Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
31 hits were found for GCACUCAAGAGAAAAAAUU (16 guide strand hits and 15 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_020893 | KIAA1529 | 425 | 443 | G | C | c | C | U | C | A | A | G | A | G | A | A | A | A | A | A | a | a | 72 | 3 | 14 | c | false | <90% | 6269 | ||
| NM_001079691 | CG018 | 577 | 595 | u | g | u | C | U | C | A | A | G | A | G | A | A | A | A | A | A | U | c | 62 | 4 | 15 | bc | false | <90% | 3043 | ||
| NM_052818 | CG018 | 585 | 603 | u | g | u | C | U | C | A | A | G | A | G | A | A | A | A | A | A | U | c | 62 | 4 | 15 | bc | false | <90% | 3051 | ||
| XM_001130495 | LOC728429 | 3221 | 3239 | a | a | A | C | U | C | A | A | G | A | G | A | A | A | A | u | A | U | U | 60 | 3 | 13 | c | false | <90% | 3784 | ||
| NM_015559 | SETBP1 | 1854 | 1872 | a | C | A | C | U | C | A | A | G | A | G | g | A | A | A | A | A | c | a | 56 | 4 | 10 | false | <90% | 5744 | |||
| NM_181489 | ZNF445 | 1868 | 1886 | a | C | A | C | U | C | A | A | G | A | G | A | A | A | g | c | A | U | U | 47 | 3 | 13 | c | false | <90% | 9105 | ||
| NM_004730 | ETF1 | 974 | 992 | u | C | A | u | U | C | A | A | G | A | G | A | A | g | A | A | A | U | U | 41 | 3 | 9 | c | false | <90% | 3653 | ||
| NM_014394 | GHITM | 2000 | 2018 | a | u | u | C | U | C | A | A | G | A | G | A | A | A | A | u | A | U | U | 40 | 4 | 12 | c | false | <90% | 2449 | ||
| NM_000337 | SGCD | 4072 | 4090 | G | u | g | g | U | C | A | A | G | A | G | A | A | A | A | A | A | U | U | 32 | 3 | 15 | bc | false | <90% | 8052 | ||
| NM_003805 | CRADD | 1176 | 1194 | u | C | A | C | U | C | A | u | G | A | G | A | A | A | A | A | A | a | a | 28 | 4 | 9 | c | false | <90% | 1201 | ||
| NM_000926 | PGR | 4586 | 4604 | c | g | A | C | U | u | A | A | G | A | G | A | A | A | A | A | A | U | c | 18 | 4 | 12 | bc | false | <90% | 5000 | ||
| NM_017593 | BMP2K | 2486 | 2504 | a | C | A | C | U | C | A | A | u | A | G | A | A | A | A | u | A | U | U | 11 | 3 | 7 | c | false | <90% | 2681 | ||
| NM_022497 | MRPS25 | 1869 | 1887 | u | g | u | C | U | C | A | A | G | A | a | A | A | A | A | A | A | U | U | 5 | 4 | 8 | c | false | <90% | 4574 | ||
| NM_182496 | CCDC38 | 1130 | 1148 | G | C | A | C | U | C | c | A | G | A | G | A | A | A | A | A | g | a | a | 2 | 4 | 9 | c | false | <90% | 1953 | ||
| NM_002974 | SERPINB4 | 667 | 685 | a | C | A | C | U | a | A | A | G | A | G | g | A | A | A | A | A | U | U | 0 | 3 | 7 | false | <90% | 1736 | |||
| NM_020791 | TAOK1 | 1783 | 1801 | c | C | A | a | U | g | A | A | G | A | G | A | A | A | A | A | A | U | U | -2 | 3 | 13 | bc | false | <90% | 4662 | ||
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_001827 | CKS2 | 538 | 556 | c | A | g | U | U | U | U | U | C | U | C | U | U | a | A | G | U | G | C | 58 | 3 | 10 | c | false | <90% | 627 | ||
| NM_206894 | ZNF790 | 2087 | 2105 | A | u | U | U | U | U | U | U | C | U | C | U | U | G | A | G | g | a | a | 57 | 4 | 14 | ac | false | <90% | 3047 | ||
| NM_182646 | CPEB2 | 3380 | 3398 | u | A | U | U | U | U | U | U | C | U | C | U | U | u | A | G | a | G | C | 54 | 3 | 12 | c | false | <90% | 5537 | ||
| NM_182485 | CPEB2 | 3470 | 3488 | u | A | U | U | U | U | U | U | C | U | C | U | U | u | A | G | a | G | C | 54 | 3 | 12 | c | false | <90% | 5627 | ||
| NM_006095 | ATP8A1 | 238 | 256 | c | A | U | U | U | U | U | U | C | U | C | U | U | u | A | u | U | G | C | 52 | 3 | 12 | c | false | <90% | 3794 | ||
| NM_152556 | FLJ31818 | 1607 | 1625 | A | c | c | U | U | U | U | U | C | U | C | U | U | u | A | G | U | G | C | 49 | 3 | 10 | c | false | <90% | 3969 | ||
| NM_000382 | ALDH3A2 | 1573 | 1591 | A | A | U | U | U | U | U | U | C | U | C | U | U | G | A | a | a | c | g | 42 | 4 | 15 | c | false | <90% | 3702 | ||
| NM_001031806 | ALDH3A2 | 1573 | 1591 | A | A | U | U | U | U | U | U | C | U | C | U | U | G | A | a | a | c | g | 42 | 4 | 15 | c | false | <90% | 3823 | ||
| NM_152546 | SRFBP1 | 1782 | 1800 | c | A | U | a | U | U | U | U | C | U | C | U | U | u | A | G | U | G | C | 41 | 3 | 9 | c | false | <90% | 2836 | ||
| NM_054105 | OR6C2 | 322 | 340 | A | A | U | U | U | U | U | U | C | U | C | U | U | G | g | c | a | G | C | 25 | 3 | 14 | c | false | <90% | 939 | ||
| NM_145034 | TOR1AIP2 | 2142 | 2160 | u | u | U | U | U | U | U | U | u | U | C | U | U | G | A | G | U | G | a | 21 | 4 | 9 | bc | false | <90% | 3073 | ||
| NM_012431 | SEMA3E | 5827 | 5845 | A | A | U | U | U | U | U | U | C | U | u | U | U | G | u | G | U | G | a | 9 | 3 | 10 | c | false | <90% | 6474 | ||
| NM_006546 | IGF2BP1 | 6896 | 6914 | A | A | U | U | U | U | U | U | u | U | C | U | U | G | A | a | U | G | a | 8 | 3 | 8 | c | false | <90% | 8769 | ||
| NM_000338 | SLC12A1 | 3855 | 3873 | A | A | U | U | U | U | U | U | g | U | u | U | U | G | A | G | U | G | u | -26 | 3 | 8 | c | false | <90% | 4717 | ||
| NM_018847 | KLHL9 | 1742 | 1760 | c | A | U | U | c | U | U | U | C | a | C | U | U | G | A | G | U | G | C | -36 | 3 | 9 | bc | false | <90% | 4412 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1430
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