Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
32 hits were found for GCACAGAGCUGCAAACAAC (20 guide strand hits and 12 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_496582 | LOC440895 | 184 | 202 | c | C | A | C | A | G | A | G | C | U | G | C | A | u | A | C | A | A | g | 73 | 3 | 12 | c | false | <90% | 1993 | ||
NM_014315 | KLHDC2 | 1435 | 1453 | u | C | A | C | A | G | A | G | C | U | G | C | A | c | A | C | A | g | u | 70 | 4 | 12 | c | false | <90% | 1808 | ||
NM_024054 | C7orf25 | 1302 | 1320 | u | g | u | C | A | G | A | G | C | U | G | C | A | A | A | C | A | A | C | 67 | 3 | 16 | bc | false | <90% | 1812 | ||
NM_152924 | ABHD2 | 4338 | 4356 | u | C | A | C | A | G | A | G | C | U | G | C | A | A | A | C | u | u | g | 66 | 4 | 15 | ac | false | <90% | 8687 | ||
NM_007011 | ABHD2 | 4736 | 4754 | u | C | A | C | A | G | A | G | C | U | G | C | A | A | A | C | u | u | g | 66 | 4 | 15 | ac | false | <90% | 9085 | ||
XR_017766 | LOC153684 | 182 | 200 | G | C | A | C | A | G | A | G | C | U | G | u | g | A | A | C | A | A | g | 50 | 3 | 11 | false | <90% | 2311 | |||
XR_018004 | LOC153684 | 757 | 775 | G | C | A | C | A | G | A | G | C | U | G | u | g | A | A | C | A | A | g | 50 | 3 | 11 | false | <90% | 2941 | |||
NM_006290 | TNFAIP3 | 1803 | 1821 | c | C | A | C | A | G | A | G | C | U | G | g | A | A | A | C | g | A | C | 40 | 3 | 10 | false | <90% | 4446 | |||
NM_014154 | ARMC8 | 552 | 570 | G | C | A | C | A | G | A | G | C | U | G | a | A | A | A | C | u | g | a | 35 | 4 | 11 | false | <90% | 3178 | |||
NM_213654 | ARMC8 | 606 | 624 | G | C | A | C | A | G | A | G | C | U | G | a | A | A | A | C | u | g | a | 35 | 4 | 11 | false | <90% | 3232 | |||
NM_015396 | ARMC8 | 552 | 570 | G | C | A | C | A | G | A | G | C | U | G | a | A | A | A | C | u | g | a | 35 | 4 | 11 | false | <90% | 3832 | |||
NM_020129 | LGALS14 | 13 | 31 | a | C | A | C | A | G | A | c | C | U | G | C | A | A | A | C | A | u | C | 33 | 3 | 9 | c | false | <90% | 794 | ||
NM_203471 | LGALS14 | 13 | 31 | a | C | A | C | A | G | A | c | C | U | G | C | A | A | A | C | A | u | C | 33 | 3 | 9 | c | false | <90% | 1099 | ||
NM_020980 | AQP9 | 994 | 1012 | c | u | u | C | A | G | A | G | C | U | G | g | A | A | A | C | A | A | C | 33 | 4 | 8 | false | <90% | 2948 | |||
XR_017358 | LOC400406 | 4338 | 4356 | G | u | A | C | A | G | A | G | C | a | G | C | A | A | A | C | A | A | g | 0 | 3 | 8 | bc | false | <90% | 5132 | ||
NM_014749 | KIAA0586 | 797 | 815 | u | u | A | C | A | G | A | G | C | a | G | C | A | A | A | C | A | A | g | -1 | 4 | 8 | bc | false | <90% | 4994 | ||
XM_001131923 | LOC731120 | 331 | 349 | G | C | A | C | u | G | A | c | C | U | G | C | A | A | A | C | A | A | a | -18 | 3 | 10 | bc | false | <90% | 1221 | ||
XM_001133791 | LOC729743 | 335 | 353 | G | C | A | C | u | G | A | c | C | U | G | C | A | A | A | C | A | A | a | -18 | 3 | 10 | bc | false | <90% | 1225 | ||
NM_014672 | KIAA0391 | 1997 | 2015 | a | C | A | C | A | G | u | G | g | U | G | C | A | A | A | C | A | A | C | -28 | 3 | 10 | bc | false | <90% | 2684 | ||
NM_013246 | CLCF1 | 1497 | 1515 | G | C | A | C | A | G | A | G | u | g | G | C | A | A | A | C | A | A | a | -47 | 3 | 8 | bc | false | <90% | 1860 |
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_019091 | PLEKHA3 | 2163 | 2181 | a | U | U | G | U | U | U | G | C | A | G | C | U | C | U | u | U | c | C | 69 | 3 | 14 | c | false | <90% | 2516 | ||
XR_015720 | LOC731190 | 4030 | 4048 | c | a | a | G | U | U | U | G | C | A | G | C | U | C | U | G | U | G | a | 62 | 4 | 15 | bc | false | <90% | 6264 | ||
XR_015267 | LOC728003 | 4031 | 4049 | c | a | a | G | U | U | U | G | C | A | G | C | U | C | U | G | U | G | a | 62 | 4 | 15 | bc | false | <90% | 6265 | ||
NM_173355 | UPP2 | 967 | 985 | a | g | U | G | U | U | U | G | C | A | G | C | U | a | U | G | U | G | u | 62 | 4 | 11 | c | false | <90% | 2236 | ||
NM_004932 | CDH6 | 2219 | 2237 | G | c | U | G | U | U | U | G | C | A | G | C | U | C | U | G | a | G | g | 60 | 3 | 14 | ac | false | <90% | 4521 | ||
NM_017968 | SLTM | 2814 | 2832 | G | U | a | G | U | U | U | G | C | A | G | C | U | g | U | G | U | G | g | 55 | 3 | 10 | c | false | <90% | 3497 | ||
NM_001013843 | SLTM | 3427 | 3445 | G | U | a | G | U | U | U | G | C | A | G | C | U | g | U | G | U | G | g | 55 | 3 | 10 | c | false | <90% | 4110 | ||
NM_024755 | SLTM | 3481 | 3499 | G | U | a | G | U | U | U | G | C | A | G | C | U | g | U | G | U | G | g | 55 | 3 | 10 | c | false | <90% | 4164 | ||
XM_001132171 | LOC730036 | 665 | 683 | c | c | U | G | U | U | U | G | C | A | G | C | U | C | U | c | U | G | g | 55 | 4 | 13 | c | false | <90% | 2479 | ||
XM_001126197 | LOC730523 | 665 | 683 | c | c | U | G | U | U | U | G | C | A | G | C | U | C | U | c | U | G | g | 55 | 4 | 13 | c | false | <90% | 2479 | ||
NM_001042555 | FRS2 | 2047 | 2065 | G | U | U | G | U | U | U | G | C | A | c | C | U | u | U | G | U | G | a | 14 | 3 | 10 | c | false | <90% | 6875 | ||
NM_006654 | FRS2 | 2054 | 2072 | G | U | U | G | U | U | U | G | C | A | c | C | U | u | U | G | U | G | a | 14 | 3 | 10 | c | false | <90% | 6882 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2415
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