Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
39 hits were found for CCAACUGUUAACAUGGAAA (19 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_001009555 | SH3D19 | 4294 | 4312 | a | C | A | A | C | U | G | U | U | A | A | g | A | U | G | G | A | A | A | 64 | 2 | 10 | false | <90% | 5193 | |||
NM_001018037 | VPS13A | 10491 | 10509 | u | u | c | A | C | U | G | U | U | A | A | C | A | U | G | G | A | A | u | 62 | 4 | 15 | bc | false | <90% | 11145 | ||
NM_033305 | VPS13A | 10608 | 10626 | u | u | c | A | C | U | G | U | U | A | A | C | A | U | G | G | A | A | u | 62 | 4 | 15 | bc | false | <90% | 11262 | ||
NM_175566 | CNTN5 | 1063 | 1081 | a | C | A | A | C | U | G | U | U | A | A | g | A | U | G | G | A | A | u | 59 | 3 | 10 | false | <90% | 3942 | |||
NM_014361 | CNTN5 | 1285 | 1303 | a | C | A | A | C | U | G | U | U | A | A | g | A | U | G | G | A | A | u | 59 | 3 | 10 | false | <90% | 4164 | |||
NM_033285 | TP53INP1 | 3740 | 3758 | u | a | A | A | C | U | G | U | U | A | A | C | A | U | a | G | A | A | u | 56 | 4 | 12 | c | false | <90% | 5587 | ||
NM_012258 | HEY1 | 1946 | 1964 | a | C | A | A | a | U | G | U | U | A | A | C | A | U | G | G | A | u | A | 43 | 3 | 12 | c | false | <90% | 2319 | ||
NM_001040708 | HEY1 | 1958 | 1976 | a | C | A | A | a | U | G | U | U | A | A | C | A | U | G | G | A | u | A | 43 | 3 | 12 | c | false | <90% | 2331 | ||
NM_014016 | SACM1L | 3221 | 3239 | C | C | A | c | C | U | G | U | U | A | A | C | A | U | G | u | A | A | A | 37 | 2 | 11 | c | false | <90% | 3550 | ||
XM_001130187 | LOC729012 | 1 | 19 | u | C | A | A | C | U | a | U | U | A | A | C | A | U | G | G | A | g | g | 24 | 4 | 10 | c | false | <90% | 799 | ||
XM_001131195 | LOC731589 | 1 | 19 | u | C | A | A | C | U | a | U | U | A | A | C | A | U | G | G | A | g | g | 24 | 4 | 10 | c | false | <90% | 799 | ||
NM_022662 | ANAPC1 | 5516 | 5534 | C | C | A | A | C | U | G | U | g | A | A | C | A | U | G | G | g | u | c | 8 | 4 | 8 | c | false | <90% | 6329 | ||
NM_001071 | TYMS | 1018 | 1036 | C | C | A | A | C | U | a | U | U | A | A | a | A | U | G | G | A | A | A | 0 | 2 | 7 | false | <90% | 1536 | |||
NM_152871 | FAS | 786 | 804 | C | C | A | A | a | U | G | U | g | A | A | C | A | U | G | G | A | A | u | -16 | 3 | 9 | bc | false | <90% | 2692 | ||
NM_152872 | FAS | 786 | 804 | C | C | A | A | a | U | G | U | g | A | A | C | A | U | G | G | A | A | u | -16 | 3 | 9 | bc | false | <90% | 2730 | ||
NM_000043 | FAS | 786 | 804 | C | C | A | A | a | U | G | U | g | A | A | C | A | U | G | G | A | A | u | -16 | 3 | 9 | bc | false | <90% | 2755 | ||
NM_003622 | PPFIBP1 | 1569 | 1587 | g | C | A | A | C | U | G | U | a | A | g | C | A | U | G | G | A | A | A | -23 | 3 | 8 | c | false | <90% | 6076 | ||
XM_001129340 | LOC284952 | 452 | 470 | C | C | A | A | C | U | G | g | U | A | g | C | A | U | G | G | A | A | u | -28 | 3 | 7 | c | false | <90% | 3218 | ||
XM_001126137 | LOC284952 | 452 | 470 | C | C | A | A | C | U | G | g | U | A | g | C | A | U | G | G | A | A | u | -28 | 3 | 7 | c | false | <90% | 3218 |
