Automatic recommendation
Not OK - siRNA is not specific
40 hits were found for GUGCUGAAGACAUAGGAAC (20 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_198465 | NRK | 4195 | 4213 | a | U | G | C | U | G | A | A | G | A | C | A | g | A | G | G | A | A | g | 82 | 3 | 11 | false | <90% | 8080 | |||
NM_001017957 | OS9 | 390 | 408 | u | U | G | C | U | G | A | A | G | A | C | A | a | A | G | G | A | c | u | 79 | 4 | 11 | false | <90% | 2511 | |||
NM_001017956 | OS9 | 390 | 408 | u | U | G | C | U | G | A | A | G | A | C | A | a | A | G | G | A | c | u | 79 | 4 | 11 | false | <90% | 2556 | |||
NM_001017958 | OS9 | 390 | 408 | u | U | G | C | U | G | A | A | G | A | C | A | a | A | G | G | A | c | u | 79 | 4 | 11 | false | <90% | 2676 | |||
NM_006812 | OS9 | 390 | 408 | u | U | G | C | U | G | A | A | G | A | C | A | a | A | G | G | A | c | u | 79 | 4 | 11 | false | <90% | 2721 | |||
NM_005492 | CST8 | 25 | 43 | G | U | G | C | U | G | A | A | G | A | C | c | U | A | G | G | A | g | a | 58 | 3 | 11 | false | <90% | 895 | |||
NM_000096 | CP | 1077 | 1095 | G | U | G | C | U | G | A | A | G | A | C | A | g | A | G | u | A | A | a | 58 | 3 | 12 | false | <90% | 4419 | |||
NM_001033514 | GPR34 | 133 | 151 | a | a | c | C | U | G | A | A | G | A | C | A | U | A | a | G | A | A | C | 42 | 4 | 11 | c | false | <90% | 1282 | ||
NM_001033513 | GPR34 | 314 | 332 | a | a | u | C | U | G | A | A | G | A | C | A | U | A | a | G | A | A | C | 42 | 4 | 11 | c | false | <90% | 1509 | ||
NM_001372 | DNAH9 | 3591 | 3609 | u | U | G | C | U | G | A | A | G | A | C | c | U | A | u | G | A | A | C | 39 | 3 | 10 | false | <90% | 13750 | |||
NM_005262 | GFER | 504 | 522 | G | U | G | C | U | G | A | A | G | A | C | c | U | A | a | G | A | A | a | 36 | 3 | 11 | false | <90% | 2447 | |||
XR_018268 | LOC647968 | 776 | 794 | G | U | G | a | U | G | A | A | G | A | C | A | U | A | G | c | A | A | g | 32 | 3 | 11 | c | false | <90% | 1235 | ||
XR_016578 | LOC400352 | 776 | 794 | G | U | G | a | U | G | A | A | G | A | C | A | U | A | G | c | A | A | g | 32 | 3 | 11 | c | false | <90% | 1634 | ||
NM_018028 | SAMD4B | 510 | 528 | a | U | c | C | a | G | A | A | G | A | C | A | U | A | G | G | A | A | C | 26 | 3 | 14 | bc | false | <90% | 4543 | ||
NM_002078 | GOLGA4 | 5492 | 5510 | G | U | G | C | a | G | A | A | G | A | C | A | U | A | u | G | A | A | g | 18 | 3 | 9 | c | false | <90% | 7717 | ||
NM_005802 | TOPORS | 47 | 65 | G | U | G | C | U | G | A | A | G | A | a | A | U | A | G | G | g | c | C | 12 | 3 | 10 | c | false | <90% | 4163 | ||
XR_017606 | LOC391387 | 837 | 855 | c | c | a | C | U | G | A | A | u | A | C | A | U | A | G | G | A | A | C | 6 | 4 | 10 | bc | false | <90% | 874 | ||
XR_019516 | LOC391387 | 837 | 855 | c | c | a | C | U | G | A | A | u | A | C | A | U | A | G | G | A | A | C | 6 | 4 | 10 | bc | false | <90% | 874 | ||
NM_152558 | IQCE | 2308 | 2326 | c | U | G | C | c | G | A | g | G | A | C | A | U | A | G | G | A | A | C | -15 | 3 | 11 | bc | false | <90% | 3032 | ||
NM_003436 | ZNF135 | 2092 | 2110 | G | U | G | C | U | G | g | g | G | A | C | A | U | A | G | G | A | A | g | -33 | 3 | 10 | bc | false | <90% | 3038 |
