Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
24 hits were found for CCUUAGAGUCUCCUGAGCU (9 guide strand hits and 15 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_018108 | LOC441811 | 2786 | 2804 | C | C | a | c | A | G | A | G | U | C | U | C | C | U | G | A | G | C | U | 43 | 2 | 15 | bc | false | <90% | 3795 | ||
XR_017184 | LOC441811 | 2786 | 2804 | C | C | a | c | A | G | A | G | U | C | U | C | C | U | G | A | G | C | U | 43 | 2 | 15 | bc | false | <90% | 3795 | ||
NM_020804 | PACSIN1 | 1815 | 1833 | C | C | a | a | A | G | A | G | U | C | U | C | C | U | G | A | G | C | c | 38 | 3 | 14 | bc | false | <90% | 4282 | ||
NM_001040456 | RHBDD2 | 1226 | 1244 | C | C | U | a | A | G | A | G | U | C | U | C | C | U | G | A | c | a | a | 32 | 4 | 12 | c | false | <90% | 1756 | ||
NM_001040457 | RHBDD2 | 1348 | 1366 | C | C | U | a | A | G | A | G | U | C | U | C | C | U | G | A | c | a | a | 32 | 4 | 12 | c | false | <90% | 1878 | ||
NM_000744 | CHRNA4 | 2404 | 2422 | u | u | c | a | A | G | A | G | U | C | U | C | C | U | G | A | G | C | U | 30 | 4 | 15 | bc | false | <90% | 5540 | ||
NM_014882 | ARHGAP25 | 1209 | 1227 | a | a | c | U | A | u | A | G | U | C | U | C | C | U | G | A | G | C | U | 3 | 4 | 13 | bc | false | <90% | 2957 | ||
NM_001007231 | ARHGAP25 | 1214 | 1232 | a | a | c | U | A | u | A | G | U | C | U | C | C | U | G | A | G | C | U | 3 | 4 | 13 | bc | false | <90% | 2962 | ||
NM_015245 | ANKS1A | 4171 | 4189 | C | C | U | U | A | G | A | G | g | C | a | C | C | U | G | A | G | C | a | -26 | 3 | 8 | c | false | <90% | 6355 |
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_015341 | NCAPH | 63 | 81 | A | G | C | U | C | A | G | G | A | G | A | C | g | C | c | A | A | G | G | 64 | 2 | 12 | false | <90% | 4495 | |||
XM_932025 | LOC644171 | 359 | 377 | A | a | C | U | C | A | G | G | A | G | A | C | U | C | c | A | A | G | a | 58 | 3 | 12 | c | false | <90% | 755 | ||
XM_944971 | LOC644171 | 359 | 377 | A | a | C | U | C | A | G | G | A | G | A | C | U | C | c | A | A | G | a | 58 | 3 | 12 | c | false | <90% | 755 | ||
NM_024854 | FLJ22028 | 1232 | 1250 | A | G | u | U | C | A | G | G | A | G | A | C | U | C | U | A | u | u | G | 54 | 3 | 13 | c | false | <90% | 3171 | ||
XR_015408 | LOC730793 | 1302 | 1320 | A | G | u | U | C | A | G | G | A | G | A | C | U | C | U | A | u | u | G | 54 | 3 | 13 | c | false | <90% | 4118 | ||
XR_016381 | LOC642732 | 1302 | 1320 | A | G | u | U | C | A | G | G | A | G | A | C | U | C | U | A | u | u | G | 54 | 3 | 13 | c | false | <90% | 4118 | ||
NM_016252 | BIRC6 | 15001 | 15019 | u | G | C | U | g | A | G | G | A | G | A | C | U | C | U | A | A | u | G | 43 | 3 | 12 | c | false | <90% | 16079 | ||
NM_182811 | PLCG1 | 4334 | 4352 | g | G | C | a | C | A | G | G | A | G | A | C | U | C | c | A | A | G | G | 36 | 3 | 10 | c | false | <90% | 5202 | ||
NM_002660 | PLCG1 | 4337 | 4355 | g | G | C | a | C | A | G | G | A | G | A | C | U | C | c | A | A | G | G | 36 | 3 | 10 | c | false | <90% | 5205 | ||
NM_019118 | C1orf91 | 636 | 654 | A | G | C | a | C | A | G | G | A | G | A | C | U | C | U | A | c | G | c | 34 | 3 | 12 | c | false | <90% | 1108 | ||
NM_015584 | POLDIP2 | 770 | 788 | g | G | C | U | C | g | G | G | A | G | A | C | g | C | U | A | A | G | G | 24 | 3 | 6 | false | <90% | 2723 | |||
NM_018178 | GOLPH3L | 291 | 309 | g | a | u | U | C | u | G | G | A | G | A | C | U | C | U | A | A | G | G | 3 | 4 | 13 | bc | false | <90% | 3127 | ||
NM_006729 | DIAPH2 | 8441 | 8459 | u | c | u | U | C | u | G | G | A | G | A | C | U | C | U | A | A | G | G | 3 | 4 | 13 | bc | false | <90% | 9335 | ||
NM_002547 | OPHN1 | 159 | 177 | u | G | g | U | C | A | G | G | A | a | A | C | U | C | U | A | A | G | G | -4 | 3 | 9 | bc | false | <90% | 7350 | ||
NM_206886 | CCDC18 | 4320 | 4338 | A | G | C | U | C | A | G | G | A | u | A | C | U | g | U | A | A | G | c | -7 | 3 | 9 | c | false | <90% | 4658 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1600
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