Automatic recommendation
Not OK - siRNA is not specific
61 hits were found for UGGUGAUGAUGUAAUUGCU (31 guide strand hits and 30 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 | |||||||||||||
XR_018820 | LOC442672 | 1286 | 1304 | g | G | G | U | G | A | U | G | A | U | G | U | c | A | U | U | G | C | U | 87 | 2 | 11 | false | <90% | 1664 | |||
XR_015334 | LOC728615 | 1285 | 1303 | g | G | G | U | G | A | U | G | A | U | G | U | c | A | U | U | G | C | U | 87 | 2 | 11 | false | <90% | 2197 | |||
XR_015187 | LOC728028 | 1346 | 1364 | g | G | G | U | G | A | U | G | A | U | G | U | c | A | U | U | G | C | U | 87 | 2 | 11 | false | <90% | 2281 | |||
XR_015613 | LOC729655 | 1521 | 1539 | g | G | G | U | G | A | U | G | A | U | G | U | c | A | U | U | G | C | U | 87 | 2 | 11 | false | <90% | 2400 | |||
XR_015337 | LOC730978 | 1285 | 1303 | g | G | G | U | G | A | U | G | A | U | G | U | c | A | U | U | G | C | U | 87 | 2 | 11 | false | <90% | 2408 | |||
XM_937807 | DYNC2H1 | 3333 | 3351 | U | G | G | U | G | A | U | G | A | U | G | U | u | A | U | U | G | a | a | 81 | 3 | 12 | false | <90% | 13436 | |||
XM_931085 | DYNC2H1 | 3333 | 3351 | U | G | G | U | G | A | U | G | A | U | G | U | u | A | U | U | G | a | a | 81 | 3 | 12 | false | <90% | 13436 | |||
NM_001080463 | DYNC2H1 | 3333 | 3351 | U | G | G | U | G | A | U | G | A | U | G | U | u | A | U | U | G | a | a | 81 | 3 | 12 | false | <90% | 13699 | |||
NM_001068 | TOP2B | 4959 | 4977 | a | u | G | U | G | A | U | G | A | U | G | U | A | A | U | U | G | a | c | 78 | 4 | 15 | ac | false | <90% | 5189 | ||
NM_004621 | TRPC6 | 3490 | 3508 | U | u | G | U | G | A | U | G | A | U | G | U | c | A | U | U | G | C | c | 73 | 3 | 10 | false | <90% | 4537 | |||
NM_152932 | GLT8D1 | 649 | 667 | g | G | a | U | G | A | U | G | A | U | G | U | A | A | U | U | G | u | g | 70 | 4 | 14 | c | false | <90% | 1635 | ||
NM_018446 | GLT8D1 | 1132 | 1150 | g | G | a | U | G | A | U | G | A | U | G | U | A | A | U | U | G | u | g | 70 | 4 | 14 | c | false | <90% | 2118 | ||
NM_001010983 | GLT8D1 | 1361 | 1379 | g | G | a | U | G | A | U | G | A | U | G | U | A | A | U | U | G | u | g | 70 | 4 | 14 | c | false | <90% | 2347 | ||
NM_015125 | CIC | 1384 | 1402 | g | G | a | U | G | A | U | G | A | U | G | U | c | A | U | U | G | C | U | 68 | 3 | 9 | false | <90% | 5473 | |||
NM_017651 | AHI1 | 513 | 531 | a | a | G | U | G | A | U | G | A | U | G | U | A | A | g | U | G | C | U | 61 | 3 | 12 | c | false | <90% | 5538 | ||
NM_018268 | WDR41 | 467 | 485 | U | G | G | U | G | A | U | G | A | U | G | g | A | A | U | U | G | u | a | 58 | 3 | 11 | false | <90% | 2608 | |||
NM_014334 | C9orf4 | 618 | 636 | U | G | G | U | G | A | U | G | A | U | G | U | c | A | U | g | G | C | c | 58 | 3 | 12 | false | <90% | 1189 | |||
NM_001416 | EIF4A1 | 307 | 325 | g | G | G | U | u | A | U | G | A | U | G | U | g | A | U | U | G | C | U | 36 | 3 | 7 | false | <90% | 1844 | |||
