Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for GCAAUUCAUUGAGUAUGCU (9 guide strand hits and 3 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_080546 | SLC44A1 | 3221 | 3239 | G | C | A | A | U | U | C | A | U | U | G | A | G | U | A | U | c | C | a | 71 | 2 | 16 | ac | false | <90% | 4540 | ||
| NM_000706 | AVPR1A | 3338 | 3356 | u | C | A | A | U | U | C | A | U | U | G | u | G | U | A | U | G | a | g | 56 | 4 | 10 | false | <90% | 4154 | |||
| NR_003257 | PDLIM5 | 2526 | 2544 | u | C | u | A | U | U | C | A | U | U | G | u | G | U | A | U | G | C | U | 44 | 3 | 8 | false | <90% | 5681 | |||
| NM_001011513 | PDLIM5 | 2618 | 2636 | u | C | u | A | U | U | C | A | U | U | G | u | G | U | A | U | G | C | U | 44 | 3 | 8 | false | <90% | 5774 | |||
| NM_006457 | PDLIM5 | 2945 | 2963 | u | C | u | A | U | U | C | A | U | U | G | u | G | U | A | U | G | C | U | 44 | 3 | 8 | false | <90% | 6101 | |||
| NM_152467 | KLHL10 | 377 | 395 | G | C | u | A | a | U | C | A | U | U | G | A | G | U | A | U | G | C | a | 23 | 3 | 13 | bc | false | <90% | 1969 | ||
| NM_024969 | FAM130A2 | 1678 | 1696 | G | C | A | A | U | U | C | g | U | U | G | A | c | U | A | U | G | C | c | 22 | 3 | 7 | false | <90% | 2965 | |||
| XM_001127470 | PABPC5 | 1428 | 1446 | G | C | A | A | U | U | g | A | U | U | G | A | G | U | A | U | a | u | U | 7 | 3 | 9 | c | false | <90% | 3005 | ||
| NM_080832 | PABPC5 | 1867 | 1885 | G | C | A | A | U | U | g | A | U | U | G | A | G | U | A | U | a | u | U | 7 | 3 | 9 | c | false | <90% | 3521 | ||
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_170662 | CBLB | 327 | 345 | g | G | C | A | a | A | C | U | C | A | A | U | G | A | A | U | g | G | C | 23 | 3 | 11 | c | false | <90% | 3976 | ||
| NM_001039840 | CHIC1 | 3768 | 3786 | A | G | C | A | U | A | a | U | a | A | A | U | G | A | A | U | U | G | g | -31 | 3 | 9 | bc | false | <90% | 4158 | ||
| NM_014618 | DBC1 | 3001 | 3019 | A | G | C | A | U | A | u | g | C | A | A | U | G | A | A | U | U | G | u | -33 | 3 | 10 | bc | false | <90% | 3158 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1397
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