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_003909 | CPNE3 | 2874 | 2892 | u | U | U | C | C | U | A | U | G | U | C | U | a | C | A | G | C | A | u | 82 | 3 | 11 | false | <90% | 4868 | |||
NM_138431 | MFSD3 | 1138 | 1156 | G | a | g | C | C | U | A | U | G | U | C | U | g | C | A | G | C | A | C | 58 | 3 | 9 | false | <90% | 1468 | |||
NM_019897 | OR2S2 | 622 | 640 | u | c | U | C | C | U | A | U | G | U | C | U | U | C | A | u | C | A | u | 55 | 4 | 13 | c | false | <90% | 930 | ||
NM_198902 | TSPAN3 | 313 | 331 | G | a | g | C | C | U | A | U | G | U | C | U | U | C | A | u | C | A | C | 42 | 3 | 12 | c | false | <90% | 1767 | ||
NM_005724 | TSPAN3 | 313 | 331 | G | a | g | C | C | U | A | U | G | U | C | U | U | C | A | u | C | A | C | 42 | 3 | 12 | c | false | <90% | 1842 | ||
NM_003941 | WASL | 443 | 461 | G | U | g | a | C | U | A | U | G | U | C | U | U | C | A | G | C | A | g | 38 | 3 | 14 | bc | false | <90% | 4430 | ||
XR_019619 | LOC648866 | 782 | 800 | u | U | U | C | C | U | A | U | G | U | a | U | U | C | A | G | C | A | C | 36 | 2 | 9 | c | false | <90% | 923 | ||
XR_016599 | LOC644129 | 782 | 800 | u | U | U | C | C | U | A | U | G | U | a | U | U | C | A | G | C | A | C | 36 | 2 | 9 | c | false | <90% | 923 | ||
NM_003323 | TULP2 | 1155 | 1173 | G | a | U | C | C | a | A | U | G | U | C | U | U | C | A | G | C | A | C | 25 | 2 | 13 | bc | false | <90% | 1733 | ||
NM_183231 | IKZF3 | 1327 | 1345 | G | c | U | C | C | U | A | U | G | U | a | U | U | C | A | G | C | A | u | 22 | 3 | 8 | c | false | <90% | 2152 | ||
NM_183232 | IKZF3 | 1378 | 1396 | G | c | U | C | C | U | A | U | G | U | a | U | U | C | A | G | C | A | u | 22 | 3 | 8 | c | false | <90% | 2203 | ||
NM_183228 | IKZF3 | 1444 | 1462 | G | c | U | C | C | U | A | U | G | U | a | U | U | C | A | G | C | A | u | 22 | 3 | 8 | c | false | <90% | 2269 | ||
NM_183230 | IKZF3 | 1495 | 1513 | G | c | U | C | C | U | A | U | G | U | a | U | U | C | A | G | C | A | u | 22 | 3 | 8 | c | false | <90% | 2320 | ||
NM_183229 | IKZF3 | 1495 | 1513 | G | c | U | C | C | U | A | U | G | U | a | U | U | C | A | G | C | A | u | 22 | 3 | 8 | c | false | <90% | 2320 | ||
NM_012481 | IKZF3 | 1612 | 1630 | G | c | U | C | C | U | A | U | G | U | a | U | U | C | A | G | C | A | u | 22 | 3 | 8 | c | false | <90% | 2437 | ||
NM_002274 | KRT13 | 1433 | 1451 | c | U | c | C | C | U | c | U | G | U | C | U | U | C | A | G | C | A | C | 12 | 3 | 12 | bc | false | <90% | 1693 | ||
NM_153490 | KRT13 | 1459 | 1477 | c | U | c | C | C | U | c | U | G | U | C | U | U | C | A | G | C | A | C | 12 | 3 | 12 | bc | false | <90% | 1719 | ||
NM_139279 | MCFD2 | 3174 | 3192 | G | U | U | C | C | U | A | U | c | U | C | U | U | C | A | G | g | c | a | 8 | 4 | 8 | c | false | <90% | 4144 | ||
NM_175737 | KLB | 1572 | 1590 | a | a | a | C | C | U | A | a | G | U | C | U | U | C | A | G | C | A | C | 4 | 4 | 11 | bc | false | <90% | 3279 | ||
NM_021141 | XRCC5 | 3235 | 3253 | u | c | a | C | C | U | c | U | G | U | C | U | U | C | A | G | C | A | C | 0 | 4 | 12 | bc | false | <90% | 3310 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2193
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