Automatic recommendation
Not OK - siRNA is not specific
15 hits were found for UAUCUACCAUGUAGACUGC (12 guide strand hits and 3 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_001025073 | C3orf17 | 4396 | 4414 | a | A | U | C | U | A | C | C | A | U | G | U | u | G | A | C | U | u | C | 84 | 3 | 11 | false | <90% | 4702 | |||
| NM_001025072 | C3orf17 | 4400 | 4418 | a | A | U | C | U | A | C | C | A | U | G | U | u | G | A | C | U | u | C | 84 | 3 | 11 | false | <90% | 4706 | |||
| NM_015412 | C3orf17 | 4551 | 4569 | a | A | U | C | U | A | C | C | A | U | G | U | u | G | A | C | U | u | C | 84 | 3 | 11 | false | <90% | 4857 | |||
| NM_018374 | TMEM106B | 5781 | 5799 | U | u | a | C | U | A | C | C | A | U | G | U | A | G | A | C | U | G | u | 64 | 3 | 15 | bc | false | <90% | 6456 | ||
| NM_001005407 | CACNA1H | 1970 | 1988 | c | A | U | C | U | A | C | C | A | U | G | c | c | G | A | C | U | G | C | 53 | 3 | 10 | false | <90% | 8079 | |||
| NM_021098 | CACNA1H | 1970 | 1988 | c | A | U | C | U | A | C | C | A | U | G | c | c | G | A | C | U | G | C | 53 | 3 | 10 | false | <90% | 8097 | |||
| NM_004742 | MAGI1 | 1648 | 1666 | U | A | U | C | U | A | C | u | A | U | G | U | A | G | A | C | c | a | C | 11 | 3 | 8 | c | false | <90% | 6178 | ||
| NM_001033057 | MAGI1 | 1648 | 1666 | U | A | U | C | U | A | C | u | A | U | G | U | A | G | A | C | c | a | C | 11 | 3 | 8 | c | false | <90% | 7062 | ||
| NM_015520 | MAGI1 | 1648 | 1666 | U | A | U | C | U | A | C | u | A | U | G | U | A | G | A | C | c | a | C | 11 | 3 | 8 | c | false | <90% | 7235 | ||
| NM_181054 | HIF1A | 2486 | 2504 | U | A | U | u | U | A | g | C | A | U | G | U | A | G | A | C | U | G | C | -3 | 2 | 12 | bc | false | <90% | 3812 | ||
| NM_019600 | KIAA1370 | 3528 | 3546 | U | A | U | a | U | u | C | C | A | U | G | U | A | G | A | C | U | G | g | -5 | 3 | 12 | bc | false | <90% | 3863 | ||
| NM_001530 | HIF1A | 2613 | 2631 | g | A | U | u | U | A | g | C | A | U | G | U | A | G | A | C | U | G | C | -5 | 3 | 12 | bc | false | <90% | 3958 | ||
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_004866 | SCAMP1 | 491 | 509 | u | C | A | G | U | C | a | A | C | A | U | G | G | U | A | G | A | a | A | 29 | 3 | 10 | c | false | <90% | 6245 | ||
| XR_017120 | LOC646090 | 2769 | 2787 | G | C | u | G | U | C | U | A | C | A | a | G | G | U | A | G | A | U | A | 19 | 2 | 8 | c | false | <90% | 2897 | ||
| NM_033103 | RHPN2 | 2767 | 2785 | G | C | u | G | U | C | U | A | C | A | a | G | G | U | A | G | A | U | A | 19 | 2 | 8 | c | false | <90% | 3516 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1065
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