Automatic recommendation
Not OK - siRNA is not specific
19 hits were found for GCUGUCAGCUUCAGUCAAU (5 guide strand hits and 14 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 | |||||||||||||
| XM_929612 | LOC646670 | 1550 | 1568 | G | C | U | G | U | C | A | G | C | U | U | C | u | G | U | C | A | g | c | 81 | 3 | 12 | false | <90% | 2097 | |||
| NM_000383 | AIRE | 676 | 694 | c | a | U | G | U | C | A | G | C | U | U | C | A | G | U | C | c | A | g | 58 | 4 | 14 | ac | false | <90% | 2252 | ||
| NM_015564 | LRRTM2 | 650 | 668 | u | u | U | G | c | C | A | G | C | U | U | C | A | G | U | C | A | A | c | 30 | 4 | 13 | bc | false | <90% | 5572 | ||
| XM_942521 | USP24 | 9445 | 9463 | G | C | U | G | a | C | A | G | C | U | a | C | A | G | U | C | A | A | U | -12 | 2 | 8 | c | false | <90% | 10051 | ||
| XM_371254 | USP24 | 9463 | 9481 | G | C | U | G | a | C | A | G | C | U | a | C | A | G | U | C | A | A | U | -12 | 2 | 8 | c | false | <90% | 10069 | ||
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_020416 | PPP2R2C | 433 | 451 | u | g | U | G | A | C | U | G | A | A | G | C | U | G | A | C | A | u | C | 83 | 3 | 15 | ac | false | <90% | 4438 | ||
| NM_015158 | ANKRD15 | 1477 | 1495 | g | a | U | G | A | C | U | G | A | A | G | C | U | G | A | C | A | a | a | 78 | 4 | 15 | ac | false | <90% | 5083 | ||
| NM_153186 | ANKRD15 | 1657 | 1675 | g | a | U | G | A | C | U | G | A | A | G | C | U | G | A | C | A | a | a | 78 | 4 | 15 | ac | false | <90% | 5263 | ||
| NM_004713 | SDCCAG1 | 1835 | 1853 | c | U | U | G | A | C | U | G | A | A | G | C | U | G | g | C | A | c | a | 65 | 4 | 13 | c | false | <90% | 4121 | ||
| NM_000297 | PKD2 | 967 | 985 | c | c | a | G | A | C | U | G | A | A | G | C | U | G | A | C | A | a | C | 64 | 4 | 14 | c | false | <90% | 5073 | ||
| NM_182914 | SYNE2 | 5249 | 5267 | A | U | U | G | A | C | U | G | A | A | G | a | g | G | A | C | A | G | a | 50 | 3 | 11 | false | <90% | 21882 | |||
| NM_015180 | SYNE2 | 5249 | 5267 | A | U | U | G | A | C | U | G | A | A | G | a | g | G | A | C | A | G | a | 50 | 3 | 11 | false | <90% | 21816 | |||
| XR_016402 | LOC643536 | 273 | 291 | A | U | g | G | A | C | U | G | A | A | G | C | U | G | A | C | c | u | u | 49 | 4 | 13 | c | false | <90% | 841 | ||
| XR_018357 | LOC643536 | 273 | 291 | A | U | g | G | A | C | U | G | A | A | G | C | U | G | A | C | c | u | u | 49 | 4 | 13 | c | false | <90% | 841 | ||
| NM_004506 | HSF2 | 1600 | 1618 | A | U | U | G | A | C | U | G | A | A | G | C | U | G | A | a | g | c | u | 42 | 4 | 15 | c | false | <90% | 2444 | ||
| NM_170752 | CDYL | 1021 | 1039 | g | U | g | G | A | C | g | G | A | A | G | C | U | G | A | C | A | G | C | 12 | 3 | 12 | bc | false | <90% | 2805 | ||
| NM_004824 | CDYL | 1647 | 1665 | g | U | g | G | A | C | g | G | A | A | G | C | U | G | A | C | A | G | C | 12 | 3 | 12 | bc | false | <90% | 3432 | ||
| NM_170751 | CDYL | 1689 | 1707 | g | U | g | G | A | C | g | G | A | A | G | C | U | G | A | C | A | G | C | 12 | 3 | 12 | bc | false | <90% | 3474 | ||
| NM_004048 | B2M | 36 | 54 | c | a | U | u | c | C | U | G | A | A | G | C | U | G | A | C | A | G | C | -1 | 4 | 14 | bc | false | <90% | 987 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2148
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