Automatic recommendation
Not OK - siRNA is not specific
33 hits were found for AGCUUCUGCUGAUUCAACU (11 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 | |||||||||||||
NM_014846 | KIAA0196 | 857 | 875 | A | u | C | U | U | C | U | G | C | U | G | A | U | U | C | A | A | a | U | 85 | 2 | 15 | ac | false | <90% | 4173 | ||
NM_001011718 | XKR7 | 1279 | 1297 | A | u | C | U | U | C | U | G | C | U | G | g | U | U | C | A | A | C | g | 49 | 3 | 9 | false | <90% | 2929 | |||
NM_001075 | UGT2B10 | 29 | 47 | c | a | g | U | U | C | U | G | C | U | G | A | U | a | C | A | A | C | U | 47 | 4 | 10 | c | false | <90% | 1619 | ||
NM_173525 | C11orf42 | 768 | 786 | A | G | C | a | U | C | U | G | C | U | G | A | U | a | C | A | A | C | U | 43 | 2 | 9 | c | false | <90% | 1168 | ||
XR_015246 | LOC730555 | 1523 | 1541 | A | G | C | U | U | C | U | G | a | U | G | A | U | U | C | A | A | a | c | 32 | 3 | 8 | c | false | <90% | 1898 | ||
XR_015538 | LOC728592 | 1523 | 1541 | A | G | C | U | U | C | U | G | a | U | G | A | U | U | C | A | A | a | c | 32 | 3 | 8 | c | false | <90% | 1898 | ||
NM_024690 | MUC16 | 18570 | 18588 | A | G | C | U | U | C | U | G | C | U | c | A | g | U | C | A | A | C | a | 23 | 3 | 10 | false | <90% | 43816 | |||
NM_015176 | FBXO28 | 1283 | 1301 | u | G | C | U | U | C | U | c | C | U | G | A | U | U | g | A | A | C | U | 11 | 3 | 6 | c | false | <90% | 2923 | ||
NM_021238 | FAM60A | 1692 | 1710 | A | G | C | U | U | C | U | G | a | U | G | A | U | U | C | A | c | a | c | 8 | 4 | 8 | c | false | <90% | 3097 | ||
NM_016596 | HDAC7A | 2127 | 2145 | g | G | C | U | U | C | U | G | C | U | u | c | U | U | C | A | A | C | U | 2 | 3 | 9 | false | <90% | 4086 | |||
NM_015401 | HDAC7A | 2247 | 2265 | g | G | C | U | U | C | U | G | C | U | u | c | U | U | C | A | A | C | U | 2 | 3 | 9 | false | <90% | 4206 |
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_139241 | FGD4 | 2327 | 2345 | g | a | U | U | G | A | A | U | C | A | G | C | A | G | A | A | G | u | a | 78 | 4 | 15 | ac | false | <90% | 2931 | ||
NM_152520 | ZNF533 | 1258 | 1276 | u | G | U | U | G | A | A | U | C | A | G | a | A | G | A | A | G | a | a | 56 | 4 | 10 | false | <90% | 3154 | |||
NM_052947 | ALPK2 | 3787 | 3805 | A | a | U | a | G | A | A | U | C | A | G | C | A | G | A | A | G | C | c | 46 | 3 | 14 | bc | false | <90% | 6496 | ||
NM_001723 | DST | 3114 | 3132 | A | G | U | U | G | A | A | U | C | A | a | C | A | G | A | A | G | a | U | 36 | 2 | 10 | c | false | <90% | 8972 | ||
NM_020388 | DST | 3114 | 3132 | A | G | U | U | G | A | A | U | C | A | a | C | A | G | A | A | G | a | U | 36 | 2 | 10 | c | false | <90% | 9348 | ||
NM_015548 | DST | 3114 | 3132 | A | G | U | U | G | A | A | U | C | A | a | C | A | G | A | A | G | a | U | 36 | 2 | 10 | c | false | <90% | 16384 | ||
NM_183380 | DST | 4510 | 4528 | A | G | U | U | G | A | A | U | C | A | a | C | A | G | A | A | G | a | U | 36 | 2 | 10 | c | false | <90% | 18036 | ||
NM_001821 | CHML | 1847 | 1865 | u | c | g | g | G | A | A | U | C | A | G | C | A | G | A | A | G | C | U | 30 | 4 | 15 | bc | false | <90% | 7082 | ||
NM_020661 | AICDA | 1249 | 1267 | g | u | U | U | u | A | A | U | C | A | G | C | A | G | A | A | G | C | a | 30 | 4 | 13 | bc | false | <90% | 2791 | ||
NM_024969 | FAM130A2 | 679 | 697 | A | G | U | a | G | A | A | U | C | A | G | a | A | G | A | A | G | C | c | 24 | 3 | 7 | false | <90% | 2965 | |||
NM_001001651 | MED8 | 1431 | 1449 | g | G | U | U | G | A | g | U | C | A | G | C | A | G | A | A | G | u | g | 24 | 4 | 10 | c | false | <90% | 1502 | ||
NM_052877 | MED8 | 1492 | 1510 | g | G | U | U | G | A | g | U | C | A | G | C | A | G | A | A | G | u | g | 24 | 4 | 10 | c | false | <90% | 1563 | ||
NM_201542 | MED8 | 1967 | 1985 | g | G | U | U | G | A | g | U | C | A | G | C | A | G | A | A | G | u | g | 24 | 4 | 10 | c | false | <90% | 2038 | ||
NM_002778 | PSAP | 544 | 562 | A | G | c | U | G | A | A | U | C | A | c | C | A | G | A | A | G | C | a | 14 | 3 | 7 | c | false | <90% | 2839 | ||
NM_001042466 | PSAP | 544 | 562 | A | G | c | U | G | A | A | U | C | A | c | C | A | G | A | A | G | C | a | 14 | 3 | 7 | c | false | <90% | 2845 | ||
NM_001042465 | PSAP | 544 | 562 | A | G | c | U | G | A | A | U | C | A | c | C | A | G | A | A | G | C | a | 14 | 3 | 7 | c | false | <90% | 2848 | ||
NM_012159 | FBXL21 | 401 | 419 | c | G | c | U | G | A | g | U | C | A | G | C | A | G | A | A | G | C | U | 12 | 3 | 12 | bc | false | <90% | 1333 | ||
NM_181727 | SPATA12 | 436 | 454 | A | G | U | g | G | A | A | a | C | A | G | C | A | G | A | A | G | C | a | -3 | 3 | 10 | bc | false | <90% | 2430 | ||
NM_004120 | GBP2 | 1752 | 1770 | g | G | c | U | G | A | A | U | C | u | G | C | A | G | A | A | G | C | U | -4 | 3 | 9 | bc | false | <90% | 2595 | ||
NM_178499 | CCDC60 | 1347 | 1365 | A | u | a | U | G | A | A | U | C | u | G | C | A | G | A | A | G | C | U | -13 | 3 | 9 | bc | false | <90% | 2465 | ||
NM_001079810 | CMYA3 | 2672 | 2690 | u | G | U | U | G | A | A | a | C | A | a | C | A | G | A | A | G | C | U | -25 | 3 | 8 | c | false | <90% | 3239 | ||
NM_152381 | CMYA3 | 12051 | 12069 | u | G | U | U | G | A | A | a | C | A | a | C | A | G | A | A | G | C | U | -25 | 3 | 8 | c | false | <90% | 12618 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2922
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