Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for CUAGGAGGCUGUAGGCAUA (7 guide strand hits and 10 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_016577 | RAB6B | 2692 | 2710 | C | U | A | G | G | A | G | G | C | U | G | U | A | u | G | C | c | a | g | 49 | 4 | 13 | c | false | <90% | 5561 | ||
NM_006371 | CRTAP | 3410 | 3428 | a | a | A | a | G | A | G | G | C | U | G | U | A | G | G | C | A | U | c | 44 | 4 | 14 | bc | false | <90% | 6622 | ||
NM_006617 | NES | 5180 | 5198 | a | a | u | G | G | A | G | G | C | U | G | U | A | G | G | a | A | U | A | 40 | 4 | 12 | c | false | <90% | 5591 | ||
NM_014425 | INVS | 2788 | 2806 | C | U | A | G | G | A | G | G | C | U | G | g | A | G | a | C | A | U | c | 36 | 3 | 11 | false | <90% | 3880 | |||
NM_015227 | POFUT2 | 1389 | 1407 | a | U | A | G | c | A | G | G | C | U | G | U | u | G | G | C | A | U | A | 36 | 3 | 7 | false | <90% | 4843 | |||
NM_019089 | HES2 | 2253 | 2271 | g | a | A | G | G | A | a | G | C | U | G | U | A | G | G | C | A | U | u | 15 | 4 | 11 | bc | false | <90% | 4259 | ||
NM_020428 | SLC44A2 | 219 | 237 | C | U | A | c | G | u | G | G | C | U | G | U | A | G | G | C | A | U | c | -5 | 3 | 12 | bc | false | <90% | 3389 |
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_002616 | PER1 | 501 | 519 | a | u | U | G | C | C | U | A | C | A | G | C | C | U | C | C | U | g | a | 78 | 4 | 15 | ac | false | <90% | 4656 | ||
NM_017736 | THUMPD1 | 316 | 334 | g | A | g | G | C | C | U | A | C | A | G | C | C | U | C | C | U | c | a | 70 | 4 | 14 | c | false | <90% | 4416 | ||
NR_003505 | PPP4R1L | 1676 | 1694 | U | g | U | G | C | C | U | A | C | A | G | C | C | U | C | C | c | A | G | 65 | 2 | 14 | ac | false | <90% | 2398 | ||
NM_001042600 | MAP4K1 | 1179 | 1197 | c | u | c | G | C | C | U | A | C | A | G | C | C | U | C | C | U | c | G | 64 | 4 | 14 | c | false | <90% | 2688 | ||
NM_007181 | MAP4K1 | 1179 | 1197 | c | u | c | G | C | C | U | A | C | A | G | C | C | U | C | C | U | c | G | 64 | 4 | 14 | c | false | <90% | 2786 | ||
NM_207320 | OTUD6A | 812 | 830 | U | A | U | G | C | C | U | A | C | A | G | C | C | U | C | g | g | c | G | 47 | 3 | 15 | c | false | <90% | 1689 | ||
XR_016984 | LOC340888 | 676 | 694 | a | u | g | G | C | C | U | A | C | A | G | C | C | c | C | C | U | A | G | 47 | 4 | 10 | c | false | <90% | 1080 | ||
XR_018726 | LOC340888 | 676 | 694 | a | u | g | G | C | C | U | A | C | A | G | C | C | c | C | C | U | A | G | 47 | 4 | 10 | c | false | <90% | 1080 | ||
NM_001017967 | MARVELD3 | 977 | 995 | g | c | c | G | C | C | U | u | C | A | G | C | C | U | C | C | U | A | G | 4 | 4 | 11 | bc | false | <90% | 2239 | ||
NM_004943 | DMWD | 2102 | 2120 | c | A | U | G | C | C | c | c | C | A | G | C | C | U | C | C | U | A | G | -30 | 3 | 11 | bc | false | <90% | 3308 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1582
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