Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for GGUGUUUCCAUUCCAUGUG (6 guide strand hits and 11 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_201428 | RTN3 | 1700 | 1718 | c | c | U | G | U | U | U | C | C | A | U | U | C | C | A | a | G | U | G | 60 | 3 | 13 | c | false | <90% | 4942 | ||
| NM_001004441 | DP58 | 3503 | 3521 | G | G | U | u | U | U | U | C | C | A | U | U | u | C | A | U | G | U | c | 47 | 3 | 8 | false | <90% | 3763 | |||
| NM_012080 | HDHD1A | 846 | 864 | G | G | a | G | U | U | U | C | C | A | U | c | C | C | A | U | G | U | u | 41 | 3 | 8 | false | <90% | 2113 | |||
| NM_017583 | TRIM44 | 2280 | 2298 | a | u | U | G | U | U | c | C | C | A | U | U | C | C | A | U | G | U | G | 20 | 3 | 12 | bc | false | <90% | 3182 | ||
| XM_001129826 | LOC730908 | 374 | 392 | G | a | a | G | U | U | U | C | C | A | g | U | C | C | A | U | G | U | G | 7 | 3 | 8 | c | false | <90% | 1069 | ||
| XM_001129848 | LOC730908 | 515 | 533 | G | a | a | G | U | U | U | C | C | A | g | U | C | C | A | U | G | U | G | 7 | 3 | 8 | c | false | <90% | 1269 | ||
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_005433 | YES1 | 1104 | 1122 | a | A | C | A | U | G | G | A | A | U | G | G | A | A | c | C | A | C | g | 68 | 3 | 13 | c | false | <90% | 4685 | ||
| NM_052896 | CSMD2 | 9023 | 9041 | g | A | C | A | U | G | G | A | A | U | G | G | A | A | c | C | A | a | g | 65 | 4 | 13 | c | false | <90% | 13108 | ||
| NM_183376 | ARRDC4 | 944 | 962 | C | A | C | A | U | G | G | A | A | U | G | G | g | A | A | a | A | C | g | 58 | 3 | 12 | false | <90% | 4071 | |||
| NM_153048 | FYN | 754 | 772 | u | A | C | c | U | G | G | A | A | U | G | G | A | A | A | C | A | C | a | 56 | 3 | 14 | bc | false | <90% | 2000 | ||
| NM_153047 | FYN | 867 | 885 | u | A | C | c | U | G | G | A | A | U | G | G | A | A | A | C | A | C | a | 56 | 3 | 14 | bc | false | <90% | 2073 | ||
| NM_002037 | FYN | 1444 | 1462 | u | A | C | c | U | G | G | A | A | U | G | G | A | A | A | C | A | C | a | 56 | 3 | 14 | bc | false | <90% | 2650 | ||
| NM_031282 | FCRL4 | 544 | 562 | u | A | C | u | U | G | G | A | A | U | G | G | A | A | A | C | A | u | u | 53 | 4 | 13 | c | false | <90% | 3459 | ||
| NM_178509 | STXBP4 | 1292 | 1310 | C | A | C | A | U | G | G | A | A | U | G | G | A | A | A | u | g | g | a | 42 | 4 | 15 | c | false | <90% | 6046 | ||
| NM_001419 | ELAVL1 | 5793 | 5811 | u | A | C | A | U | G | u | A | A | U | G | G | A | A | A | C | A | u | g | 24 | 4 | 10 | c | false | <90% | 6075 | ||
| NM_001039937 | INTS6 | 3838 | 3856 | u | A | a | A | U | G | G | A | A | a | G | G | A | A | A | C | A | C | C | -4 | 3 | 9 | bc | false | <90% | 6973 | ||
| NM_012141 | INTS6 | 4330 | 4348 | u | A | a | A | U | G | G | A | A | a | G | G | A | A | A | C | A | C | C | -4 | 3 | 9 | bc | false | <90% | 7465 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2739
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