Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
25 hits were found for GAAAUUCAACUCCUGGCAG (10 guide strand hits and 15 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_001031807 | LBXCOR1 | 693 | 711 | c | A | A | c | U | U | C | A | A | C | U | C | C | U | G | G | C | g | u | 53 | 4 | 13 | c | false | <90% | 2766 | ||
| NM_203375 | LOC284912 | 515 | 533 | G | A | A | A | c | U | C | A | A | C | U | C | C | U | G | G | C | A | G | 48 | 1 | 14 | bc | false | <90% | 899 | ||
| XR_017373 | LOC647002 | 79 | 97 | c | A | g | g | U | U | C | A | A | C | U | C | C | U | G | G | C | A | G | 41 | 3 | 15 | bc | false | <90% | 700 | ||
| XR_019616 | LOC647002 | 79 | 97 | c | A | g | g | U | U | C | A | A | C | U | C | C | U | G | G | C | A | G | 41 | 3 | 15 | bc | false | <90% | 700 | ||
| NM_004508 | IDI1 | 326 | 344 | c | A | g | g | U | U | C | A | A | C | U | C | C | U | G | G | C | A | G | 41 | 3 | 15 | bc | false | <90% | 2150 | ||
| NM_173215 | NFAT5 | 1433 | 1451 | G | A | A | A | U | a | C | A | A | C | U | C | C | U | u | G | C | A | a | 7 | 3 | 8 | c | false | <90% | 5304 | ||
| NM_006599 | NFAT5 | 2263 | 2281 | G | A | A | A | U | a | C | A | A | C | U | C | C | U | u | G | C | A | a | 7 | 3 | 8 | c | false | <90% | 14123 | ||
| NM_138713 | NFAT5 | 2317 | 2335 | G | A | A | A | U | a | C | A | A | C | U | C | C | U | u | G | C | A | a | 7 | 3 | 8 | c | false | <90% | 14177 | ||
| NM_173214 | NFAT5 | 2325 | 2343 | G | A | A | A | U | a | C | A | A | C | U | C | C | U | u | G | C | A | a | 7 | 3 | 8 | c | false | <90% | 14185 | ||
| NM_138714 | NFAT5 | 2379 | 2397 | G | A | A | A | U | a | C | A | A | C | U | C | C | U | u | G | C | A | a | 7 | 3 | 8 | c | false | <90% | 14239 | ||
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_002811 | PSMD7 | 1415 | 1433 | a | a | a | C | C | A | G | G | A | G | U | U | G | A | A | U | U | U | u | 62 | 4 | 15 | bc | false | <90% | 1678 | ||
| NM_020650 | RCN3 | 163 | 181 | C | U | G | C | C | A | G | G | A | G | U | U | G | u | A | g | U | U | C | 54 | 2 | 13 | c | false | <90% | 1882 | ||
| NR_002723 | GABPAP | 75913 | 75931 | a | g | G | C | C | A | G | G | A | G | U | g | G | A | A | U | U | U | u | 47 | 4 | 9 | false | <90% | 194142 | |||
| NM_015215 | CAMTA1 | 8029 | 8047 | g | U | G | C | C | A | G | G | A | G | U | a | G | g | A | U | U | U | C | 44 | 3 | 10 | false | <90% | 8457 | |||
| NM_202003 | FOXM1 | 3180 | 3198 | g | g | G | u | C | A | G | G | A | G | U | U | G | A | A | U | U | U | g | 44 | 4 | 14 | bc | false | <90% | 3487 | ||
| NM_021953 | FOXM1 | 3225 | 3243 | g | g | G | u | C | A | G | G | A | G | U | U | G | A | A | U | U | U | g | 44 | 4 | 14 | bc | false | <90% | 3527 | ||
| NM_202002 | FOXM1 | 3339 | 3357 | g | g | G | u | C | A | G | G | A | G | U | U | G | A | A | U | U | U | g | 44 | 4 | 14 | bc | false | <90% | 3641 | ||
| NM_001555 | IGSF1 | 3694 | 3712 | C | U | G | C | C | A | G | G | u | G | U | U | G | A | A | U | U | U | g | 34 | 2 | 9 | bc | false | <90% | 4492 | ||
| NM_021209 | NLRC4 | 3078 | 3096 | C | U | u | C | C | A | G | c | A | G | U | U | G | A | A | U | U | U | g | 13 | 3 | 10 | bc | false | <90% | 3384 | ||
| NM_018080 | VPS13C | 7041 | 7059 | C | U | G | C | C | A | G | G | A | G | a | U | G | A | u | U | U | U | a | 9 | 3 | 10 | c | false | <90% | 11012 | ||
| NM_001018088 | VPS13C | 7170 | 7188 | C | U | G | C | C | A | G | G | A | G | a | U | G | A | u | U | U | U | a | 9 | 3 | 10 | c | false | <90% | 11141 | ||
| NM_017684 | VPS13C | 7041 | 7059 | C | U | G | C | C | A | G | G | A | G | a | U | G | A | u | U | U | U | a | 9 | 3 | 10 | c | false | <90% | 13295 | ||
| NM_020821 | VPS13C | 7170 | 7188 | C | U | G | C | C | A | G | G | A | G | a | U | G | A | u | U | U | U | a | 9 | 3 | 10 | c | false | <90% | 13400 | ||
| NM_198336 | INSIG1 | 970 | 988 | C | U | G | u | g | A | G | G | A | G | U | U | G | A | A | U | U | U | g | 6 | 3 | 13 | bc | false | <90% | 3049 | ||
| NM_018370 | DRAM | 1297 | 1315 | C | a | u | C | C | A | G | G | A | c | U | U | G | A | A | U | U | U | C | -13 | 3 | 9 | bc | false | <90% | 3553 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2403
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