Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
26 hits were found for ACCCUUAUAAAGAAUUUGG (16 guide strand hits and 10 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_000673 | ADH7 | 1391 | 1409 | A | C | C | C | U | U | A | U | A | A | A | G | A | A | U | U | a | u | u | 68 | 3 | 16 | ac | false | <90% | 2147 | ||
| XR_000668 | CXorf30 | 593 | 611 | A | C | C | C | U | U | A | U | A | A | A | G | A | A | a | U | U | c | u | 67 | 3 | 14 | c | false | <90% | 903 | ||
| XR_017930 | LOC158730 | 593 | 611 | A | C | C | C | U | U | A | U | A | A | A | G | A | A | a | U | U | c | u | 67 | 3 | 14 | c | false | <90% | 903 | ||
| NM_019605 | SERTAD4 | 567 | 585 | g | u | C | C | U | U | A | U | A | A | A | c | A | A | U | U | U | G | a | 47 | 4 | 9 | false | <90% | 2038 | |||
| NM_194314 | ZBTB41 | 5194 | 5212 | c | a | C | u | U | U | A | U | A | A | A | G | A | A | U | U | U | G | a | 44 | 4 | 14 | bc | false | <90% | 8474 | ||
| NM_001005746 | CACNB4 | 2860 | 2878 | A | a | a | a | U | U | A | U | A | A | A | G | A | A | U | U | U | G | G | 32 | 3 | 15 | bc | false | <90% | 3062 | ||
| NM_000726 | CACNB4 | 2877 | 2895 | A | a | a | a | U | U | A | U | A | A | A | G | A | A | U | U | U | G | G | 32 | 3 | 15 | bc | false | <90% | 3079 | ||
| NM_001005747 | CACNB4 | 2983 | 3001 | A | a | a | a | U | U | A | U | A | A | A | G | A | A | U | U | U | G | G | 32 | 3 | 15 | bc | false | <90% | 3185 | ||
| NM_000891 | KCNJ2 | 4657 | 4675 | u | C | C | C | U | U | u | U | A | A | A | G | A | A | U | U | U | u | u | 24 | 4 | 10 | c | false | <90% | 5397 | ||
| NM_017667 | CCDC132 | 2818 | 2836 | u | u | C | C | U | g | A | U | A | A | A | G | A | A | U | U | U | G | u | 18 | 4 | 12 | bc | false | <90% | 3625 | ||
| NM_000128 | F11 | 287 | 305 | A | C | C | C | U | U | A | U | u | A | A | G | A | A | U | U | g | c | a | 8 | 4 | 8 | c | false | <90% | 3278 | ||
| NM_138638 | CFL2 | 2095 | 2113 | c | u | C | C | U | U | A | U | A | g | A | G | A | A | U | U | U | G | a | -1 | 4 | 8 | bc | false | <90% | 3093 | ||
| NM_021914 | CFL2 | 2095 | 2113 | c | u | C | C | U | U | A | U | A | g | A | G | A | A | U | U | U | G | a | -1 | 4 | 8 | bc | false | <90% | 3093 | ||
| NM_080630 | COL11A1 | 1388 | 1406 | c | C | C | C | U | a | A | U | g | A | A | G | A | A | U | U | U | G | G | -25 | 3 | 10 | bc | false | <90% | 7174 | ||
| NM_001854 | COL11A1 | 1505 | 1523 | c | C | C | C | U | a | A | U | g | A | A | G | A | A | U | U | U | G | G | -25 | 3 | 10 | bc | false | <90% | 7291 | ||
| NM_080629 | COL11A1 | 1541 | 1559 | c | C | C | C | U | a | A | U | g | A | A | G | A | A | U | U | U | G | G | -25 | 3 | 10 | bc | false | <90% | 7327 | ||
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_173560 | RFXDC1 | 1024 | 1042 | C | u | c | A | A | U | U | C | U | U | U | A | U | A | A | G | G | u | U | 66 | 3 | 14 | c | false | <90% | 3538 | ||
| NM_002757 | MAP2K5 | 1294 | 1312 | g | g | A | A | A | U | U | C | U | U | U | A | U | A | A | G | u | G | c | 58 | 4 | 14 | ac | false | <90% | 2334 | ||
| NM_145160 | MAP2K5 | 1294 | 1312 | g | g | A | A | A | U | U | C | U | U | U | A | U | A | A | G | u | G | c | 58 | 4 | 14 | ac | false | <90% | 2381 | ||
| NM_007167 | ZMYM6 | 518 | 536 | a | a | A | A | A | U | g | C | U | U | U | A | U | A | A | G | G | G | c | 15 | 4 | 11 | bc | false | <90% | 5159 | ||
| NM_016275 | SELT | 1129 | 1147 | C | C | A | A | A | U | a | C | U | U | U | A | U | A | A | G | a | G | U | 10 | 2 | 9 | c | false | <90% | 3498 | ||
| NM_152279 | ZNF585B | 2853 | 2871 | C | C | A | A | A | U | U | C | U | U | c | A | U | A | A | G | a | a | a | 7 | 4 | 10 | c | false | <90% | 2992 | ||
| NM_024763 | WDR78 | 2960 | 2978 | C | C | A | A | A | a | U | C | U | U | U | A | U | A | A | G | a | c | a | 5 | 4 | 10 | c | false | <90% | 3871 | ||
| XM_001126090 | LOC728146 | 524 | 542 | a | u | c | A | A | U | U | a | U | U | U | A | U | A | A | G | G | G | U | 4 | 4 | 11 | bc | false | <90% | 2194 | ||
| XM_001129476 | LOC286434 | 527 | 545 | a | u | c | A | A | U | U | a | U | U | U | A | U | A | A | G | G | G | U | 4 | 4 | 11 | bc | false | <90% | 2197 | ||
| XM_001129423 | LOC729137 | 527 | 545 | a | u | c | A | A | U | U | a | U | U | U | A | U | A | A | G | G | G | U | 4 | 4 | 11 | bc | false | <90% | 2198 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1147
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