NM_080604 | TJAP1 | 2405 | 2423 | g | G | G | U | G | A | U | G | g | U | G | U | A | A | U | U | G | u | U | 35 | 3 | 8 | c | false | <90% | 2720 | ||
XR_018892 | LOC442676 | 1330 | 1348 | g | G | G | U | G | A | c | G | A | U | G | U | c | A | U | U | G | C | U | 21 | 3 | 6 | false | <90% | 2382 | |||
XR_016831 | LOC645808 | 441 | 459 | U | G | u | U | G | A | U | G | c | U | G | U | A | A | U | U | G | C | U | 20 | 2 | 10 | bc | false | <90% | 1702 | ||
XR_018107 | LOC642237 | 513 | 531 | U | G | u | U | G | A | U | G | c | U | G | U | A | A | U | U | G | C | U | 20 | 2 | 10 | bc | false | <90% | 2259 | ||
XR_016534 | LOC643300 | 517 | 535 | U | G | u | U | G | A | U | G | c | U | G | U | A | A | U | U | G | C | U | 20 | 2 | 10 | bc | false | <90% | 2263 | ||
NM_199440 | HSPD1 | 558 | 576 | U | G | u | U | G | A | U | G | c | U | G | U | A | A | U | U | G | C | U | 20 | 2 | 10 | bc | false | <90% | 2319 | ||
NM_002156 | HSPD1 | 578 | 596 | U | G | u | U | G | A | U | G | c | U | G | U | A | A | U | U | G | C | U | 20 | 2 | 10 | bc | false | <90% | 2339 | ||
XR_018757 | LOC644745 | 501 | 519 | U | G | u | U | G | A | U | G | c | U | G | U | A | A | U | U | G | C | U | 20 | 2 | 10 | bc | false | <90% | 2379 | ||
XR_016744 | LOC644745 | 501 | 519 | U | G | u | U | G | A | U | G | c | U | G | U | A | A | U | U | G | C | U | 20 | 2 | 10 | bc | false | <90% | 2379 | ||
NM_017654 | SAMD9 | 3691 | 3709 | a | G | u | U | G | A | U | G | A | U | c | U | A | A | U | U | G | C | U | 17 | 3 | 8 | c | false | <90% | 6853 | ||
NM_183387 | EML5 | 4365 | 4383 | U | G | G | U | G | A | U | G | A | U | a | U | A | A | U | U | u | a | U | 12 | 3 | 10 | c | false | <90% | 7091 | ||
NM_025132 | WDR19 | 2518 | 2536 | g | G | G | U | G | A | U | u | A | U | G | U | A | A | a | U | G | C | U | 11 | 3 | 6 | c | false | <90% | 4534 | ||
NM_004660 | DDX3Y | 2247 | 2265 | g | u | u | U | G | A | a | G | A | U | G | U | A | A | U | U | G | C | U | 0 | 4 | 12 | bc | false | <90% | 4416 |
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_198397 | CACNA1G | 4311 | 4329 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 5243 | |||
NM_198376 | CACNA1G | 4242 | 4260 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7207 | |||
NM_198388 | CACNA1G | 4242 | 4260 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7450 | |||
NM_198387 | CACNA1G | 4242 | 4260 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7471 | |||
NM_198382 | CACNA1G | 4242 | 4260 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7477 | |||
NM_198386 | CACNA1G | 4311 | 4329 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7492 | |||
NM_198378 | CACNA1G | 4311 | 4329 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7513 | |||
NM_198384 | CACNA1G | 4311 | 4329 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7546 | |||
NM_198379 | CACNA1G | 4242 | 4260 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7588 | |||
NM_198383 | CACNA1G | 4242 | 4260 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7612 | |||
