Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GAGAUCACUGUGGCUACAU (10 guide strand hits and 10 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_004275 | TRFP | 1636 | 1654 | c | A | G | A | U | C | A | C | U | G | U | G | G | C | c | A | C | A | c | 68 | 3 | 13 | c | false | <90% | 2478 | ||
| NM_001084 | PLOD3 | 577 | 595 | G | u | G | A | U | C | A | C | U | G | U | G | G | C | c | A | C | A | g | 58 | 3 | 12 | c | false | <90% | 2995 | ||
| XR_015306 | LOC730888 | 1950 | 1968 | G | A | G | A | U | C | A | C | U | G | U | u | G | a | U | A | C | A | U | 46 | 2 | 11 | false | <90% | 2601 | |||
| NM_012392 | PEF1 | 395 | 413 | c | A | G | A | U | C | A | C | a | G | U | G | G | C | U | A | u | A | U | 14 | 3 | 7 | c | false | <90% | 1640 | ||
| NM_005402 | RALA | 2094 | 2112 | a | A | G | A | a | C | A | C | U | G | U | a | G | C | U | A | C | A | U | 12 | 3 | 7 | false | <90% | 2818 | |||
| NM_001079872 | CUL4B | 3304 | 3322 | G | A | G | A | U | C | c | C | U | G | U | G | G | C | U | A | u | u | a | 2 | 4 | 9 | c | false | <90% | 5198 | ||
| NM_003588 | CUL4B | 3471 | 3489 | G | A | G | A | U | C | c | C | U | G | U | G | G | C | U | A | u | u | a | 2 | 4 | 9 | c | false | <90% | 5365 | ||
| XM_940984 | SNED1 | 4825 | 4843 | G | A | G | g | U | C | c | C | U | G | U | G | G | C | U | A | C | A | g | -8 | 3 | 11 | bc | false | <90% | 6714 | ||
| NM_001080437 | SNED1 | 4945 | 4963 | G | A | G | g | U | C | c | C | U | G | U | G | G | C | U | A | C | A | g | -8 | 3 | 11 | bc | false | <90% | 6834 | ||
| NM_152359 | CPT1C | 1652 | 1670 | G | A | G | u | U | C | A | C | U | c | U | G | G | C | U | A | C | A | g | -24 | 3 | 8 | bc | false | <90% | 2772 | ||
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_014390 | SND1 | 1599 | 1617 | g | U | c | U | A | G | C | C | A | C | A | G | U | G | A | U | C | a | g | 70 | 4 | 14 | c | false | <90% | 3522 | ||
| NM_002548 | OR1D2 | 814 | 832 | c | a | G | U | A | G | C | C | A | C | A | G | U | G | A | U | g | U | a | 58 | 4 | 14 | ac | false | <90% | 939 | ||
| NM_014566 | OR1D5 | 814 | 832 | c | a | G | U | A | G | C | C | A | C | A | G | U | G | A | U | g | U | a | 58 | 4 | 14 | ac | false | <90% | 939 | ||
| NM_003552 | OR1D4 | 868 | 886 | c | a | G | U | A | G | C | C | A | C | A | G | U | G | A | U | g | U | a | 58 | 4 | 14 | ac | false | <90% | 993 | ||
| XM_001127446 | LOC648187 | 3835 | 3853 | A | U | u | U | A | G | C | C | A | C | A | G | U | G | A | U | g | c | C | 54 | 3 | 13 | c | false | <90% | 5430 | ||
| NM_001014342 | FLG2 | 4104 | 4122 | A | U | u | U | A | G | C | C | A | C | A | G | U | G | A | U | g | c | C | 54 | 3 | 13 | c | false | <90% | 9147 | ||
| NM_001004704 | OR4C6 | 96 | 114 | A | U | G | U | A | G | C | C | A | C | A | G | U | G | c | U | g | g | a | 44 | 4 | 14 | c | false | <90% | 930 | ||
| NM_001838 | CCR7 | 618 | 636 | u | a | c | U | A | G | C | C | A | C | A | G | U | G | c | U | C | U | C | 42 | 4 | 11 | c | false | <90% | 2188 | ||
| NM_005773 | ZNF256 | 988 | 1006 | c | U | G | U | A | G | C | C | u | C | A | G | U | G | A | U | C | a | u | 30 | 4 | 8 | c | false | <90% | 2228 | ||
| NM_005478 | INSL5 | 594 | 612 | u | U | G | a | A | a | C | C | A | C | A | G | U | G | A | U | C | U | C | -2 | 3 | 13 | bc | false | <90% | 715 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1766
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