Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
52 hits were found for GAAGCAAAGCAGAAAGUUU (32 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 | |||||||||||||
NM_017412 | FZD3 | 2193 | 2211 | G | A | A | G | C | A | A | A | G | C | A | G | g | A | A | G | c | a | U | 63 | 3 | 12 | false | <90% | 3933 | |||
NM_002395 | ME1 | 1335 | 1353 | c | u | A | G | C | A | A | A | G | C | A | G | A | A | u | G | U | U | c | 56 | 4 | 12 | c | false | <90% | 3360 | ||
NM_001042430 | C14orf140 | 1335 | 1353 | G | A | u | G | C | A | A | A | G | C | A | G | A | A | A | G | a | a | a | 49 | 4 | 13 | c | false | <90% | 1578 | ||
NM_024643 | C14orf140 | 1850 | 1868 | G | A | u | G | C | A | A | A | G | C | A | G | A | A | A | G | a | a | a | 49 | 4 | 13 | c | false | <90% | 2093 | ||
NM_003622 | PPFIBP1 | 4900 | 4918 | a | A | A | G | C | A | A | A | G | C | A | G | A | A | A | c | c | U | U | 48 | 3 | 14 | c | false | <90% | 6076 | ||
NM_024940 | DOCK5 | 7079 | 7097 | G | u | g | G | C | A | A | A | G | C | A | G | A | A | A | G | c | U | U | 45 | 3 | 13 | c | false | <90% | 7555 | ||
NM_001148 | ANK2 | 7825 | 7843 | G | A | A | G | C | A | A | A | G | C | A | G | A | A | A | a | g | g | g | 42 | 4 | 15 | c | false | <90% | 14166 | ||
NM_001033910 | TRAF5 | 2371 | 2389 | G | A | A | G | u | A | A | A | G | C | A | G | A | A | A | G | U | a | c | 40 | 3 | 12 | c | false | <90% | 3982 | ||
NM_004619 | TRAF5 | 2377 | 2395 | G | A | A | G | u | A | A | A | G | C | A | G | A | A | A | G | U | a | c | 40 | 3 | 12 | c | false | <90% | 3988 | ||
NM_145759 | TRAF5 | 2377 | 2395 | G | A | A | G | u | A | A | A | G | C | A | G | A | A | A | G | U | a | c | 40 | 3 | 12 | c | false | <90% | 3988 | ||
NM_017553 | INOC1 | 570 | 588 | G | A | A | G | a | A | A | A | G | C | A | G | A | A | A | G | U | g | g | 40 | 3 | 12 | c | false | <90% | 6249 | ||
NM_002855 | PVRL1 | 4012 | 4030 | c | A | A | G | C | A | A | A | G | C | A | c | A | A | A | u | U | U | U | 38 | 3 | 10 | false | <90% | 5493 | |||
NM_015065 | EXPH5 | 3054 | 3072 | u | A | A | G | C | A | A | A | a | C | A | G | A | A | A | G | U | a | U | 35 | 3 | 8 | c | false | <90% | 6655 | ||
NM_007153 | ZNF208 | 5762 | 5780 | a | A | A | G | C | A | A | A | u | C | A | G | A | A | A | G | U | U | a | 32 | 3 | 9 | bc | false | <90% | 8241 | ||
XM_001133612 | LOC731873 | 115 | 133 | a | A | A | G | C | c | A | A | G | C | A | G | A | A | A | G | U | g | a | 27 | 4 | 11 | c | false | <90% | 541 | ||
XM_001128627 | LOC728183 | 115 | 133 | a | A | A | G | C | c | A | A | G | C | A | G | A | A | A | G | U | g | a | 27 | 4 | 11 | c | false | <90% | 541 | ||
NM_002976 | SCN7A | 1322 | 1340 | G | A | A | G | a | A | A | A | G | C | A | G | A | g | A | G | U | U | g | 24 | 3 | 8 | c | false | <90% | 5727 | ||
