Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
36 hits were found for GGAUAGAACUUGAUGAAAU (25 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_024873 | TNIP3 | 289 | 307 | a | G | A | a | A | G | A | A | C | U | U | G | A | U | G | A | A | u | U | 58 | 3 | 13 | c | false | <90% | 2425 | ||
| NM_031366 | COL4A3 | 653 | 671 | a | u | A | U | A | G | A | A | C | U | U | G | A | U | G | c | A | A | a | 55 | 4 | 13 | c | false | <90% | 7420 | ||
| NM_031365 | COL4A3 | 653 | 671 | a | u | A | U | A | G | A | A | C | U | U | G | A | U | G | c | A | A | a | 55 | 4 | 13 | c | false | <90% | 7630 | ||
| NM_031362 | COL4A3 | 653 | 671 | a | u | A | U | A | G | A | A | C | U | U | G | A | U | G | c | A | A | a | 55 | 4 | 13 | c | false | <90% | 7923 | ||
| NM_000091 | COL4A3 | 653 | 671 | a | u | A | U | A | G | A | A | C | U | U | G | A | U | G | c | A | A | a | 55 | 4 | 13 | c | false | <90% | 8096 | ||
| NM_001077501 | LRRCC1 | 2617 | 2635 | a | a | g | U | A | G | A | A | C | U | U | G | A | a | G | A | A | A | U | 47 | 4 | 10 | c | false | <90% | 3619 | ||
| NM_033402 | LRRCC1 | 2823 | 2841 | a | a | g | U | A | G | A | A | C | U | U | G | A | a | G | A | A | A | U | 47 | 4 | 10 | c | false | <90% | 3825 | ||
| NM_004011 | DMD | 637 | 655 | c | c | A | a | A | G | A | A | C | U | U | G | A | U | G | A | A | A | g | 44 | 4 | 14 | bc | false | <90% | 9773 | ||
| NM_004012 | DMD | 780 | 798 | c | c | A | a | A | G | A | A | C | U | U | G | A | U | G | A | A | A | g | 44 | 4 | 14 | bc | false | <90% | 9916 | ||
| NM_004007 | DMD | 4628 | 4646 | c | c | A | a | A | G | A | A | C | U | U | G | A | U | G | A | A | A | g | 44 | 4 | 14 | bc | false | <90% | 13764 | ||
| NM_004006 | DMD | 4857 | 4875 | c | c | A | a | A | G | A | A | C | U | U | G | A | U | G | A | A | A | g | 44 | 4 | 14 | bc | false | <90% | 13993 | ||
| NM_004009 | DMD | 4864 | 4882 | c | c | A | a | A | G | A | A | C | U | U | G | A | U | G | A | A | A | g | 44 | 4 | 14 | bc | false | <90% | 14000 | ||
| NM_000109 | DMD | 4933 | 4951 | c | c | A | a | A | G | A | A | C | U | U | G | A | U | G | A | A | A | g | 44 | 4 | 14 | bc | false | <90% | 14069 | ||
| NM_004010 | DMD | 4946 | 4964 | c | c | A | a | A | G | A | A | C | U | U | G | A | U | G | A | A | A | g | 44 | 4 | 14 | bc | false | <90% | 14082 | ||
| NM_017691 | LRRC49 | 1590 | 1608 | u | c | A | U | A | G | A | A | u | U | U | G | A | U | G | A | A | A | U | 26 | 3 | 10 | bc | false | <90% | 2809 | ||
| NM_006642 | SDCCAG8 | 1646 | 1664 | G | a | A | U | A | G | A | A | C | U | g | G | A | U | G | A | A | A | g | 22 | 3 | 8 | c | false | <90% | 2614 | ||
| NM_019062 | RNF186 | 1173 | 1191 | u | u | A | U | A | u | A | A | C | U | U | G | A | U | G | A | A | A | g | 18 | 4 | 12 | bc | false | <90% | 1268 | ||
| NM_004886 | APBA3 | 323 | 341 | G | G | A | U | g | G | A | A | C | U | U | G | A | U | G | A | g | u | c | 17 | 4 | 11 | c | false | <90% | 2158 | ||
