Automatic recommendation
Not OK - siRNA is not specific
33 hits were found for GGGAAAGGACCCAAAGUCA (22 guide strand hits and 11 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_001620 | AHNAK | 8446 | 8464 | c | u | G | A | A | A | G | G | A | C | C | C | A | A | A | G | U | g | A | 83 | 3 | 15 | ac | false | <90% | 18815 | ||
NM_001620 | AHNAK | 11944 | 11962 | c | u | G | A | A | A | G | G | A | C | C | C | A | A | A | G | U | g | A | 83 | 3 | 15 | ac | false | <90% | 18815 | ||
NM_001620 | AHNAK | 14488 | 14506 | c | u | G | A | A | A | G | G | A | C | C | C | A | A | A | G | U | g | A | 83 | 3 | 15 | ac | false | <90% | 18815 | ||
NM_001620 | AHNAK | 14872 | 14890 | u | u | G | A | A | A | G | G | A | C | C | C | A | A | A | G | U | a | A | 83 | 3 | 15 | ac | false | <90% | 18815 | ||
NM_018271 | FLJ10916 | 1102 | 1120 | u | u | G | A | A | A | G | G | A | C | C | C | A | A | A | G | U | g | u | 78 | 4 | 15 | ac | false | <90% | 2091 | ||
XM_938118 | OVOS2 | 2699 | 2717 | a | G | G | A | A | A | G | G | A | C | C | C | A | g | A | G | U | u | u | 70 | 4 | 12 | c | false | <90% | 3348 | ||
XR_015368 | LOC728735 | 2552 | 2570 | a | G | G | A | A | A | G | G | A | C | C | C | A | g | A | G | U | u | u | 70 | 4 | 12 | c | false | <90% | 4286 | ||
NM_001080502 | OVOS2 | 2699 | 2717 | a | G | G | A | A | A | G | G | A | C | C | C | A | g | A | G | U | u | u | 70 | 4 | 12 | c | false | <90% | 4409 | ||
NM_002468 | MYD88 | 2286 | 2304 | u | G | G | A | A | A | G | G | A | C | C | C | A | A | u | G | U | a | c | 65 | 4 | 13 | c | false | <90% | 2826 | ||
NM_001620 | AHNAK | 7684 | 7702 | c | u | c | A | A | A | G | G | A | C | C | C | A | A | A | a | U | C | A | 40 | 4 | 12 | c | false | <90% | 18815 | ||
NM_019063 | EML4 | 1710 | 1728 | G | G | G | A | A | A | G | G | A | C | C | u | A | A | A | G | g | u | g | 35 | 4 | 11 | false | <90% | 5539 | |||
NM_014351 | SULT4A1 | 2150 | 2168 | u | G | G | A | A | A | G | c | A | C | C | C | A | A | A | G | U | g | g | 28 | 4 | 9 | c | false | <90% | 2465 | ||
NM_001620 | AHNAK | 3910 | 3928 | u | u | G | A | A | A | G | G | c | C | C | C | A | A | A | G | U | C | A | 26 | 3 | 10 | bc | false | <90% | 18815 | ||
NM_001620 | AHNAK | 5284 | 5302 | u | u | G | A | A | A | G | G | c | C | C | C | A | A | A | G | U | C | A | 26 | 3 | 10 | bc | false | <90% | 18815 | ||
NM_001620 | AHNAK | 5890 | 5908 | c | u | G | A | A | A | G | G | c | C | C | C | A | A | A | G | U | C | A | 26 | 3 | 10 | bc | false | <90% | 18815 | ||
NM_001620 | AHNAK | 6091 | 6109 | u | u | G | A | A | A | G | G | c | C | C | C | A | A | A | G | U | C | A | 26 | 3 | 10 | bc | false | <90% | 18815 | ||
NM_001620 | AHNAK | 6292 | 6310 | c | u | G | A | A | A | G | G | c | C | C | C | A | A | A | G | U | C | A | 26 | 3 | 10 | bc | false | <90% | 18815 | ||
NM_001620 | AHNAK | 6676 | 6694 | u | u | G | A | A | A | G | G | c | C | C | C | A | A | A | G | U | C | A | 26 | 3 | 10 | bc | false | <90% | 18815 | ||
NM_001620 | AHNAK | 6877 | 6895 | u | u | G | A | A | A | G | G | c | C | C | C | A | A | A | G | U | C | A | 26 | 3 | 10 | bc | false | <90% | 18815 | ||
NM_019072 | SGTB | 1531 | 1549 | G | G | G | A | A | A | u | G | A | C | C | C | A | A | A | G | g | a | A | 7 | 3 | 9 | c | false | <90% | 5453 | ||
NR_003255 | TSIX | 31923 | 31941 | a | G | G | A | A | A | G | G | A | g | C | C | A | A | A | G | U | u | g | 7 | 4 | 8 | c | false | <90% | 36861 | ||
NM_173535 | CLEC4F | 1450 | 1468 | u | a | c | A | A | A | G | a | A | C | C | C | A | A | A | G | U | C | A | 4 | 4 | 11 | bc | false | <90% | 2486 |
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_015509 | NECAP1 | 2258 | 2276 | U | G | A | C | U | U | U | G | G | G | U | C | C | a | U | U | u | u | C | 54 | 3 | 13 | c | false | <90% | 2563 | ||
NR_003366 | ANKRD20B | 53148 | 53166 | g | a | c | C | U | U | U | G | G | G | U | u | C | U | U | U | C | C | C | 33 | 4 | 8 | false | <90% | 96524 | |||
NM_003171 | SUPV3L1 | 148 | 166 | c | c | A | C | U | U | U | G | G | G | c | C | C | U | U | U | C | C | C | 25 | 3 | 8 | c | false | <90% | 2490 | ||
NR_003491 | MIAT | 3929 | 3947 | c | u | A | C | U | U | U | G | G | G | c | C | C | U | U | U | C | C | C | 25 | 3 | 8 | c | false | <90% | 10142 | ||
NM_006105 | RAPGEF3 | 645 | 663 | g | G | A | C | U | U | g | G | G | G | U | C | C | a | U | U | C | C | C | 12 | 3 | 6 | c | false | <90% | 3327 | ||
NM_001734 | C1S | 2503 | 2521 | c | u | c | C | U | U | g | G | G | G | U | C | C | U | U | U | C | C | C | 0 | 4 | 12 | bc | false | <90% | 2714 | ||
NM_201442 | C1S | 2594 | 2612 | c | u | c | C | U | U | g | G | G | G | U | C | C | U | U | U | C | C | C | 0 | 4 | 12 | bc | false | <90% | 2813 | ||
NM_001024466 | SOD2 | 404 | 422 | U | G | A | C | U | U | U | G | G | u | U | C | C | U | U | U | g | a | C | -8 | 3 | 9 | c | false | <90% | 918 | ||
NM_001024465 | SOD2 | 521 | 539 | U | G | A | C | U | U | U | G | G | u | U | C | C | U | U | U | g | a | C | -8 | 3 | 9 | c | false | <90% | 1035 | ||
NM_000636 | SOD2 | 521 | 539 | U | G | A | C | U | U | U | G | G | u | U | C | C | U | U | U | g | a | C | -8 | 3 | 9 | c | false | <90% | 1593 | ||
NM_002055 | GFAP | 2910 | 2928 | a | G | A | C | U | U | g | G | u | G | U | C | C | U | U | U | C | C | C | -28 | 3 | 10 | bc | false | <90% | 3035 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3268
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