Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
25 hits were found for GUCUGUACAACAUCUUGAG (5 guide strand hits and 20 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_198407 | GHSR | 962 | 980 | u | U | C | U | G | U | A | C | A | A | C | A | U | C | a | U | G | u | c | 65 | 4 | 13 | c | false | <90% | 1101 | ||
| NM_032448 | FAM120B | 1880 | 1898 | u | g | g | U | G | U | A | C | A | A | C | A | U | C | a | U | G | A | G | 42 | 4 | 11 | c | false | <90% | 3261 | ||
| NM_130838 | UBE3A | 3187 | 3205 | u | U | C | U | G | U | g | C | A | A | a | A | U | C | U | U | G | A | G | -29 | 3 | 8 | c | false | <90% | 4491 | ||
| NM_000462 | UBE3A | 3212 | 3230 | u | U | C | U | G | U | g | C | A | A | a | A | U | C | U | U | G | A | G | -29 | 3 | 8 | c | false | <90% | 4516 | ||
| NM_130839 | UBE3A | 3860 | 3878 | u | U | C | U | G | U | g | C | A | A | a | A | U | C | U | U | G | A | G | -29 | 3 | 8 | c | false | <90% | 5164 | ||
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 | |||||||||||||
| XM_001128575 | LOC731136 | 564 | 582 | u | U | C | A | A | G | A | U | G | U | U | G | U | A | C | A | u | g | u | 66 | 4 | 15 | ac | false | <90% | 692 | ||
| NM_152336 | AGBL1 | 3365 | 3383 | u | U | C | A | A | G | A | U | G | U | U | G | U | A | C | A | u | g | u | 66 | 4 | 15 | ac | false | <90% | 3493 | ||
| NM_004071 | CLK1 | 1459 | 1477 | C | U | C | A | A | G | A | U | G | U | U | G | a | A | C | A | u | g | a | 58 | 4 | 12 | false | <90% | 1887 | |||
| NM_001037126 | EXOC4 | 1203 | 1221 | u | c | C | A | A | G | A | U | G | U | U | c | U | A | C | A | G | A | u | 47 | 4 | 9 | false | <90% | 1620 | |||
| NM_021807 | EXOC4 | 1203 | 1221 | u | c | C | A | A | G | A | U | G | U | U | c | U | A | C | A | G | A | u | 47 | 4 | 9 | false | <90% | 4203 | |||
| NM_001001692 | FLJ45139 | 3519 | 3537 | g | c | a | A | A | G | A | U | G | U | U | u | U | A | C | A | G | A | C | 33 | 4 | 8 | false | <90% | 3822 | |||
| XR_015405 | LOC728895 | 329 | 347 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 1819 | ||
| XM_939560 | NBPF7 | 138 | 156 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 1887 | ||
| NM_001047980 | NBPF7 | 138 | 156 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 1887 | ||
| XM_001133092 | LOC728912 | 586 | 604 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 2950 | ||
| XM_001133097 | LOC728912 | 586 | 604 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 3194 | ||
| XM_001133188 | LOC728936 | 70 | 88 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 4492 | ||
| XM_001133155 | LOC728936 | 591 | 609 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 4784 | ||
| XM_001133176 | LOC728936 | 591 | 609 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 4898 | ||
| XM_001133169 | LOC728936 | 591 | 609 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 4922 | ||
| XM_001133179 | LOC728936 | 591 | 609 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 5093 | ||
| XM_001133191 | LOC728936 | 591 | 609 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 5111 | ||
| XR_015220 | LOC730476 | 643 | 661 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 5174 | ||
| XM_001133181 | LOC728936 | 591 | 609 | u | U | g | A | u | G | A | U | G | U | U | G | U | A | C | A | G | A | C | 26 | 3 | 14 | bc | false | <90% | 5622 | ||
| NM_001042475 | C6orf204 | 2147 | 2165 | C | U | C | u | A | G | A | U | G | a | U | G | U | A | C | A | G | A | g | -24 | 3 | 8 | bc | false | <90% | 3335 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1915
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