Automatic recommendation
Not OK - siRNA is not specific
20 hits were found for CAUCACAUCAGGAUUCCUA (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 | |||||||||||||
XR_017031 | LOC441654 | 46 | 64 | C | A | U | C | A | C | A | U | C | A | G | G | g | U | U | C | C | U | u | 84 | 2 | 12 | false | <90% | 2199 | |||
XR_018855 | LOC650452 | 46 | 64 | C | A | U | C | A | C | A | U | C | A | G | G | g | U | U | C | C | U | u | 84 | 2 | 12 | false | <90% | 2218 | |||
NM_178150 | FBXO18 | 2622 | 2640 | u | A | U | a | A | C | A | U | C | A | G | G | A | U | U | C | C | a | g | 53 | 4 | 13 | c | false | <90% | 3540 | ||
NM_032807 | FBXO18 | 2784 | 2802 | u | A | U | a | A | C | A | U | C | A | G | G | A | U | U | C | C | a | g | 53 | 4 | 13 | c | false | <90% | 3727 | ||
XM_938779 | LOC653972 | 1337 | 1355 | C | A | U | C | A | C | A | g | C | A | G | G | u | U | U | C | C | U | c | 22 | 3 | 7 | false | <90% | 1814 | |||
NM_007276 | CBX3 | 1340 | 1358 | C | A | U | C | A | C | A | g | C | A | G | G | u | U | U | C | C | U | c | 22 | 3 | 7 | false | <90% | 1837 | |||
NM_016587 | CBX3 | 1380 | 1398 | C | A | U | C | A | C | A | g | C | A | G | G | u | U | U | C | C | U | c | 22 | 3 | 7 | false | <90% | 1851 | |||
NM_015074 | KIF1B | 6356 | 6374 | C | c | U | C | A | C | A | g | C | A | G | G | A | U | U | C | C | U | g | 21 | 3 | 10 | bc | false | <90% | 10551 | ||
NM_000097 | CPOX | 2464 | 2482 | a | A | U | C | A | C | A | a | C | A | G | G | A | U | U | C | u | U | A | 12 | 3 | 8 | c | false | <90% | 2714 | ||
NM_152552 | SAMD3 | 820 | 838 | u | u | g | C | A | C | A | U | u | A | G | G | A | U | U | C | C | U | A | 6 | 4 | 10 | bc | false | <90% | 1052 | ||
NM_173808 | NEGR1 | 3584 | 3602 | u | A | U | C | A | C | A | g | C | A | G | c | A | U | U | C | C | U | A | 2 | 3 | 7 | false | <90% | 5669 | |||
NM_013988 | PARK2 | 558 | 576 | C | A | U | C | A | C | u | U | C | A | G | G | A | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 2513 | ||
NM_013987 | PARK2 | 921 | 939 | C | A | U | C | A | C | u | U | C | A | G | G | A | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 2876 | ||
NM_004562 | PARK2 | 1005 | 1023 | C | A | U | C | A | C | u | U | C | A | G | G | A | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 2960 |
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_001007189 | LOC492311 | 1736 | 1754 | a | A | G | G | A | A | U | C | C | U | G | c | U | G | U | G | A | a | a | 56 | 4 | 10 | false | <90% | 2900 | |||
NM_080687 | UPF3A | 391 | 409 | U | A | G | G | A | A | U | C | C | U | G | A | U | G | a | c | A | U | c | 44 | 3 | 14 | c | false | <90% | 2282 | ||
NM_023011 | UPF3A | 391 | 409 | U | A | G | G | A | A | U | C | C | U | G | A | U | G | a | c | A | U | c | 44 | 3 | 14 | c | false | <90% | 2381 | ||
XR_015324 | LOC730944 | 249 | 267 | a | A | G | G | A | A | U | C | C | U | G | g | U | G | g | G | A | U | G | 39 | 3 | 10 | false | <90% | 1976 | |||
NM_001023587 | ABCC5 | 108 | 126 | c | A | G | G | A | A | U | u | C | U | G | A | U | G | U | G | A | a | a | 28 | 4 | 9 | c | false | <90% | 2007 | ||
NM_005688 | ABCC5 | 108 | 126 | c | A | G | G | A | A | U | u | C | U | G | A | U | G | U | G | A | a | a | 28 | 4 | 9 | c | false | <90% | 5851 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1975
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