NM_024297 | PHF23 | 1916 | 1934 | G | A | A | G | g | A | A | A | G | C | A | G | A | A | A | G | g | U | g | 20 | 3 | 11 | c | false | <90% | 2041 | ||
NM_152998 | EZH2 | 638 | 656 | G | A | A | G | a | A | A | A | G | C | A | G | A | A | A | G | a | U | c | 20 | 3 | 11 | c | false | <90% | 2563 | ||
NM_004456 | EZH2 | 755 | 773 | G | A | A | G | a | A | A | A | G | C | A | G | A | A | A | G | a | U | c | 20 | 3 | 11 | c | false | <90% | 2695 | ||
NM_001522 | GUCY2F | 3563 | 3581 | G | A | A | G | a | A | A | A | G | C | A | G | A | A | A | G | g | c | a | 17 | 4 | 11 | c | false | <90% | 3698 | ||
NM_005445 | SMC3 | 1138 | 1156 | G | A | A | G | a | A | A | A | G | C | A | G | A | A | A | G | a | a | c | 17 | 4 | 11 | c | false | <90% | 4131 | ||
NM_017439 | LOC54103 | 1757 | 1775 | a | c | u | G | a | A | A | A | G | C | A | G | A | A | A | G | U | U | U | 15 | 4 | 14 | bc | false | <90% | 2282 | ||
NM_002291 | LAMB1 | 4847 | 4865 | c | A | A | G | C | A | A | A | u | C | A | G | A | A | A | c | U | U | U | 11 | 3 | 7 | c | false | <90% | 5831 | ||
NM_152453 | TMCO5 | 188 | 206 | G | A | A | G | C | A | A | A | c | C | A | G | A | A | A | c | U | U | c | 8 | 3 | 8 | c | false | <90% | 1186 | ||
NM_032991 | CASP3 | 2010 | 2028 | G | A | A | G | C | A | A | A | u | C | A | G | A | A | A | c | U | U | g | 8 | 3 | 8 | c | false | <90% | 2522 | ||
NM_004346 | CASP3 | 2177 | 2195 | G | A | A | G | C | A | A | A | u | C | A | G | A | A | A | c | U | U | g | 8 | 3 | 8 | c | false | <90% | 2689 | ||
NM_015496 | KIAA1429 | 4341 | 4359 | a | A | A | G | C | A | A | A | G | a | A | G | A | A | A | G | U | c | c | 7 | 4 | 8 | c | false | <90% | 5786 | ||
XM_937970 | C10orf18 | 1879 | 1897 | a | A | A | G | C | A | A | A | G | a | A | G | A | g | A | G | U | U | U | -4 | 3 | 8 | c | false | <90% | 10129 | ||
XM_374765 | C10orf18 | 1879 | 1897 | a | A | A | G | C | A | A | A | G | a | A | G | A | g | A | G | U | U | U | -4 | 3 | 8 | c | false | <90% | 10129 | ||
NM_021239 | RBM25 | 678 | 696 | a | A | A | G | C | A | A | A | G | a | A | G | A | A | A | G | c | U | U | -8 | 3 | 8 | c | false | <90% | 4189 | ||
NM_144571 | CNOT6L | 5480 | 5498 | G | A | A | G | C | A | A | g | G | g | A | G | A | A | A | G | U | U | g | -49 | 3 | 8 | bc | false | <90% | 8794 |
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_004613 | TGM2 | 3740 | 3758 | g | A | A | C | U | U | U | C | U | G | C | U | U | U | G | C | a | c | a | 66 | 4 | 15 | ac | false | <90% | 3937 | ||
NM_001546 | ID4 | 2083 | 2101 | A | c | A | C | U | U | U | C | U | G | C | U | U | U | c | C | U | U | C | 63 | 2 | 12 | c | false | <90% | 2389 | ||
XM_001125843 | LOC727804 | 571 | 589 | u | g | g | C | U | U | U | C | U | G | C | U | U | U | G | C | U | U | u | 62 | 4 | 15 | bc | false | <90% | 2060 | ||
