Automatic recommendation
Not OK - siRNA is not specific
32 hits were found for CUUUUUCACCUCUGCCUAA (12 guide strand hits and 20 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_016664 | LOC347281 | 1238 | 1256 | C | U | g | U | U | U | C | A | C | C | U | C | U | G | C | C | U | A | A | 80 | 1 | 16 | bc | false | <90% | 2606 | ||
XR_019067 | LOC347281 | 1238 | 1256 | C | U | g | U | U | U | C | A | C | C | U | C | U | G | C | C | U | A | A | 80 | 1 | 16 | bc | false | <90% | 2606 | ||
NM_005436 | CCDC6 | 3172 | 3190 | u | U | U | U | U | U | C | A | C | C | U | C | U | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 5702 | ||
NM_006373 | VAT1 | 1632 | 1650 | u | g | c | U | U | U | C | A | C | C | U | C | U | G | C | C | U | c | A | 64 | 4 | 14 | c | false | <90% | 2758 | ||
NM_017522 | LRP8 | 3052 | 3070 | u | c | U | U | U | U | C | A | C | C | U | C | U | G | g | C | U | A | u | 56 | 4 | 12 | c | false | <90% | 3739 | ||
NM_033300 | LRP8 | 3426 | 3444 | u | c | U | U | U | U | C | A | C | C | U | C | U | G | g | C | U | A | u | 56 | 4 | 12 | c | false | <90% | 4097 | ||
NM_001018054 | LRP8 | 3664 | 3682 | u | c | U | U | U | U | C | A | C | C | U | C | U | G | g | C | U | A | u | 56 | 4 | 12 | c | false | <90% | 4351 | ||
NM_004631 | LRP8 | 3841 | 3859 | u | c | U | U | U | U | C | A | C | C | U | C | U | G | g | C | U | A | u | 56 | 4 | 12 | c | false | <90% | 4528 | ||
NM_000790 | DDC | 57 | 75 | C | U | U | U | U | U | C | A | C | C | U | C | U | G | a | C | a | g | A | 49 | 3 | 14 | c | false | <90% | 1975 | ||
NM_153211 | C18orf17 | 772 | 790 | C | U | U | U | U | U | C | A | C | C | U | u | U | G | C | a | U | A | u | 35 | 3 | 11 | false | <90% | 2304 | |||
NM_002737 | PRKCA | 8203 | 8221 | C | U | U | U | g | U | C | A | C | C | U | C | U | G | C | u | U | A | A | 22 | 2 | 10 | c | false | <90% | 8787 | ||
NM_007112 | THBS3 | 71 | 89 | C | U | U | U | U | U | C | A | C | a | U | C | U | G | C | C | a | g | u | -13 | 4 | 9 | c | false | <90% | 3176 |
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_006281 | STK3 | 1720 | 1738 | U | U | A | G | G | C | A | G | A | G | G | U | c | A | A | A | A | A | G | 89 | 1 | 12 | false | <90% | 2826 | |||
NM_144681 | CCDC42 | 1135 | 1153 | c | U | g | G | G | C | A | G | A | G | G | U | G | A | A | A | A | A | G | 78 | 2 | 16 | bc | false | <90% | 1374 | ||
NM_005048 | PTHR2 | 1474 | 1492 | U | c | A | G | G | C | A | G | A | G | G | U | G | A | A | g | A | A | G | 62 | 2 | 13 | c | false | <90% | 2810 | ||
NM_006946 | SPTBN2 | 4944 | 4962 | c | c | A | G | G | C | A | G | A | G | G | U | G | A | A | g | A | A | G | 60 | 3 | 13 | c | false | <90% | 7864 | ||
NM_001033520 | WIPI2 | 2901 | 2919 | U | U | A | G | G | C | A | G | A | G | G | U | G | c | A | A | g | u | G | 54 | 3 | 13 | c | false | <90% | 4295 | ||
NM_001033519 | WIPI2 | 3008 | 3026 | U | U | A | G | G | C | A | G | A | G | G | U | G | c | A | A | g | u | G | 54 | 3 | 13 | c | false | <90% | 4402 | ||
NM_016003 | WIPI2 | 3041 | 3059 | U | U | A | G | G | C | A | G | A | G | G | U | G | c | A | A | g | u | G | 54 | 3 | 13 | c | false | <90% | 4435 | ||
NM_001033518 | WIPI2 | 3062 | 3080 | U | U | A | G | G | C | A | G | A | G | G | U | G | c | A | A | g | u | G | 54 | 3 | 13 | c | false | <90% | 4456 | ||
NM_015610 | WIPI2 | 3095 | 3113 | U | U | A | G | G | C | A | G | A | G | G | U | G | c | A | A | g | u | G | 54 | 3 | 13 | c | false | <90% | 4489 | ||
XM_496344 | LOC440563 | 506 | 524 | a | g | A | G | G | u | A | G | A | G | G | U | G | A | A | A | A | A | u | 18 | 4 | 12 | bc | false | <90% | 753 | ||
NM_030811 | MRPS26 | 522 | 540 | g | c | A | G | G | a | A | G | A | G | G | U | G | A | A | A | A | A | c | 18 | 4 | 12 | bc | false | <90% | 1062 | ||
NM_001013631 | HNRPCL1 | 861 | 879 | a | g | A | G | G | u | A | G | A | G | G | U | G | A | A | A | A | A | u | 18 | 4 | 12 | bc | false | <90% | 1108 | ||
XM_938404 | LOC649330 | 842 | 860 | a | g | A | G | G | u | A | G | A | G | G | U | G | A | A | A | A | A | u | 18 | 4 | 12 | bc | false | <90% | 1292 | ||
NM_032010 | MAP1B | 1997 | 2015 | a | a | A | G | G | a | A | G | A | G | G | U | G | A | A | A | A | A | a | 18 | 4 | 12 | bc | false | <90% | 9161 | ||
NM_005909 | MAP1B | 2252 | 2270 | a | a | A | G | G | a | A | G | A | G | G | U | G | A | A | A | A | A | a | 18 | 4 | 12 | bc | false | <90% | 9416 | ||
XR_015996 | LOC731899 | 1052 | 1070 | U | c | A | G | G | C | u | G | A | G | G | U | G | A | A | A | A | A | a | 17 | 3 | 11 | bc | false | <90% | 3357 | ||
XR_015706 | LOC728913 | 1054 | 1072 | U | c | A | G | G | C | u | G | A | G | G | U | G | A | A | A | A | A | a | 17 | 3 | 11 | bc | false | <90% | 3360 | ||
NM_020977 | ANK2 | 73 | 91 | g | U | A | G | u | C | A | G | A | G | G | a | G | A | A | A | A | A | G | 12 | 3 | 7 | false | <90% | 7911 | |||
NM_001148 | ANK2 | 73 | 91 | g | U | A | G | u | C | A | G | A | G | G | a | G | A | A | A | A | A | G | 12 | 3 | 7 | false | <90% | 14166 | |||
NM_024038 | C19orf43 | 521 | 539 | c | a | u | G | G | C | A | G | A | a | G | U | G | A | A | A | A | A | G | -15 | 4 | 9 | bc | false | <90% | 945 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4873
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