Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for CCUACACCUGAAGAACCAG (19 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_207414 | FLJ43860 | 3600 | 3618 | C | C | U | A | C | A | C | C | U | G | A | A | G | g | A | C | C | A | a | 75 | 2 | 13 | c | false | <90% | 4164 | ||
NM_000885 | ITGA4 | 105 | 123 | C | C | U | A | C | A | C | C | U | G | A | A | a | A | A | C | a | A | G | 66 | 2 | 12 | false | <90% | 6082 | |||
NM_023085 | CAPN10 | 817 | 835 | g | C | U | c | C | A | C | C | U | G | A | A | G | g | A | C | C | A | G | 41 | 3 | 9 | c | false | <90% | 2161 | ||
NM_023083 | CAPN10 | 817 | 835 | g | C | U | c | C | A | C | C | U | G | A | A | G | g | A | C | C | A | G | 41 | 3 | 9 | c | false | <90% | 2626 | ||
NM_080414 | VPS16 | 355 | 373 | g | C | U | g | C | A | C | C | U | G | A | A | G | A | A | C | g | A | G | 37 | 3 | 12 | c | false | <90% | 1301 | ||
NM_080413 | VPS16 | 1350 | 1368 | g | C | U | g | C | A | C | C | U | G | A | A | G | A | A | C | g | A | G | 37 | 3 | 12 | c | false | <90% | 2337 | ||
NM_022575 | VPS16 | 1782 | 1800 | g | C | U | g | C | A | C | C | U | G | A | A | G | A | A | C | g | A | G | 37 | 3 | 12 | c | false | <90% | 2769 | ||
NM_002836 | PTPRA | 107 | 125 | g | C | U | g | C | A | C | C | U | G | A | A | G | A | A | C | g | A | G | 37 | 3 | 12 | c | false | <90% | 3637 | ||
NM_032797 | AIFM2 | 466 | 484 | g | a | U | A | g | A | C | C | U | G | A | A | G | A | A | C | C | A | G | 35 | 3 | 14 | bc | false | <90% | 3240 | ||
NM_178555 | FLJ25770 | 1659 | 1677 | u | u | U | A | C | A | g | C | U | G | A | A | G | A | A | C | C | A | a | 15 | 4 | 11 | bc | false | <90% | 1931 | ||
NM_001042784 | FLJ25770 | 3399 | 3417 | u | u | U | A | C | A | g | C | U | G | A | A | G | A | A | C | C | A | a | 15 | 4 | 11 | bc | false | <90% | 3626 | ||
NM_033438 | SLAMF9 | 673 | 691 | C | C | U | A | C | A | C | C | U | G | c | A | G | A | g | C | C | A | a | 9 | 3 | 10 | c | false | <90% | 1137 | ||
XR_017291 | LOC646773 | 1703 | 1721 | g | C | U | A | C | A | C | g | U | G | A | A | G | A | A | a | C | A | G | 9 | 3 | 7 | c | false | <90% | 1750 | ||
NM_000087 | CNGA1 | 156 | 174 | u | C | U | A | C | A | u | C | U | G | A | A | G | A | A | u | C | A | G | 5 | 3 | 8 | c | false | <90% | 2532 | ||
NM_031366 | COL4A3 | 4252 | 4270 | g | g | c | A | C | A | C | C | U | G | g | A | G | A | A | C | C | A | G | 5 | 4 | 8 | c | false | <90% | 7420 | ||
NM_031365 | COL4A3 | 4252 | 4270 | g | g | c | A | C | A | C | C | U | G | g | A | G | A | A | C | C | A | G | 5 | 4 | 8 | c | false | <90% | 7630 | ||
NM_031362 | COL4A3 | 4252 | 4270 | g | g | c | A | C | A | C | C | U | G | g | A | G | A | A | C | C | A | G | 5 | 4 | 8 | c | false | <90% | 7923 | ||
NM_000091 | COL4A3 | 4252 | 4270 | g | g | c | A | C | A | C | C | U | G | g | A | G | A | A | C | C | A | G | 5 | 4 | 8 | c | false | <90% | 8096 | ||
NM_153697 | ANKRD44 | 1066 | 1084 | u | u | a | A | C | A | C | C | U | u | A | A | G | A | A | C | C | A | G | -15 | 4 | 9 | bc | false | <90% | 3686 |
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_052900 | CSMD3 | 7379 | 7397 | g | a | u | G | U | U | C | U | U | C | A | G | G | U | G | U | A | u | G | 64 | 4 | 14 | c | false | <90% | 12643 | ||
NM_198124 | CSMD3 | 7583 | 7601 | g | a | u | G | U | U | C | U | U | C | A | G | G | U | G | U | A | u | G | 64 | 4 | 14 | c | false | <90% | 13042 | ||
NM_198123 | CSMD3 | 7691 | 7709 | g | a | u | G | U | U | C | U | U | C | A | G | G | U | G | U | A | u | G | 64 | 4 | 14 | c | false | <90% | 13150 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 999
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