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_012160 | FBXL4 | 371 | 389 | U | U | c | C | C | A | U | G | U | U | A | A | C | A | G | U | U | c | u | 72 | 3 | 14 | c | false | <90% | 2777 | ||
NM_207383 | FLJ42289 | 1096 | 1114 | a | U | U | C | C | A | U | G | U | U | A | A | C | A | G | g | U | G | c | 66 | 3 | 14 | c | false | <90% | 1657 | ||
NM_152701 | ABCA13 | 5743 | 5761 | c | U | U | C | C | A | U | G | U | U | A | A | C | A | u | U | U | c | u | 65 | 4 | 13 | c | false | <90% | 17208 | ||
NM_017420 | SIX4 | 5558 | 5576 | c | U | U | g | C | A | U | G | U | U | A | A | a | A | G | U | U | G | G | 50 | 3 | 8 | false | <90% | 6217 | |||
NM_173591 | C12orf64 | 1924 | 1942 | a | a | U | u | C | A | U | G | U | U | A | A | C | A | G | U | U | G | G | 49 | 3 | 15 | bc | false | <90% | 2361 | ||
NM_020148 | SPIRE1 | 3807 | 3825 | a | a | U | g | C | A | U | G | U | U | A | A | C | A | G | U | U | G | G | 49 | 3 | 15 | bc | false | <90% | 5402 | ||
XM_001130901 | LOC650655 | 663 | 681 | U | U | U | C | C | A | U | G | U | U | g | A | C | A | G | U | c | a | G | 12 | 3 | 10 | c | false | <90% | 1140 | ||
XM_001130687 | LOC650655 | 663 | 681 | U | U | U | C | C | A | U | G | U | U | g | A | C | A | G | U | c | a | G | 12 | 3 | 10 | c | false | <90% | 1140 | ||
NM_014676 | PUM1 | 702 | 720 | U | U | U | C | C | A | U | G | U | g | A | A | C | A | G | U | g | a | G | -8 | 3 | 9 | c | false | <90% | 5410 | ||
NM_001020658 | PUM1 | 702 | 720 | U | U | U | C | C | A | U | G | U | g | A | A | C | A | G | U | g | a | G | -8 | 3 | 9 | c | false | <90% | 5416 | ||
NM_030668 | PTPRO | 2328 | 2346 | c | U | U | C | C | u | U | a | U | U | A | A | C | A | G | U | U | G | G | -27 | 3 | 11 | bc | false | <90% | 2948 | ||
NM_030669 | PTPRO | 2412 | 2430 | c | U | U | C | C | u | U | a | U | U | A | A | C | A | G | U | U | G | G | -27 | 3 | 11 | bc | false | <90% | 3032 | ||
NM_030670 | PTPRO | 3360 | 3378 | c | U | U | C | C | u | U | a | U | U | A | A | C | A | G | U | U | G | G | -27 | 3 | 11 | bc | false | <90% | 3980 | ||
NM_030671 | PTPRO | 3444 | 3462 | c | U | U | C | C | u | U | a | U | U | A | A | C | A | G | U | U | G | G | -27 | 3 | 11 | bc | false | <90% | 4064 | ||
NM_002848 | PTPRO | 4449 | 4467 | c | U | U | C | C | u | U | a | U | U | A | A | C | A | G | U | U | G | G | -27 | 3 | 11 | bc | false | <90% | 5069 | ||
NM_030667 | PTPRO | 4533 | 4551 | c | U | U | C | C | u | U | a | U | U | A | A | C | A | G | U | U | G | G | -27 | 3 | 11 | bc | false | <90% | 5153 | ||
NM_152322 | BTBD11 | 1131 | 1149 | g | U | U | C | C | A | g | G | U | U | g | A | C | A | G | U | U | G | G | -29 | 3 | 8 | c | false | <90% | 2711 | ||
NM_001017523 | BTBD11 | 2296 | 2314 | g | U | U | C | C | A | g | G | U | U | g | A | C | A | G | U | U | G | G | -29 | 3 | 8 | c | false | <90% | 3900 | ||
NM_001018072 | BTBD11 | 4156 | 4174 | g | U | U | C | C | A | g | G | U | U | g | A | C | A | G | U | U | G | G | -29 | 3 | 8 | c | false | <90% | 5760 | ||
NM_020872 | CNTN3 | 87 | 105 | U | U | U | C | C | A | U | G | g | a | A | A | C | A | G | U | U | G | a | -47 | 3 | 8 | bc | false | <90% | 4997 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1686
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