Automatic recommendation
Not OK - siRNA is not specific
20 hits were found for AGAAGGAGAGCUAGGCCUA (10 guide strand hits and 10 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_015106 | RAD54L2 | 1611 | 1629 | A | G | A | A | G | G | A | G | A | G | C | U | u | G | G | C | C | a | A | 86 | 2 | 12 | false | <90% | 4319 | |||
NM_206873 | PPP1CA | 36 | 54 | g | G | A | A | G | G | A | G | A | G | C | c | A | G | G | C | C | g | g | 56 | 4 | 10 | false | <90% | 1356 | |||
NM_002708 | PPP1CA | 36 | 54 | g | G | A | A | G | G | A | G | A | G | C | c | A | G | G | C | C | g | g | 56 | 4 | 10 | false | <90% | 1488 | |||
NM_001008709 | PPP1CA | 36 | 54 | g | G | A | A | G | G | A | G | A | G | C | c | A | G | G | C | C | g | g | 56 | 4 | 10 | false | <90% | 1521 | |||
NM_182831 | TNT | 364 | 382 | g | G | A | A | G | G | A | G | A | G | C | c | A | a | G | C | C | U | A | 44 | 3 | 10 | false | <90% | 2486 | |||
NM_004809 | STOML1 | 1536 | 1554 | A | G | g | A | G | G | A | G | A | G | C | c | A | G | G | C | C | U | g | 41 | 3 | 8 | false | <90% | 2116 | |||
XM_001130371 | LOC729474 | 1058 | 1076 | A | G | A | A | G | G | A | G | A | G | C | a | A | G | G | C | u | g | g | 35 | 4 | 11 | false | <90% | 1149 | |||
XM_001132139 | LOC732188 | 1067 | 1085 | A | G | A | A | G | G | A | G | A | G | C | a | A | G | G | C | u | g | g | 35 | 4 | 11 | false | <90% | 1158 | |||
NM_000139 | MS4A2 | 557 | 575 | u | G | A | A | G | a | A | G | A | G | C | U | u | G | G | C | C | U | A | 24 | 3 | 6 | false | <90% | 3723 | |||
NM_133463 | AMZ1 | 3485 | 3503 | A | G | A | u | G | a | A | G | A | G | C | U | A | G | G | C | C | U | u | -5 | 3 | 12 | bc | false | <90% | 4415 |
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_000403 | GALE | 95 | 113 | a | c | G | G | C | C | U | A | G | C | U | C | c | C | C | U | U | C | c | 71 | 4 | 10 | false | <90% | 1647 | |||
NM_016151 | TAOK2 | 3946 | 3964 | c | A | G | G | C | C | U | A | G | C | U | C | U | a | C | c | U | C | U | 52 | 3 | 12 | c | false | <90% | 4920 | ||
NM_030623 | SKIP | 3558 | 3576 | g | A | G | G | C | C | U | A | G | C | U | g | U | C | C | c | U | C | U | 38 | 3 | 10 | false | <90% | 6824 | |||
NM_153252 | BRWD3 | 4730 | 4748 | c | A | G | G | a | C | U | A | G | C | U | C | U | C | C | U | U | u | c | 38 | 4 | 12 | c | false | <90% | 6085 | ||
NM_199420 | POLQ | 1638 | 1656 | a | A | G | G | C | a | U | A | G | C | U | C | U | C | C | U | U | C | a | 29 | 3 | 12 | bc | false | <90% | 8787 | ||
NM_153823 | GSG1 | 810 | 828 | a | u | G | G | C | C | U | g | G | C | U | C | U | C | C | U | U | C | a | 19 | 4 | 10 | bc | false | <90% | 1942 | ||
NM_001080555 | GSG1 | 923 | 941 | a | u | G | G | C | C | U | g | G | C | U | C | U | C | C | U | U | C | a | 19 | 4 | 10 | bc | false | <90% | 2055 | ||
NM_031289 | GSG1 | 934 | 952 | a | u | G | G | C | C | U | g | G | C | U | C | U | C | C | U | U | C | a | 19 | 4 | 10 | bc | false | <90% | 2066 | ||
NM_001080554 | GSG1 | 1047 | 1065 | a | u | G | G | C | C | U | g | G | C | U | C | U | C | C | U | U | C | a | 19 | 4 | 10 | bc | false | <90% | 2179 | ||
NM_005229 | ELK1 | 1403 | 1421 | c | c | G | G | C | C | a | A | G | C | U | C | U | C | C | U | U | C | c | 15 | 4 | 11 | bc | false | <90% | 2828 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3305
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