Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
19 hits were found for AUAGUGACCUGUUGCUGUG (3 guide strand hits and 16 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_014832 | TBC1D4 | 4174 | 4192 | A | U | u | G | U | G | A | C | C | U | G | U | U | G | C | U | G | a | G | 77 | 2 | 14 | c | false | <90% | 6363 | ||
| NM_006226 | PLCL1 | 3606 | 3624 | A | c | u | G | U | a | A | C | C | U | G | U | U | G | C | U | G | U | G | 5 | 3 | 13 | bc | false | <90% | 4565 | ||
| NM_024086 | METT10D | 2912 | 2930 | g | g | g | G | U | G | A | C | C | U | u | U | U | G | C | U | G | U | G | 5 | 4 | 8 | c | false | <90% | 5758 | ||
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 | |||||||||||||
| NR_003252 | INPP5F | 2032 | 2050 | u | u | C | A | G | C | A | A | C | A | G | G | U | C | A | C | U | u | U | 83 | 3 | 15 | ac | false | <90% | 3161 | ||
| NM_014937 | INPP5F | 3818 | 3836 | u | u | C | A | G | C | A | A | C | A | G | G | U | C | A | C | U | u | U | 83 | 3 | 15 | ac | false | <90% | 4955 | ||
| XR_018982 | LOC645474 | 544 | 562 | u | A | C | A | G | C | A | A | C | A | G | G | U | C | A | C | c | A | g | 69 | 3 | 15 | ac | false | <90% | 1440 | ||
| NM_022093 | TNN | 224 | 242 | a | g | g | A | G | C | A | A | C | A | G | G | U | C | A | C | U | g | U | 64 | 4 | 14 | c | false | <90% | 5008 | ||
| NM_145048 | C4orf28 | 181 | 199 | C | A | g | A | G | C | A | A | C | A | G | G | U | a | A | C | U | A | U | 60 | 2 | 10 | c | false | <90% | 1825 | ||
| NM_016231 | NLK | 790 | 808 | a | g | C | A | G | C | A | A | C | A | G | G | U | C | A | C | c | A | c | 58 | 4 | 14 | ac | false | <90% | 4059 | ||
| NM_014337 | PPIL2 | 1235 | 1253 | a | A | C | A | G | C | A | A | C | A | G | G | U | C | u | C | a | A | U | 49 | 3 | 13 | c | false | <90% | 2609 | ||
| NM_148176 | PPIL2 | 1201 | 1219 | a | A | C | A | G | C | A | A | C | A | G | G | U | C | u | C | a | A | U | 49 | 3 | 13 | c | false | <90% | 2648 | ||
| NM_148175 | PPIL2 | 1200 | 1218 | a | A | C | A | G | C | A | A | C | A | G | G | U | C | u | C | a | A | U | 49 | 3 | 13 | c | false | <90% | 2789 | ||
| NM_004467 | FGL1 | 245 | 263 | a | A | C | A | G | C | A | A | C | A | G | G | U | C | A | a | g | A | U | 48 | 3 | 14 | c | false | <90% | 1285 | ||
| NM_147203 | FGL1 | 333 | 351 | a | A | C | A | G | C | A | A | C | A | G | G | U | C | A | a | g | A | U | 48 | 3 | 14 | c | false | <90% | 1373 | ||
| NM_201552 | FGL1 | 372 | 390 | a | A | C | A | G | C | A | A | C | A | G | G | U | C | A | a | g | A | U | 48 | 3 | 14 | c | false | <90% | 1412 | ||
| NM_201553 | FGL1 | 460 | 478 | a | A | C | A | G | C | A | A | C | A | G | G | U | C | A | a | g | A | U | 48 | 3 | 14 | c | false | <90% | 1500 | ||
| XM_001130828 | LOC731791 | 535 | 553 | u | A | C | A | G | C | A | A | C | A | u | G | U | C | A | C | U | A | g | 31 | 3 | 9 | c | false | <90% | 561 | ||
| XR_018982 | LOC645474 | 98 | 116 | u | A | C | A | G | C | A | A | C | A | u | G | U | C | A | C | U | A | g | 31 | 3 | 9 | c | false | <90% | 1440 | ||
| NM_173672 | PPIL6 | 790 | 808 | C | A | C | A | G | C | A | A | C | g | G | G | U | C | A | C | a | A | U | -6 | 2 | 9 | c | false | <90% | 1106 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1676
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