Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
37 hits were found for AAGCCUCUUCUCGCUCCUC (15 guide strand hits and 22 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 | |||||||||||||
XM_944355 | LOC645495 | 52 | 70 | g | u | G | C | C | U | C | U | U | C | U | C | c | C | U | C | C | U | g | 71 | 4 | 10 | false | <90% | 543 | |||
XM_932940 | LOC645495 | 52 | 70 | g | u | G | C | C | U | C | U | U | C | U | C | c | C | U | C | C | U | g | 71 | 4 | 10 | false | <90% | 543 | |||
NM_003278 | CLEC3B | 123 | 141 | c | u | G | C | C | U | C | U | U | C | U | C | c | C | U | C | C | U | g | 71 | 4 | 10 | false | <90% | 874 | |||
XM_001133550 | C14orf128 | 829 | 847 | A | c | u | C | C | U | C | U | U | C | U | C | G | C | U | C | C | U | g | 64 | 3 | 15 | bc | false | <90% | 1441 | ||
NM_198493 | ANKRD45 | 2164 | 2182 | c | c | u | C | C | U | C | U | U | C | U | C | u | C | U | C | C | U | C | 56 | 4 | 9 | false | <90% | 2670 | |||
NM_001008393 | LOC201725 | 272 | 290 | c | u | c | C | C | U | C | U | U | C | U | C | c | C | U | C | C | U | C | 56 | 4 | 9 | false | <90% | 3503 | |||
NM_001004474 | OR10S1 | 111 | 129 | u | A | G | C | C | U | C | U | U | C | U | u | c | C | U | C | C | U | C | 53 | 3 | 10 | false | <90% | 996 | |||
XM_001128061 | LOC728454 | 51 | 69 | u | c | u | C | C | U | C | U | U | C | U | C | G | u | U | C | C | U | C | 47 | 4 | 10 | c | false | <90% | 336 | ||
NM_004942 | DEFB4 | 51 | 69 | u | c | u | C | C | U | C | U | U | C | U | C | G | u | U | C | C | U | C | 47 | 4 | 10 | c | false | <90% | 336 | ||
NM_000721 | CACNA1E | 6304 | 6322 | A | A | G | C | a | U | C | U | U | C | U | C | u | C | U | C | C | U | g | 33 | 3 | 7 | false | <90% | 9734 | |||
NM_001942 | DSG1 | 2682 | 2700 | A | A | G | C | C | U | a | U | U | C | U | C | G | a | U | C | C | U | C | 14 | 2 | 6 | c | false | <90% | 5447 | ||
NM_006804 | STARD3 | 214 | 232 | g | A | G | C | C | U | C | U | c | C | U | C | G | C | a | C | C | U | C | 13 | 3 | 7 | c | false | <90% | 2073 | ||
NM_006492 | ALX3 | 1057 | 1075 | A | A | G | C | C | U | C | g | U | C | U | C | G | C | U | C | a | g | g | 6 | 4 | 8 | c | false | <90% | 1478 | ||
XM_372775 | LOC391025 | 544 | 562 | A | A | G | C | C | U | C | g | U | C | U | g | G | C | U | C | C | U | C | 4 | 2 | 7 | false | <90% | 579 | |||
XM_001131226 | LOC391025 | 544 | 562 | A | A | G | C | C | U | C | g | U | C | U | g | G | C | U | C | C | U | C | 4 | 2 | 7 | false | <90% | 579 |
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_003576 | STK24 | 187 | 205 | a | A | G | G | A | G | C | G | A | G | A | A | G | g | G | G | g | U | U | 54 | 3 | 12 | c | false | <90% | 4539 | ||
NM_033266 | ERN2 | 1778 | 1796 | G | A | G | G | A | G | C | c | A | G | A | A | G | A | G | G | C | U | U | 37 | 1 | 11 | bc | false | <90% | 3634 | ||
NM_032572 | RNASE7 | 90 | 108 | c | A | G | G | A | G | u | G | A | G | A | A | G | A | G | G | C | c | c | 24 | 4 | 10 | c | false | <90% | 1465 | ||
