Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
26 hits were found for UUCCUAGGACCCCUUCUCG (3 guide strand hits and 23 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_016333 | SRRM2 | 3194 | 3212 | a | a | u | C | U | A | G | G | A | C | C | C | C | U | U | C | U | a | G | 64 | 4 | 14 | c | false | <90% | 9379 | ||
NM_017564 | STAB2 | 7773 | 7791 | U | U | C | C | U | A | c | G | A | C | C | C | C | U | U | C | a | C | G | 10 | 2 | 9 | c | false | <90% | 8266 | ||
XM_001129224 | ITGB5 | 4150 | 4168 | U | U | C | C | U | A | a | G | A | C | C | C | C | a | U | C | U | C | a | 9 | 3 | 6 | c | false | <90% | 4599 |
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_001127146 | IL7R | 2823 | 2841 | a | G | A | G | A | A | G | G | G | G | U | C | a | U | A | G | G | u | u | 79 | 4 | 11 | false | <90% | 4493 | |||
NM_016428 | ABI3 | 1745 | 1763 | g | G | A | G | A | A | G | G | G | G | U | C | C | U | g | G | G | g | A | 70 | 3 | 13 | c | false | <90% | 2129 | ||
XM_929785 | LOC340204 | 253 | 271 | g | G | A | G | A | A | G | G | G | G | U | C | C | g | A | G | G | g | c | 70 | 4 | 12 | c | false | <90% | 575 | ||
XM_941299 | LOC340204 | 253 | 271 | g | G | A | G | A | A | G | G | G | G | U | C | C | g | A | G | G | g | c | 70 | 4 | 12 | c | false | <90% | 575 | ||
NM_001010886 | LOC340204 | 253 | 271 | g | G | A | G | A | A | G | G | G | G | U | C | C | g | A | G | G | g | c | 70 | 4 | 12 | c | false | <90% | 584 | ||
NM_207380 | FLJ43339 | 274 | 292 | g | c | A | G | A | A | G | G | G | G | U | C | C | c | A | G | G | A | g | 62 | 4 | 11 | c | false | <90% | 4707 | ||
NM_021191 | NEUROD4 | 690 | 708 | a | G | A | G | A | A | G | G | G | G | U | C | C | c | A | a | G | A | A | 52 | 3 | 12 | c | false | <90% | 1481 | ||
NM_006339 | HMG20B | 191 | 209 | C | G | A | G | A | A | G | G | G | G | U | C | C | c | A | c | G | A | g | 49 | 3 | 13 | c | false | <90% | 1584 | ||
NM_001017404 | LGR6 | 1641 | 1659 | C | G | A | G | c | A | G | G | G | G | U | C | C | U | A | G | G | c | u | 40 | 3 | 12 | c | false | <90% | 3041 | ||
NM_021636 | LGR6 | 1945 | 1963 | C | G | A | G | c | A | G | G | G | G | U | C | C | U | A | G | G | c | u | 40 | 3 | 12 | c | false | <90% | 3345 | ||
NM_001017403 | LGR6 | 2058 | 2076 | C | G | A | G | c | A | G | G | G | G | U | C | C | U | A | G | G | c | u | 40 | 3 | 12 | c | false | <90% | 3458 | ||
NM_000164 | GIPR | 1709 | 1727 | C | G | A | G | A | A | G | G | G | G | g | C | C | U | A | G | G | g | u | 31 | 3 | 10 | c | false | <90% | 2024 | ||
NM_022843 | PCDH20 | 2347 | 2365 | g | G | A | G | A | A | G | a | G | G | U | C | C | U | A | G | G | c | c | 28 | 4 | 9 | c | false | <90% | 4412 | ||
NM_000405 | GM2A | 2350 | 2368 | g | G | A | G | c | A | G | G | G | G | U | C | C | a | A | G | G | A | A | 27 | 3 | 8 | c | false | <90% | 2521 | ||
NM_007050 | PTPRT | 11034 | 11052 | g | G | A | G | A | A | a | G | G | G | U | C | a | U | A | G | G | A | A | 21 | 3 | 6 | false | <90% | 12653 | |||
NM_133170 | PTPRT | 11091 | 11109 | g | G | A | G | A | A | a | G | G | G | U | C | a | U | A | G | G | A | A | 21 | 3 | 6 | false | <90% | 12710 | |||
XM_376903 | KIAA0674 | 2573 | 2591 | u | G | A | G | A | A | G | G | a | G | U | C | C | U | u | G | G | A | A | 13 | 3 | 7 | c | false | <90% | 4588 | ||
XM_936355 | KIAA0674 | 2573 | 2591 | u | G | A | G | A | A | G | G | a | G | U | C | C | U | u | G | G | A | A | 13 | 3 | 7 | c | false | <90% | 4588 | ||
NM_014460 | CSDC2 | 558 | 576 | C | G | A | G | A | A | c | G | G | G | U | C | C | g | A | G | G | A | c | 9 | 3 | 6 | c | false | <90% | 2545 | ||
XR_019479 | LOC650018 | 1024 | 1042 | C | G | A | G | A | A | G | G | u | G | U | C | C | U | A | G | a | u | c | 8 | 4 | 8 | c | false | <90% | 1489 | ||
XR_017586 | LOC644988 | 1024 | 1042 | C | G | A | G | A | A | G | G | u | G | U | C | C | U | A | G | a | u | c | 8 | 4 | 8 | c | false | <90% | 1489 | ||
XR_016450 | LOC139748 | 552 | 570 | g | G | A | G | A | A | G | G | G | a | U | C | C | U | A | G | G | u | c | 7 | 4 | 8 | c | false | <90% | 1489 | ||
XR_018559 | LOC649375 | 552 | 570 | g | G | A | G | A | A | G | G | G | a | U | C | C | U | A | G | G | u | c | 7 | 4 | 8 | c | false | <90% | 1489 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2082
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