NM_198380 | CACNA1G | 4311 | 4329 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7657 | |||
NM_198385 | CACNA1G | 4311 | 4329 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7690 | |||
NM_198377 | CACNA1G | 4242 | 4260 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7756 | |||
NM_018896 | CACNA1G | 4311 | 4329 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7825 | |||
NM_198396 | CACNA1G | 4242 | 4260 | u | c | C | A | A | U | U | A | C | A | U | C | u | U | C | A | C | C | g | 71 | 4 | 10 | false | <90% | 7834 | |||
NM_017662 | TRPM6 | 2865 | 2883 | A | G | C | A | u | U | U | A | C | A | U | C | u | U | C | A | C | C | A | 38 | 2 | 7 | false | <90% | 8429 | |||
NM_144652 | LETM2 | 1221 | 1239 | A | c | C | A | g | U | U | A | C | A | U | C | A | U | C | A | C | C | c | 32 | 3 | 13 | bc | false | <90% | 1631 | ||
XM_940936 | SLFN5 | 2082 | 2100 | A | G | C | A | A | g | U | A | C | A | U | C | A | U | C | A | C | C | u | 31 | 2 | 12 | bc | false | <90% | 2834 | ||
XM_496206 | SLFN5 | 2082 | 2100 | A | G | C | A | A | g | U | A | C | A | U | C | A | U | C | A | C | C | u | 31 | 2 | 12 | bc | false | <90% | 2836 | ||
NM_002350 | LYN | 1239 | 1257 | c | c | C | A | u | U | U | A | C | A | U | C | A | U | C | A | C | C | g | 30 | 4 | 13 | bc | false | <90% | 2298 | ||
XM_941265 | C6orf94 | 145 | 163 | g | G | C | A | A | U | g | A | C | A | U | C | A | U | C | A | C | a | A | 29 | 3 | 10 | c | false | <90% | 1192 | ||
XM_928657 | C6orf94 | 145 | 163 | g | G | C | A | A | U | g | A | C | A | U | C | A | U | C | A | C | a | A | 29 | 3 | 10 | c | false | <90% | 1192 | ||
NM_001039682 | FLJ45340 | 1846 | 1864 | A | G | C | A | A | U | g | A | C | A | U | C | A | U | C | A | C | C | c | 28 | 2 | 11 | bc | false | <90% | 3497 | ||
NM_001039935 | ANKRD55 | 507 | 525 | g | u | C | A | A | U | g | A | C | A | U | C | A | U | C | A | C | C | A | 20 | 3 | 12 | bc | false | <90% | 1722 | ||
NM_024669 | ANKRD55 | 1287 | 1305 | g | u | C | A | A | U | g | A | C | A | U | C | A | U | C | A | C | C | A | 20 | 3 | 12 | bc | false | <90% | 2502 | ||
NM_018455 | CENPN | 959 | 977 | u | G | C | A | A | U | U | u | C | A | U | C | A | g | C | A | C | C | A | 16 | 3 | 6 | c | false | <90% | 1405 | ||
NM_032034 | SLC4A11 | 1167 | 1185 | g | G | C | A | A | a | U | A | C | A | U | C | A | c | C | A | C | C | A | 15 | 3 | 7 | c | false | <90% | 3138 | ||
NM_001456 | FLNA | 6350 | 6368 | g | G | C | A | A | c | U | A | C | A | U | C | A | U | C | A | a | C | A | 11 | 3 | 10 | c | false | <90% | 8278 | ||
NM_001386 | DPYSL2 | 2622 | 2640 | u | G | C | A | A | U | U | A | C | g | U | C | A | U | C | A | C | C | c | 10 | 3 | 8 | bc | false | <90% | 4567 | ||
NM_001458 | FLNC | 5345 | 5363 | g | G | C | A | A | g | U | A | C | g | U | C | A | U | C | A | C | C | A | -48 | 3 | 9 | bc | false | <90% | 9146 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2089
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