NM_015904 | EIF5B | 2546 | 2564 | G | A | G | G | A | G | C | G | A | G | c | A | a | A | G | G | C | U | a | 23 | 3 | 10 | false | <90% | 4698 | |||
NM_017775 | TTC19 | 709 | 727 | G | A | u | G | A | G | C | c | A | G | A | A | G | A | G | G | C | U | g | 13 | 3 | 10 | bc | false | <90% | 2784 | ||
NM_032010 | MAP1B | 2821 | 2839 | G | A | G | G | A | G | C | c | A | G | A | A | G | A | G | G | a | U | g | 9 | 3 | 8 | c | false | <90% | 9161 | ||
NM_005909 | MAP1B | 3076 | 3094 | G | A | G | G | A | G | C | c | A | G | A | A | G | A | G | G | a | U | g | 9 | 3 | 8 | c | false | <90% | 9416 | ||
NM_033081 | DIDO1 | 4806 | 4824 | G | A | G | G | A | G | C | a | A | G | A | A | G | A | a | G | C | U | c | 8 | 3 | 7 | c | false | <90% | 8562 | ||
NM_152536 | FGD5 | 70 | 88 | G | A | G | G | A | G | C | G | u | G | A | A | G | A | G | G | g | a | g | 8 | 4 | 8 | c | false | <90% | 5384 | ||
NM_001080426 | DUSP27 | 836 | 854 | G | A | G | G | A | G | a | G | A | G | A | A | G | A | G | G | a | c | U | 7 | 3 | 9 | c | false | <90% | 4034 | ||
XM_942428 | DUSP27 | 836 | 854 | G | A | G | G | A | G | a | G | A | G | A | A | G | A | G | G | a | c | U | 7 | 3 | 9 | c | false | <90% | 4034 | ||
NM_006617 | NES | 4188 | 4206 | G | A | G | G | A | G | g | G | A | G | A | A | G | A | G | G | a | g | U | 7 | 3 | 9 | c | false | <90% | 5591 | ||
NM_001080521 | LOC644943 | 1196 | 1214 | G | A | G | G | A | G | C | c | A | G | A | A | G | A | G | G | u | g | g | 6 | 4 | 8 | c | false | <90% | 1848 | ||
XM_940771 | LOC651593 | 1403 | 1421 | G | A | G | G | A | G | C | c | A | G | A | A | G | A | G | G | u | g | g | 6 | 4 | 8 | c | false | <90% | 2055 | ||
NM_014909 | VASH1 | 758 | 776 | G | A | G | G | A | G | C | c | A | G | A | A | G | A | G | G | a | a | g | 6 | 4 | 8 | c | false | <90% | 5746 | ||
NM_015238 | WWC1 | 2656 | 2674 | G | A | G | G | A | G | g | G | A | G | A | A | G | A | G | G | a | U | g | 5 | 3 | 9 | c | false | <90% | 4171 | ||
NM_004798 | KIF3B | 1359 | 1377 | G | A | G | G | A | G | g | G | A | G | A | A | G | A | G | G | g | U | g | 5 | 3 | 9 | c | false | <90% | 6103 | ||
NM_006763 | BTG2 | 162 | 180 | c | g | u | G | A | G | C | G | A | G | c | A | G | A | G | G | C | U | U | 5 | 4 | 8 | c | false | <90% | 2718 | ||
NM_015284 | KIAA0467 | 7294 | 7312 | G | A | G | G | A | G | C | a | A | G | g | A | G | A | G | G | C | U | g | -28 | 3 | 7 | c | false | <90% | 10217 | ||
NM_017986 | GPR172B | 1408 | 1426 | a | A | G | G | A | G | g | a | A | G | A | A | G | A | G | G | C | U | U | -30 | 3 | 11 | bc | false | <90% | 2305 | ||
NM_001001329 | PRKCSH | 1297 | 1315 | G | A | G | G | A | G | g | a | A | G | A | A | G | A | G | G | C | U | g | -33 | 3 | 10 | bc | false | <90% | 2253 | ||
NM_002743 | PRKCSH | 1297 | 1315 | G | A | G | G | A | G | g | a | A | G | A | A | G | A | G | G | C | U | g | -33 | 3 | 10 | bc | false | <90% | 2262 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2033
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