Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
23 hits were found for CUUAAACAACUCCUGGAAC (12 guide strand hits and 11 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_001044 | SLC6A3 | 658 | 676 | C | U | g | c | A | A | C | A | A | C | U | C | C | U | G | G | A | A | C | 43 | 2 | 15 | bc | false | <90% | 3925 | ||
NM_015030 | FRYL | 3669 | 3687 | a | c | U | A | g | A | C | A | A | C | U | C | C | U | G | G | A | A | g | 30 | 4 | 13 | bc | false | <90% | 11706 | ||
NM_032503 | MCHR2 | 136 | 154 | u | U | U | A | A | A | C | A | A | a | U | C | C | U | G | G | A | A | u | 10 | 3 | 8 | bc | false | <90% | 2144 | ||
NM_001040179 | MCHR2 | 360 | 378 | u | U | U | A | A | A | C | A | A | a | U | C | C | U | G | G | A | A | u | 10 | 3 | 8 | bc | false | <90% | 2368 | ||
NM_001744 | CAMK4 | 533 | 551 | g | U | U | A | A | A | C | A | A | a | U | C | C | U | G | G | A | g | g | 7 | 4 | 8 | c | false | <90% | 2168 | ||
NM_000303 | PMM2 | 1269 | 1287 | u | a | c | A | A | A | C | A | c | C | U | C | C | U | G | G | A | A | C | 6 | 4 | 10 | bc | false | <90% | 2302 | ||
NM_003611 | OFD1 | 1671 | 1689 | C | U | U | A | A | A | C | A | A | C | a | a | C | U | G | G | A | A | g | 0 | 3 | 10 | false | <90% | 3615 | |||
NM_020647 | JPH1 | 2608 | 2626 | C | U | U | u | A | A | C | A | u | C | U | C | C | U | G | G | A | A | u | -1 | 3 | 9 | bc | false | <90% | 4373 | ||
NM_019857 | CTPS2 | 3452 | 3470 | C | U | U | A | A | A | C | A | A | u | U | C | C | a | G | G | A | A | C | -2 | 2 | 9 | c | false | <90% | 3844 | ||
NM_175859 | CTPS2 | 3555 | 3573 | C | U | U | A | A | A | C | A | A | u | U | C | C | a | G | G | A | A | C | -2 | 2 | 9 | c | false | <90% | 3947 | ||
NM_001009877 | BRD9 | 274 | 292 | a | U | U | c | A | g | C | A | A | C | U | C | C | U | G | G | A | A | C | -2 | 3 | 13 | bc | false | <90% | 2395 | ||
NM_023924 | BRD9 | 683 | 701 | a | U | U | c | A | g | C | A | A | C | U | C | C | U | G | G | A | A | C | -2 | 3 | 13 | bc | false | <90% | 2843 |
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_001032395 | GPR126 | 4831 | 4849 | c | U | c | C | C | A | G | G | A | G | U | U | G | U | U | U | A | A | G | 78 | 2 | 16 | bc | false | <90% | 6818 | ||
NM_001032394 | GPR126 | 4877 | 4895 | c | U | c | C | C | A | G | G | A | G | U | U | G | U | U | U | A | A | G | 78 | 2 | 16 | bc | false | <90% | 6864 | ||
NM_198569 | GPR126 | 4915 | 4933 | c | U | c | C | C | A | G | G | A | G | U | U | G | U | U | U | A | A | G | 78 | 2 | 16 | bc | false | <90% | 6902 | ||
NM_020455 | GPR126 | 4961 | 4979 | c | U | c | C | C | A | G | G | A | G | U | U | G | U | U | U | A | A | G | 78 | 2 | 16 | bc | false | <90% | 6948 | ||
NM_001039592 | SPAG8 | 61 | 79 | G | c | U | C | C | A | G | G | A | G | U | U | G | U | U | U | g | c | u | 57 | 4 | 14 | ac | false | <90% | 1715 | ||
NM_172312 | SPAG8 | 61 | 79 | G | c | U | C | C | A | G | G | A | G | U | U | G | U | U | U | g | c | u | 57 | 4 | 14 | ac | false | <90% | 2010 | ||
NM_003307 | TRPM2 | 1260 | 1278 | c | U | U | C | C | A | G | G | A | G | a | U | G | U | U | U | g | A | G | 13 | 3 | 9 | c | false | <90% | 5876 | ||
XR_016284 | LOC402422 | 1120 | 1138 | c | U | U | C | C | A | G | G | A | G | c | U | G | U | U | c | A | A | G | 10 | 3 | 9 | c | false | <90% | 1334 | ||
XR_018492 | LOC402422 | 1120 | 1138 | c | U | U | C | C | A | G | G | A | G | c | U | G | U | U | c | A | A | G | 10 | 3 | 9 | c | false | <90% | 1334 | ||
NM_001080853 | LOC728758 | 1489 | 1507 | G | U | U | C | C | A | u | G | A | G | U | U | G | U | U | U | u | g | u | 2 | 4 | 9 | c | false | <90% | 1729 | ||
NM_030576 | LIMD2 | 419 | 437 | c | U | U | C | C | A | G | c | A | G | c | U | G | U | U | U | A | A | G | -25 | 3 | 8 | c | false | <90% | 3178 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1895
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