Automatic recommendation
Not OK - siRNA is not specific
26 hits were found for CCUGUGUAUAUUGCAAGAC (17 guide strand hits and 9 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_138319 | PCSK6 | 4138 | 4156 | u | C | U | G | U | G | U | A | U | A | U | U | a | C | A | A | G | c | C | 84 | 3 | 11 | false | <90% | 4520 | |||
| NM_002570 | PCSK6 | 4177 | 4195 | u | C | U | G | U | G | U | A | U | A | U | U | a | C | A | A | G | c | C | 84 | 3 | 11 | false | <90% | 4559 | |||
| XM_044434 | KIAA1458 | 4549 | 4567 | C | C | U | u | U | G | U | A | U | A | U | U | G | C | A | A | u | u | u | 32 | 4 | 12 | c | false | <90% | 6472 | ||
| XM_941571 | KIAA1458 | 4549 | 4567 | C | C | U | u | U | G | U | A | U | A | U | U | G | C | A | A | u | u | u | 32 | 4 | 12 | c | false | <90% | 6472 | ||
| XM_936707 | LOC647654 | 365 | 383 | g | a | c | a | U | G | U | A | U | A | U | U | G | C | A | A | G | A | C | 30 | 4 | 15 | bc | false | <90% | 1065 | ||
| XR_015172 | LOC730535 | 364 | 382 | g | a | c | a | U | G | U | A | U | A | U | U | G | C | A | A | G | A | C | 30 | 4 | 15 | bc | false | <90% | 1914 | ||
| XR_018282 | LOC647696 | 389 | 407 | a | a | c | a | U | G | U | A | U | A | U | U | G | C | A | A | G | A | C | 30 | 4 | 15 | bc | false | <90% | 1939 | ||
| NM_001256 | CDC27 | 493 | 511 | g | a | c | a | U | G | U | A | U | A | U | U | G | C | A | A | G | A | C | 30 | 4 | 15 | bc | false | <90% | 3277 | ||
| NM_002717 | PPP2R2A | 1616 | 1634 | u | C | U | G | U | a | U | A | U | A | U | U | u | C | A | A | G | A | C | 24 | 3 | 6 | false | <90% | 2385 | |||
| NM_005726 | TSFM | 205 | 223 | C | C | U | u | U | G | U | A | a | A | U | U | G | C | A | A | G | A | a | -1 | 3 | 9 | bc | false | <90% | 1247 | ||
| NM_000641 | IL11 | 2302 | 2320 | a | C | U | G | U | G | U | A | U | u | U | U | G | C | A | u | G | A | C | -10 | 3 | 8 | c | false | <90% | 2354 | ||
| NM_173200 | NR4A3 | 3287 | 3305 | C | C | U | G | U | a | U | u | U | A | U | U | G | C | A | A | G | A | C | -25 | 2 | 11 | bc | false | <90% | 4983 | ||
| NM_006981 | NR4A3 | 3939 | 3957 | C | C | U | G | U | a | U | u | U | A | U | U | G | C | A | A | G | A | C | -25 | 2 | 11 | bc | false | <90% | 5635 | ||
| NM_173198 | NR4A3 | 4686 | 4704 | C | C | U | G | U | a | U | u | U | A | U | U | G | C | A | A | G | A | C | -25 | 2 | 11 | bc | false | <90% | 6382 | ||
| XM_938853 | LOC285484 | 1851 | 1869 | C | C | U | G | U | G | U | u | U | c | U | U | G | C | A | A | G | A | g | -49 | 3 | 8 | bc | false | <90% | 2756 | ||
| XM_376303 | LOC285484 | 1851 | 1869 | C | C | U | G | U | G | U | u | U | c | U | U | G | C | A | A | G | A | g | -49 | 3 | 8 | bc | false | <90% | 2756 | ||
| NM_007271 | STK38 | 3418 | 3436 | C | C | U | G | U | G | U | g | U | u | U | U | G | C | A | A | G | A | a | -49 | 3 | 8 | bc | false | <90% | 3593 | ||
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_012167 | FBXO11 | 1368 | 1386 | a | a | g | U | U | G | C | A | A | U | A | U | A | C | A | C | A | G | a | 62 | 4 | 15 | bc | false | <90% | 2154 | ||
| NM_018693 | FBXO11 | 1368 | 1386 | a | a | g | U | U | G | C | A | A | U | A | U | A | C | A | C | A | G | a | 62 | 4 | 15 | bc | false | <90% | 2567 | ||
| NM_025133 | FBXO11 | 1368 | 1386 | a | a | g | U | U | G | C | A | A | U | A | U | A | C | A | C | A | G | a | 62 | 4 | 15 | bc | false | <90% | 3951 | ||
| NM_002001 | FCER1A | 950 | 968 | a | g | C | U | U | G | C | A | A | U | A | U | A | C | A | u | A | G | a | 55 | 4 | 13 | c | false | <90% | 1191 | ||
| XM_937669 | ZBTB34 | 6247 | 6265 | a | U | C | U | U | G | C | A | A | U | A | U | A | a | A | C | u | G | G | 54 | 3 | 12 | c | false | <90% | 6559 | ||
| XM_928961 | ZBTB34 | 6774 | 6792 | a | U | C | U | U | G | C | A | A | U | A | U | A | a | A | C | u | G | G | 54 | 3 | 12 | c | false | <90% | 7086 | ||
| NM_181539 | KRT26 | 734 | 752 | G | U | C | U | U | G | C | A | A | U | A | U | A | C | A | g | c | u | G | 47 | 3 | 15 | c | false | <90% | 1748 | ||
| NM_020946 | DENND1A | 3811 | 3829 | u | U | C | U | a | G | C | A | A | U | A | U | A | C | A | C | A | c | a | 38 | 4 | 12 | c | false | <90% | 5041 | ||
| NM_001008742 | LOC401410 | 2136 | 2154 | G | a | a | U | U | G | g | A | A | U | A | U | A | C | A | C | A | G | G | 2 | 3 | 12 | bc | false | <90% | 3045 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3763
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)
Motif found in guide strand
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