| XM_001130919 | LOC729652 | 2852 | 2870 | u | G | A | U | A | u | A | A | C | U | U | G | A | U | a | A | A | A | U | 9 | 3 | 8 | c | false | <90% | 3264 | ||
| NM_005822 | DSCR1L1 | 518 | 536 | G | G | A | U | A | G | A | g | C | U | U | c | A | U | G | A | A | A | c | 0 | 3 | 7 | false | <90% | 3318 | |||
| NM_001024674 | LIN52 | 346 | 364 | a | G | A | U | A | G | A | A | C | g | U | G | A | U | G | A | c | A | U | -8 | 3 | 8 | c | false | <90% | 576 | ||
| NM_032435 | KIAA1804 | 1082 | 1100 | a | G | A | U | A | G | A | A | C | a | U | G | A | U | G | A | c | A | U | -8 | 3 | 8 | c | false | <90% | 4667 | ||
| XM_045911 | STXBP5L | 3809 | 3827 | G | G | A | U | u | G | c | A | C | U | U | G | A | U | G | A | A | A | g | -22 | 3 | 11 | bc | false | <90% | 5179 | ||
| XM_938898 | STXBP5L | 3809 | 3827 | G | G | A | U | u | G | c | A | C | U | U | G | A | U | G | A | A | A | g | -22 | 3 | 11 | bc | false | <90% | 5179 | ||
| XM_943718 | LOC440905 | 518 | 536 | a | G | A | U | A | G | A | A | g | U | g | G | A | U | G | A | A | A | U | -23 | 3 | 8 | c | false | <90% | 1553 | ||
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_024767 | DLC1 | 340 | 358 | c | U | U | U | C | A | U | C | A | A | G | U | U | C | c | A | U | C | u | 68 | 3 | 13 | c | false | <90% | 1975 | ||
| NM_182643 | DLC1 | 340 | 358 | c | U | U | U | C | A | U | C | A | A | G | U | U | C | c | A | U | C | u | 68 | 3 | 13 | c | false | <90% | 7445 | ||
| NM_002658 | PLAU | 187 | 205 | A | c | U | U | C | A | U | C | A | A | G | U | U | C | c | A | U | C | g | 58 | 3 | 12 | c | false | <90% | 2360 | ||
| NM_014992 | DAAM1 | 4047 | 4065 | A | U | U | U | C | A | U | C | A | A | G | U | U | a | U | c | U | C | u | 49 | 3 | 13 | c | false | <90% | 4256 | ||
| XR_018242 | LOC390183 | 503 | 521 | A | U | U | U | C | A | U | C | A | A | G | U | U | C | a | A | c | a | C | 49 | 3 | 14 | c | false | <90% | 843 | ||
| XR_016275 | LOC390183 | 503 | 521 | A | U | U | U | C | A | U | C | A | A | G | U | U | C | a | A | c | a | C | 49 | 3 | 14 | c | false | <90% | 843 | ||
| NM_001007 | RPS4X | 606 | 624 | A | U | U | U | C | A | U | C | A | A | G | U | U | C | g | A | c | a | C | 49 | 3 | 14 | c | false | <90% | 977 | ||
| NM_025191 | EDEM3 | 2379 | 2397 | A | U | U | U | C | A | U | C | A | A | G | U | U | C | U | c | a | g | g | 42 | 4 | 15 | c | false | <90% | 6298 | ||
| NM_006727 | CDH10 | 3180 | 3198 | A | U | U | U | C | A | U | C | A | A | a | U | U | C | U | A | U | C | u | 33 | 2 | 10 | c | false | <90% | 3261 | ||
| XM_001132934 | LOC731452 | 395 | 413 | A | U | U | U | u | A | U | C | A | A | G | U | U | a | U | A | U | C | a | 24 | 3 | 8 | c | false | <90% | 3264 | ||
| NM_033418 | C1orf156 | 214 | 232 | g | U | a | U | C | A | U | C | A | A | a | U | U | C | U | A | U | C | C | 17 | 3 | 8 | c | false | <90% | 1445 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1147
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