Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
12 hits were found for GUAGAUUUGCCUCCCUGGU (4 guide strand hits and 8 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_016235 | GPRC5B | 1356 | 1374 | a | c | c | G | A | U | U | U | G | C | C | U | C | C | C | U | G | G | c | 62 | 4 | 15 | bc | false | <90% | 2870 | ||
| NM_014286 | FREQ | 3083 | 3101 | c | U | c | G | A | U | U | U | G | C | C | U | C | u | C | U | G | G | U | 58 | 3 | 10 | c | false | <90% | 4341 | ||
| NM_130440 | PTPRF | 7242 | 7260 | G | a | u | G | A | U | U | U | u | C | C | U | C | C | C | U | G | G | U | 8 | 3 | 10 | bc | false | <90% | 7706 | ||
| NM_002840 | PTPRF | 7269 | 7287 | G | a | u | G | A | U | U | U | u | C | C | U | C | C | C | U | G | G | U | 8 | 3 | 10 | bc | false | <90% | 7733 | ||
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 | |||||||||||||
| XM_001127087 | FLJ43950 | 4684 | 4702 | u | g | C | A | G | G | G | A | G | G | C | A | A | A | U | C | U | c | C | 83 | 3 | 15 | ac | false | <90% | 4762 | ||
| XR_015253 | FLJ43859 | 4790 | 4808 | u | g | C | A | G | G | G | A | G | G | C | A | A | A | U | C | U | c | C | 83 | 3 | 15 | ac | false | <90% | 4871 | ||
| NM_182484 | BAGE5 | 1273 | 1291 | A | C | C | A | a | G | G | A | G | G | C | A | A | A | U | C | U | A | u | 43 | 2 | 13 | bc | false | <90% | 1840 | ||
| NM_181704 | BAGE4 | 1273 | 1291 | A | C | C | A | a | G | G | A | G | G | C | A | A | A | U | C | U | A | u | 43 | 2 | 13 | bc | false | <90% | 1840 | ||
| NM_182482 | BAGE2 | 1204 | 1222 | A | C | C | A | a | G | G | A | G | G | C | A | A | A | U | C | U | A | u | 43 | 2 | 13 | bc | false | <90% | 1891 | ||
| NM_182481 | BAGE3 | 1204 | 1222 | A | C | C | A | a | G | G | A | G | G | C | A | A | A | U | C | U | A | u | 43 | 2 | 13 | bc | false | <90% | 1891 | ||
| NM_170606 | MLL3 | 2480 | 2498 | A | C | C | A | a | G | G | A | G | G | C | A | A | A | U | C | U | A | u | 43 | 2 | 13 | bc | false | <90% | 16872 | ||
| NM_013255 | MKLN1 | 1031 | 1049 | u | C | a | A | c | G | G | A | G | G | C | A | A | A | U | C | U | A | C | 26 | 3 | 14 | bc | false | <90% | 11157 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1631
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