Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GAACAAUUAUAGUAAAUCA (14 guide strand hits and 6 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 | |||||||||||||
| XM_932026 | LOC644173 | 1237 | 1255 | u | g | A | C | A | A | U | U | A | U | A | G | g | A | A | A | U | C | c | 71 | 4 | 10 | false | <90% | 1373 | |||
| XM_942992 | LOC644173 | 1237 | 1255 | u | g | A | C | A | A | U | U | A | U | A | G | g | A | A | A | U | C | c | 71 | 4 | 10 | false | <90% | 1373 | |||
| NM_024617 | ZCCHC6 | 3256 | 3274 | c | A | A | C | A | A | U | U | A | U | A | G | a | A | g | A | U | C | A | 62 | 3 | 11 | false | <90% | 5648 | |||
| NM_004999 | MYO6 | 6034 | 6052 | a | u | A | C | A | A | U | U | A | U | A | G | U | u | A | A | U | C | u | 62 | 4 | 11 | c | false | <90% | 8662 | ||
| NM_021111 | RECK | 686 | 704 | G | A | A | C | A | A | U | U | A | U | A | c | U | c | A | A | U | C | u | 41 | 3 | 11 | false | <90% | 4414 | |||
| NM_005079 | TPD52 | 948 | 966 | a | A | A | C | A | c | U | U | A | U | A | G | U | A | A | A | U | g | g | 27 | 4 | 11 | c | false | <90% | 3966 | ||
| NM_001025253 | TPD52 | 1017 | 1035 | a | A | A | C | A | c | U | U | A | U | A | G | U | A | A | A | U | g | g | 27 | 4 | 11 | c | false | <90% | 4035 | ||
| NM_001025252 | TPD52 | 1232 | 1250 | a | A | A | C | A | c | U | U | A | U | A | G | U | A | A | A | U | g | g | 27 | 4 | 11 | c | false | <90% | 4250 | ||
| NM_183236 | RAB27A | 1106 | 1124 | a | g | c | C | u | A | U | U | A | U | A | G | U | A | A | A | U | C | A | 15 | 4 | 14 | bc | false | <90% | 2772 | ||
| NM_183235 | RAB27A | 1143 | 1161 | a | g | c | C | u | A | U | U | A | U | A | G | U | A | A | A | U | C | A | 15 | 4 | 14 | bc | false | <90% | 2809 | ||
| NM_183234 | RAB27A | 1146 | 1164 | a | g | c | C | u | A | U | U | A | U | A | G | U | A | A | A | U | C | A | 15 | 4 | 14 | bc | false | <90% | 2812 | ||
| NM_004580 | RAB27A | 1158 | 1176 | a | g | c | C | u | A | U | U | A | U | A | G | U | A | A | A | U | C | A | 15 | 4 | 14 | bc | false | <90% | 2824 | ||
| NM_001010942 | RAP1B | 1541 | 1559 | u | A | A | C | A | A | U | U | u | U | u | G | U | A | A | A | U | C | A | -23 | 3 | 8 | c | false | <90% | 2117 | ||
| NM_015646 | RAP1B | 1550 | 1568 | u | A | A | C | A | A | U | U | u | U | u | G | U | A | A | A | U | C | A | -23 | 3 | 8 | c | false | <90% | 2126 | ||
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_054034 | FN1 | 2322 | 2340 | g | c | A | U | U | U | A | C | U | A | U | A | u | U | U | G | U | U | u | 71 | 4 | 10 | false | <90% | 2402 | |||
| NM_001039780 | FLJ16793 | 2247 | 2265 | a | G | A | U | a | U | A | C | U | A | U | A | A | U | U | G | U | c | u | 38 | 4 | 12 | c | false | <90% | 2355 | ||
| NM_182620 | FAM33A | 1057 | 1075 | U | u | u | a | U | U | A | C | U | A | U | A | A | U | U | G | U | U | C | 32 | 3 | 15 | bc | false | <90% | 2710 | ||
| NM_199072 | MDFIC | 3145 | 3163 | U | G | A | U | U | U | A | a | U | A | U | A | A | U | U | c | U | U | a | 6 | 3 | 7 | c | false | <90% | 4607 | ||
| NM_173488 | SLCO6A1 | 1799 | 1817 | a | G | A | U | g | U | A | C | U | A | c | A | A | U | U | G | U | U | C | -14 | 3 | 8 | c | false | <90% | 2544 | ||
| NM_006526 | ZNF217 | 5507 | 5525 | U | G | A | U | U | U | A | u | U | u | U | A | A | U | U | G | U | U | g | -49 | 3 | 8 | bc | false | <90% | 5653 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1655
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