Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for UACAGCAAAAUGGGAGCUC (12 guide strand hits and 4 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_194431 | RNASE4 | 1125 | 1143 | g | c | C | A | G | C | A | A | A | A | U | G | u | G | A | G | C | U | C | 76 | 3 | 10 | false | <90% | 1361 | |||
| NM_002937 | RNASE4 | 1569 | 1587 | g | c | C | A | G | C | A | A | A | A | U | G | u | G | A | G | C | U | C | 76 | 3 | 10 | false | <90% | 1805 | |||
| NM_194430 | RNASE4 | 1673 | 1691 | g | c | C | A | G | C | A | A | A | A | U | G | u | G | A | G | C | U | C | 76 | 3 | 10 | false | <90% | 1909 | |||
| NM_153365 | TAPT1 | 2477 | 2495 | U | A | a | A | G | C | A | A | A | A | U | G | u | G | A | G | C | U | g | 65 | 3 | 9 | false | <90% | 4610 | |||
| NM_024786 | ZDHHC11 | 2110 | 2128 | c | A | C | u | G | C | A | A | A | A | U | G | G | G | A | G | C | a | C | 58 | 3 | 13 | c | false | <90% | 2623 | ||
| NM_012347 | FBXO9 | 508 | 526 | g | A | C | A | G | C | A | A | A | A | U | G | G | c | A | G | a | U | C | 54 | 3 | 12 | c | false | <90% | 4438 | ||
| NM_033481 | FBXO9 | 635 | 653 | g | A | C | A | G | C | A | A | A | A | U | G | G | c | A | G | a | U | C | 54 | 3 | 12 | c | false | <90% | 4565 | ||
| NM_033480 | FBXO9 | 758 | 776 | g | A | C | A | G | C | A | A | A | A | U | G | G | c | A | G | a | U | C | 54 | 3 | 12 | c | false | <90% | 4688 | ||
| NM_017693 | BIVM | 1358 | 1376 | U | A | C | A | G | C | A | c | A | A | U | G | G | G | A | G | C | U | g | 32 | 2 | 10 | bc | false | <90% | 3857 | ||
| NM_001024596 | ZNF772 | 2141 | 2159 | g | c | C | A | G | a | A | A | A | A | U | G | G | G | A | G | C | U | u | 18 | 4 | 12 | bc | false | <90% | 5420 | ||
| NM_017637 | BNC2 | 8590 | 8608 | U | u | g | A | u | C | A | A | A | A | U | G | G | G | A | G | C | U | C | 17 | 3 | 14 | bc | false | <90% | 12926 | ||
| XM_001129325 | LOC731354 | 13 | 31 | U | A | C | u | G | g | A | A | A | A | U | G | G | G | A | G | C | U | C | 0 | 2 | 13 | bc | false | <90% | 423 | ||
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_001032393 | HNRPH2 | 511 | 529 | G | g | a | C | U | C | C | C | A | U | U | U | g | G | C | U | G | U | A | 58 | 3 | 9 | false | <90% | 2315 | |||
| NM_019597 | HNRPH2 | 523 | 541 | G | g | a | C | U | C | C | C | A | U | U | U | g | G | C | U | G | U | A | 58 | 3 | 9 | false | <90% | 2327 | |||
| NM_020652 | ZNF286A | 1660 | 1678 | G | A | G | C | U | C | C | a | A | U | U | U | U | G | C | U | a | a | A | 11 | 3 | 8 | c | false | <90% | 2515 | ||
| NM_021186 | ZP4 | 112 | 130 | G | A | G | C | U | u | C | C | A | g | U | U | U | G | C | U | G | U | A | -46 | 2 | 9 | bc | false | <90% | 1635 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1811
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