Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for GGGUGAACAGCAUGUAAUA (5 guide strand hits and 9 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_000621 | HTR2A | 11 | 29 | G | G | G | a | G | A | A | C | A | G | C | A | U | G | U | A | c | a | c | 32 | 4 | 12 | c | false | <90% | 3009 | ||
| NM_001005407 | CACNA1H | 4765 | 4783 | G | G | G | U | G | A | A | C | A | u | C | A | U | G | U | A | c | g | A | -8 | 3 | 9 | c | false | <90% | 8079 | ||
| NM_021098 | CACNA1H | 4765 | 4783 | G | G | G | U | G | A | A | C | A | u | C | A | U | G | U | A | c | g | A | -8 | 3 | 9 | c | false | <90% | 8097 | ||
| NM_001003406 | CACNA1I | 4040 | 4058 | G | G | G | U | G | A | A | C | A | u | C | A | U | G | U | A | c | a | A | -8 | 3 | 9 | c | false | <90% | 9902 | ||
| NM_021096 | CACNA1I | 4145 | 4163 | G | G | G | U | G | A | A | C | A | u | C | A | U | G | U | A | c | a | A | -8 | 3 | 9 | c | false | <90% | 10007 | ||
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_000079 | CHRNA1 | 946 | 964 | a | A | a | U | A | C | A | U | G | C | U | G | U | U | C | A | C | C | a | 73 | 3 | 15 | bc | false | <90% | 1965 | ||
| NM_001039523 | CHRNA1 | 1021 | 1039 | a | A | a | U | A | C | A | U | G | C | U | G | U | U | C | A | C | C | a | 73 | 3 | 15 | bc | false | <90% | 2040 | ||
| NM_030805 | LMAN2L | 2261 | 2279 | g | g | U | U | A | C | A | U | G | C | U | G | c | U | C | A | C | C | u | 71 | 4 | 10 | false | <90% | 2412 | |||
| NM_053041 | COMMD7 | 1130 | 1148 | g | A | U | a | A | C | A | U | G | C | U | G | a | U | C | A | C | C | C | 50 | 3 | 8 | false | <90% | 1476 | |||
| NM_001079524 | PAICS | 2521 | 2539 | a | u | a | U | A | C | A | U | G | C | U | G | U | U | g | A | C | C | C | 42 | 4 | 11 | c | false | <90% | 3329 | ||
| NM_006452 | PAICS | 2542 | 2560 | a | u | a | U | A | C | A | U | G | C | U | G | U | U | g | A | C | C | C | 42 | 4 | 11 | c | false | <90% | 3350 | ||
| NM_001079525 | PAICS | 2542 | 2560 | a | u | a | U | A | C | A | U | G | C | U | G | U | U | g | A | C | C | C | 42 | 4 | 11 | c | false | <90% | 3350 | ||
| NM_014632 | MICAL2 | 230 | 248 | U | A | c | U | u | C | A | U | G | C | U | G | U | U | C | A | C | C | u | 23 | 3 | 13 | bc | false | <90% | 3934 | ||
| NM_024763 | WDR78 | 2667 | 2685 | U | A | U | U | A | C | A | U | a | C | U | G | U | a | C | A | C | C | a | 15 | 3 | 8 | c | false | <90% | 3871 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1578
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