Automatic recommendation
Not OK - siRNA is not specific
15 hits were found for UCCAUGUGCACUGCCUUGG (5 guide strand hits and 10 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_017580 | ZRANB1 | 2251 | 2269 | U | C | C | A | U | G | U | G | C | A | C | U | u | C | C | U | U | u | c | 81 | 3 | 12 | false | <90% | 4942 | |||
| NM_018689 | KIAA1199 | 5146 | 5164 | U | C | C | A | U | G | U | G | C | A | C | U | G | C | a | a | U | G | c | 44 | 3 | 14 | c | false | <90% | 7080 | ||
| NM_182894 | CHX10 | 2141 | 2159 | c | a | C | A | U | G | U | G | C | c | C | U | G | C | C | U | U | G | a | -1 | 4 | 8 | bc | false | <90% | 3005 | ||
| NM_138368 | DKFZp761E198 | 1708 | 1726 | U | C | C | A | U | G | U | G | C | c | C | U | G | C | C | U | g | u | G | -8 | 3 | 9 | c | false | <90% | 4181 | ||
| NM_012384 | GMEB2 | 395 | 413 | U | C | C | c | U | G | U | G | C | c | C | U | G | C | C | U | U | G | c | -24 | 3 | 8 | bc | false | <90% | 4559 | ||
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_005291 | GPR17 | 849 | 867 | C | C | A | A | G | G | C | A | G | U | G | C | g | C | A | U | G | a | u | 81 | 3 | 12 | false | <90% | 2070 | |||
| NM_014868 | RNF10 | 933 | 951 | u | g | A | A | G | G | C | A | G | U | G | g | A | C | A | U | G | G | u | 47 | 4 | 9 | false | <90% | 3784 | |||
| NM_003947 | KALRN | 1602 | 1620 | C | C | A | A | G | G | C | A | G | U | G | C | A | C | c | a | G | G | u | 44 | 3 | 14 | c | false | <90% | 6481 | ||
| NM_001024660 | KALRN | 1602 | 1620 | C | C | A | A | G | G | C | A | G | U | G | C | A | C | c | a | G | G | u | 44 | 3 | 14 | c | false | <90% | 10777 | ||
| NR_003288 | LOC729603 | 54 | 72 | g | u | g | u | G | G | C | A | G | U | G | C | A | C | A | U | G | G | A | 30 | 4 | 15 | bc | false | <90% | 1798 | ||
| NM_033512 | TSPYL5 | 1813 | 1831 | u | g | A | A | G | c | C | A | G | U | G | C | A | C | A | U | G | G | u | 18 | 4 | 12 | bc | false | <90% | 4478 | ||
| XR_015979 | LOC731655 | 1009 | 1027 | a | g | A | A | G | G | C | A | G | a | G | C | A | C | A | U | G | G | A | 3 | 3 | 9 | bc | false | <90% | 3802 | ||
| XR_015907 | LOC729143 | 1009 | 1027 | a | g | A | A | G | G | C | A | G | a | G | C | A | C | A | U | G | G | A | 3 | 3 | 9 | bc | false | <90% | 3802 | ||
| NM_015134 | M-RIP | 997 | 1015 | a | g | A | A | G | G | C | A | G | a | G | C | A | C | A | U | G | G | A | 3 | 3 | 9 | bc | false | <90% | 3858 | ||
| NM_201274 | M-RIP | 997 | 1015 | a | g | A | A | G | G | C | A | G | a | G | C | A | C | A | U | G | G | A | 3 | 3 | 9 | bc | false | <90% | 3923 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2537
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