Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
32 hits were found for UGAUGGAAAGUGCCAGACC (22 guide strand hits and 10 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_001221 | CAMK2D | 1878 | 1896 | g | G | A | U | G | G | A | A | A | G | U | G | g | C | A | G | A | a | u | 79 | 4 | 11 | false | <90% | 2140 | |||
NM_172115 | CAMK2D | 1878 | 1896 | g | G | A | U | G | G | A | A | A | G | U | G | g | C | A | G | A | a | u | 79 | 4 | 11 | false | <90% | 2151 | |||
NM_172128 | CAMK2D | 1878 | 1896 | g | G | A | U | G | G | A | A | A | G | U | G | g | C | A | G | A | a | u | 79 | 4 | 11 | false | <90% | 4054 | |||
NM_172127 | CAMK2D | 1878 | 1896 | g | G | A | U | G | G | A | A | A | G | U | G | g | C | A | G | A | a | u | 79 | 4 | 11 | false | <90% | 4098 | |||
NR_003095 | E2F6 | 1611 | 1629 | a | u | A | U | G | G | A | A | A | G | U | G | a | C | A | G | A | C | a | 71 | 4 | 10 | false | <90% | 3185 | |||
NM_198256 | E2F6 | 1666 | 1684 | a | u | A | U | G | G | A | A | A | G | U | G | a | C | A | G | A | C | a | 71 | 4 | 10 | false | <90% | 3240 | |||
NR_003092 | E2F6 | 1737 | 1755 | a | u | A | U | G | G | A | A | A | G | U | G | a | C | A | G | A | C | a | 71 | 4 | 10 | false | <90% | 3311 | |||
NR_003093 | E2F6 | 1799 | 1817 | a | u | A | U | G | G | A | A | A | G | U | G | a | C | A | G | A | C | a | 71 | 4 | 10 | false | <90% | 3373 | |||
NR_003094 | E2F6 | 1870 | 1888 | a | u | A | U | G | G | A | A | A | G | U | G | a | C | A | G | A | C | a | 71 | 4 | 10 | false | <90% | 3444 | |||
NM_016248 | AKAP11 | 5765 | 5783 | g | G | A | U | G | G | A | A | A | G | U | G | g | g | A | G | A | C | C | 68 | 3 | 11 | false | <90% | 9919 | |||
NM_007218 | RNF139 | 3261 | 3279 | U | G | A | U | G | G | A | A | A | G | U | G | g | a | A | G | A | C | a | 65 | 3 | 12 | false | <90% | 3312 | |||
NM_032638 | GATA2 | 997 | 1015 | a | G | A | U | G | G | A | A | A | G | U | G | g | C | A | G | u | C | C | 64 | 3 | 11 | false | <90% | 3383 | |||
NM_018666 | SAGE1 | 1642 | 1660 | a | G | A | U | G | G | A | A | A | G | U | G | g | C | A | a | A | C | C | 61 | 3 | 11 | false | <90% | 3069 | |||
NM_017820 | FLJ20433 | 2845 | 2863 | a | c | A | U | G | G | A | A | A | G | U | G | C | C | c | G | A | C | u | 56 | 4 | 12 | c | false | <90% | 2887 | ||
XM_938203 | C1orf167 | 2946 | 2964 | g | c | A | U | G | a | A | A | A | G | U | G | C | C | A | G | A | C | a | 18 | 4 | 12 | bc | false | <90% | 5515 | ||
XM_209234 | C1orf167 | 2946 | 2964 | g | c | A | U | G | a | A | A | A | G | U | G | C | C | A | G | A | C | a | 18 | 4 | 12 | bc | false | <90% | 5515 | ||
NM_020860 | STIM2 | 2236 | 2254 | c | a | A | U | G | G | g | A | A | G | U | G | C | C | A | G | A | C | a | 15 | 4 | 11 | bc | false | <90% | 3924 | ||
NM_199170 | TMEPAI | 581 | 599 | U | G | A | U | G | G | A | u | A | G | U | G | C | C | A | G | g | C | u | 9 | 3 | 8 | c | false | <90% | 4531 | ||
NM_199169 | TMEPAI | 588 | 606 | U | G | A | U | G | G | A | u | A | G | U | G | C | C | A | G | g | C | u | 9 | 3 | 8 | c | false | <90% | 4538 | ||
NM_199171 | TMEPAI | 640 | 658 | U | G | A | U | G | G | A | u | A | G | U | G | C | C | A | G | g | C | u | 9 | 3 | 8 | c | false | <90% | 4590 | ||
NM_020182 | TMEPAI | 980 | 998 | U | G | A | U | G | G | A | u | A | G | U | G | C | C | A | G | g | C | u | 9 | 3 | 8 | c | false | <90% | 4930 | ||
NM_032552 | DAB2IP | 5023 | 5041 | U | G | A | U | G | G | A | A | A | c | U | G | C | C | A | a | A | C | C | -8 | 2 | 9 | c | false | <90% | 5472 |
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_001004441 | DP58 | 1309 | 1327 | G | G | g | C | U | G | G | C | A | C | U | U | U | C | C | A | a | g | c | 49 | 4 | 13 | c | false | <90% | 3763 | ||
NM_003127 | SPTAN1 | 4272 | 4290 | G | G | g | C | U | G | G | C | A | C | U | U | U | C | C | A | g | g | c | 49 | 4 | 13 | c | false | <90% | 7787 | ||
NM_001005178 | OR52W1 | 606 | 624 | G | G | U | C | U | G | G | C | A | C | U | U | U | C | a | c | U | g | g | 41 | 4 | 14 | c | false | <90% | 963 | ||
NM_004161 | RAB1A | 1249 | 1267 | u | G | U | C | U | G | u | C | A | C | U | U | U | C | C | A | U | g | c | 24 | 4 | 10 | c | false | <90% | 2496 | ||
NM_001963 | EGF | 64 | 82 | u | a | g | C | U | G | G | a | A | C | U | U | U | C | C | A | U | C | A | 4 | 4 | 11 | bc | false | <90% | 4877 | ||
NM_017975 | ZWILCH | 3071 | 3089 | G | G | U | C | U | c | G | C | A | C | c | U | U | C | C | A | U | C | u | -29 | 3 | 7 | c | false | <90% | 3194 | ||
NR_003105 | ZWILCH | 3166 | 3184 | G | G | U | C | U | c | G | C | A | C | c | U | U | C | C | A | U | C | u | -29 | 3 | 7 | c | false | <90% | 3289 | ||
XM_001130324 | LOC728737 | 936 | 954 | u | G | U | C | U | u | c | C | A | C | U | U | U | C | C | A | U | C | A | -31 | 3 | 12 | bc | false | <90% | 1027 | ||
NM_032026 | TATDN1 | 929 | 947 | u | G | U | C | U | u | c | C | A | C | U | U | U | C | C | A | U | C | A | -31 | 3 | 12 | bc | false | <90% | 1038 | ||
XM_001129287 | LOC730828 | 936 | 954 | u | G | U | C | U | u | c | C | A | C | U | U | U | C | C | A | U | C | A | -31 | 3 | 12 | bc | false | <90% | 1039 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2306
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