | ||
| NM_001030011 | OPN3 | 1443 | 1461 | u | A | C | U | G | u | U | G | G | A | C | U | C | U | A | U | U | c | a | 27 | 4 | 11 | c | false | <90% | 2312 | ||
| NM_001030012 | OPN3 | 1603 | 1621 | u | A | C | U | G | u | U | G | G | A | C | U | C | U | A | U | U | c | a | 27 | 4 | 11 | c | false | <90% | 2472 | ||
| NM_014322 | OPN3 | 1763 | 1781 | u | A | C | U | G | u | U | G | G | A | C | U | C | U | A | U | U | c | a | 27 | 4 | 11 | c | false | <90% | 2632 | ||
| NR_002144 | LOC407835 | 1203 | 1221 | A | A | C | U | G | c | U | G | G | A | C | U | a | U | A | U | U | G | u | 21 | 3 | 6 | false | <90% | 1737 | |||
| XM_945774 | LOC649930 | 412 | 430 | u | c | C | U | G | G | a | G | G | A | C | U | C | U | A | U | U | G | u | 15 | 4 | 11 | bc | false | <90% | 838 | ||
| XM_945775 | LOC649930 | 402 | 420 | u | c | C | U | G | G | a | G | G | A | C | U | C | U | A | U | U | G | u | 15 | 4 | 11 | bc | false | <90% | 949 | ||
| NR_003131 | LOC388955 | 435 | 453 | u | c | C | U | G | G | a | G | G | A | C | U | C | U | A | U | U | G | u | 15 | 4 | 11 | bc | false | <90% | 978 | ||
| XM_942189 | LOC649930 | 435 | 453 | u | c | C | U | G | G | a | G | G | A | C | U | C | U | A | U | U | G | u | 15 | 4 | 11 | bc | false | <90% | 982 | ||
| NM_013237 | PRELID1 | 393 | 411 | u | c | C | U | G | G | a | G | G | A | C | U | C | U | A | U | U | G | u | 15 | 4 | 11 | bc | false | <90% | 1287 | ||
| NM_005071 | SLC1A6 | 1536 | 1554 | u | A | C | U | G | G | g | G | G | A | C | U | C | a | A | U | U | G | G | 12 | 3 | 6 | c | false | <90% | 1719 | ||
| NR_003135 | CEP170L | 28257 | 28275 | g | A | C | U | G | G | U | G | G | A | a | a | C | U | A | U | U | G | G | 2 | 3 | 9 | false | <90% | 90477 | |||
| NM_005084 | PLA2G7 | 986 | 1004 | A | A | C | U | G | a | a | G | G | A | C | U | C | U | A | U | U | G | a | -34 | 3 | 11 | bc | false | <90% | 1561 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 877
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