Automatic recommendation
Not OK - siRNA is not specific
23 hits were found for GGUGUGAGCAUGGUGUCAU (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_020792 | AADACL1 | 1263 | 1281 | c | G | U | G | U | G | A | G | C | A | U | G | a | U | G | U | C | c | U | 84 | 3 | 11 | false | <90% | 4289 | |||
NM_015318 | ARHGEF18 | 2828 | 2846 | c | G | U | G | U | G | A | G | C | A | U | G | c | U | G | c | C | A | U | 61 | 3 | 11 | false | <90% | 5386 | |||
NM_003281 | TNNI1 | 5040 | 5058 | G | G | g | G | U | G | A | G | C | A | U | G | G | U | G | U | g | u | a | 49 | 4 | 13 | c | false | <90% | 6162 | ||
NM_199170 | TMEPAI | 3282 | 3300 | u | G | U | G | U | G | u | G | C | A | U | G | G | U | G | U | C | A | g | 26 | 3 | 11 | bc | false | <90% | 4531 | ||
NM_199169 | TMEPAI | 3289 | 3307 | u | G | U | G | U | G | u | G | C | A | U | G | G | U | G | U | C | A | g | 26 | 3 | 11 | bc | false | <90% | 4538 | ||
NM_199171 | TMEPAI | 3341 | 3359 | u | G | U | G | U | G | u | G | C | A | U | G | G | U | G | U | C | A | g | 26 | 3 | 11 | bc | false | <90% | 4590 | ||
NM_020182 | TMEPAI | 3681 | 3699 | u | G | U | G | U | G | u | G | C | A | U | G | G | U | G | U | C | A | g | 26 | 3 | 11 | bc | false | <90% | 4930 | ||
NM_004424 | E4F1 | 2296 | 2314 | a | c | U | G | U | G | A | c | C | A | U | G | G | U | G | U | C | A | U | 24 | 3 | 11 | bc | false | <90% | 2573 | ||
XR_016571 | LOC643996 | 224 | 242 | G | G | U | G | U | G | A | G | u | A | U | G | G | U | G | U | g | A | c | 11 | 3 | 8 | c | false | <90% | 895 | ||
XR_018494 | LOC648942 | 224 | 242 | G | G | U | G | U | G | A | G | u | A | U | G | G | U | G | U | g | A | c | 11 | 3 | 8 | c | false | <90% | 895 | ||
NM_152750 | FLJ23834 | 2801 | 2819 | G | G | U | G | U | G | g | G | C | A | U | G | G | U | G | U | a | g | g | 2 | 4 | 9 | c | false | <90% | 3810 | ||
XM_940433 | LOC651302 | 404 | 422 | G | G | U | G | U | G | A | a | C | A | a | G | G | U | G | U | C | A | g | -28 | 3 | 7 | c | false | <90% | 1636 |
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_024901 | DENND2D | 1813 | 1831 | c | U | G | A | C | A | C | C | A | U | G | C | U | C | A | C | A | g | a | 90 | 3 | 16 | ac | false | <90% | 2062 | ||
NM_015512 | DNAH1 | 8668 | 8686 | A | g | G | A | C | A | C | C | A | U | G | C | U | C | A | C | c | a | u | 57 | 4 | 14 | ac | false | <90% | 13114 | ||
XR_018836 | LOC650778 | 1351 | 1369 | A | U | G | g | C | A | C | C | A | U | G | C | U | C | A | C | A | a | g | 55 | 3 | 13 | c | false | <90% | 2059 | ||
XR_016707 | LOC391681 | 1351 | 1369 | A | U | G | g | C | A | C | C | A | U | G | C | U | C | A | C | A | a | g | 55 | 3 | 13 | c | false | <90% | 2059 | ||
NM_032932 | RAB11FIP4 | 7291 | 7309 | A | U | G | u | C | A | C | C | A | U | G | C | U | C | A | C | c | a | g | 32 | 4 | 12 | c | false | <90% | 8665 | ||
NM_030904 | OR2T1 | 982 | 1000 | u | U | u | A | C | A | C | C | A | U | u | C | U | C | A | C | A | C | C | 17 | 3 | 8 | c | false | <90% | 1110 | ||
XM_001133324 | LOC729268 | 449 | 467 | A | U | G | A | C | A | C | C | A | c | G | C | U | C | A | C | c | g | C | -8 | 3 | 9 | c | false | <90% | 492 | ||
NM_001012706 | LOC283551 | 165 | 183 | A | U | G | A | C | A | C | C | A | c | G | C | U | C | A | C | c | g | C | -8 | 3 | 9 | c | false | <90% | 2686 | ||
NM_018411 | HR | 3715 | 3733 | g | U | G | c | C | A | C | C | A | a | G | C | U | C | A | C | A | C | C | -21 | 3 | 9 | bc | false | <90% | 4816 | ||
NM_005144 | HR | 3880 | 3898 | g | U | G | c | C | A | C | C | A | a | G | C | U | C | A | C | A | C | C | -21 | 3 | 9 | bc | false | <90% | 4981 | ||
NM_015457 | ZDHHC5 | 2666 | 2684 | A | U | G | A | C | A | g | C | u | U | G | C | U | C | A | C | A | C | C | -26 | 2 | 10 | bc | false | <90% | 4582 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2092
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