XM_001131467 | LOC731976 | 573 | 591 | u | g | g | C | U | U | U | C | U | G | C | U | U | U | G | C | U | U | u | 62 | 4 | 15 | bc | false | <90% | 2062 | ||
NM_006546 | IGF2BP1 | 7174 | 7192 | c | c | A | C | U | U | U | C | U | G | C | U | U | U | c | C | U | U | g | 56 | 4 | 12 | c | false | <90% | 8769 | ||
NM_018656 | SLC35E3 | 882 | 900 | u | c | A | g | U | U | U | C | U | G | C | U | U | U | G | C | U | U | a | 44 | 4 | 14 | bc | false | <90% | 2347 | ||
NM_015065 | EXPH5 | 6357 | 6375 | g | g | g | C | U | U | U | C | U | G | C | U | U | U | a | C | U | U | C | 42 | 4 | 11 | c | false | <90% | 6655 | ||
NM_033049 | MUC13 | 1095 | 1113 | g | c | c | C | U | U | U | C | U | G | C | g | U | U | G | C | U | U | C | 33 | 4 | 8 | false | <90% | 2961 | |||
NM_004863 | SPTLC2 | 4902 | 4920 | c | A | A | C | U | U | U | u | U | G | C | U | U | U | G | C | U | U | u | 30 | 3 | 10 | bc | false | <90% | 7250 | ||
NM_014571 | HEYL | 1114 | 1132 | g | c | c | u | U | U | U | C | U | G | C | U | U | U | G | C | U | U | C | 30 | 4 | 15 | bc | false | <90% | 4131 | ||
NM_130846 | PTPRR | 263 | 281 | g | g | A | C | U | U | U | C | U | G | u | U | U | U | G | C | U | U | u | 20 | 4 | 8 | c | false | <90% | 2733 | ||
NM_018186 | C1orf112 | 2434 | 2452 | g | u | A | C | U | g | U | C | U | G | C | U | U | U | G | C | U | U | g | 18 | 4 | 12 | bc | false | <90% | 3363 | ||
NM_000828 | GRIA3 | 3193 | 3211 | A | A | u | C | U | U | U | u | U | G | C | U | U | U | G | C | U | U | g | 13 | 3 | 10 | bc | false | <90% | 5183 | ||
NM_007325 | GRIA3 | 3193 | 3211 | A | A | u | C | U | U | U | u | U | G | C | U | U | U | G | C | U | U | g | 13 | 3 | 10 | bc | false | <90% | 5183 | ||
NM_012471 | TRPC5 | 4123 | 4141 | A | A | c | C | U | U | U | u | U | G | C | U | U | U | G | C | U | U | u | 13 | 3 | 10 | bc | false | <90% | 5840 | ||
NM_033407 | DOCK7 | 736 | 754 | g | A | A | C | U | U | U | u | U | G | C | U | U | U | G | C | a | U | C | 12 | 3 | 8 | c | false | <90% | 7063 | ||
NR_003366 | ANKRD20B | 19343 | 19361 | A | A | A | C | U | U | U | C | U | u | C | U | c | U | G | C | U | U | u | 1 | 3 | 9 | false | <90% | 96524 | |||
NM_206594 | ESRRG | 284 | 302 | c | A | A | C | U | U | U | C | U | u | C | U | U | U | u | C | U | U | C | -9 | 3 | 8 | c | false | <90% | 5369 | ||
NM_001001395 | LMO3 | 2058 | 2076 | A | A | A | C | U | U | g | C | U | u | C | U | U | U | G | C | U | U | u | -54 | 3 | 8 | bc | false | <90% | 3450 | ||
NM_018640 | LMO3 | 2335 | 2353 | A | A | A | C | U | U | g | C | U | u | C | U | U | U | G | C | U | U | u | -54 | 3 | 8 | bc | false | <90% | 3727 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2347
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