Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for UUUGGAAGAGAAACCGUUA (11 guide strand hits and 3 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_153235 | TXLNB | 438 | 456 | g | c | U | G | G | A | A | G | A | G | A | A | c | C | C | G | U | U | g | 71 | 4 | 10 | false | <90% | 4647 | |||
| NM_001011649 | CDK5RAP2 | 2860 | 2878 | U | U | g | G | G | A | A | G | A | G | A | A | A | C | C | G | a | U | c | 51 | 3 | 13 | c | false | <90% | 5993 | ||
| NM_018249 | CDK5RAP2 | 2860 | 2878 | U | U | g | G | G | A | A | G | A | G | A | A | A | C | C | G | a | U | c | 51 | 3 | 13 | c | false | <90% | 6230 | ||
| NM_001042399 | CCDC41 | 2114 | 2132 | a | U | U | G | G | A | A | G | A | G | A | A | A | C | a | G | a | U | A | 49 | 3 | 13 | c | false | <90% | 3182 | ||
| NM_016122 | CCDC41 | 2167 | 2185 | a | U | U | G | G | A | A | G | A | G | A | A | A | C | a | G | a | U | A | 49 | 3 | 13 | c | false | <90% | 3235 | ||
| NM_033044 | MACF1 | 3572 | 3590 | U | U | U | G | G | A | A | G | A | G | A | A | A | C | u | G | g | U | g | 46 | 3 | 14 | c | false | <90% | 19271 | ||
| XR_017107 | LOC442058 | 208 | 226 | g | U | U | G | G | A | A | G | A | G | u | A | A | C | C | G | c | U | A | 13 | 3 | 9 | c | false | <90% | 364 | ||
| XR_019279 | LOC442058 | 208 | 226 | g | U | U | G | G | A | A | G | A | G | u | A | A | C | C | G | c | U | A | 13 | 3 | 9 | c | false | <90% | 364 | ||
| NM_005316 | GTF2H1 | 973 | 991 | U | U | U | G | G | A | A | G | A | u | A | A | A | C | C | a | U | U | A | -8 | 2 | 9 | c | false | <90% | 2989 | ||
| NM_173157 | NR4A1 | 2199 | 2217 | U | U | U | G | u | A | A | G | A | u | A | A | A | C | C | G | U | U | u | -39 | 3 | 8 | bc | false | <90% | 2549 | ||
| NM_002135 | NR4A1 | 2349 | 2367 | U | U | U | G | u | A | A | G | A | u | A | A | A | C | C | G | U | U | u | -39 | 3 | 8 | bc | false | <90% | 2699 | ||
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_031473 | IFT81 | 284 | 302 | g | c | A | C | G | G | U | U | U | C | U | C | U | c | C | C | A | A | A | 67 | 3 | 11 | c | false | <90% | 2906 | ||
| NM_014055 | IFT81 | 406 | 424 | g | c | A | C | G | G | U | U | U | C | U | C | U | c | C | C | A | A | A | 67 | 3 | 11 | c | false | <90% | 3118 | ||
| NM_014910 | ZNF507 | 7031 | 7049 | g | u | u | C | a | G | U | U | U | C | U | C | U | U | C | C | A | A | A | 15 | 4 | 14 | bc | false | <90% | 7604 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4747
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