Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
20 hits were found for GGGAAUCCAUAUGCUGUAU (12 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_152263 | TPM3 | 4895 | 4913 | G | G | G | A | A | U | C | C | A | U | A | U | G | g | g | G | U | A | c | 50 | 3 | 13 | c | false | <90% | 7116 | ||
| NM_018405 | C17orf79 | 411 | 429 | G | G | G | A | A | U | C | C | A | U | A | U | G | a | U | G | c | u | g | 49 | 4 | 13 | c | false | <90% | 861 | ||
| NM_002526 | NT5E | 1408 | 1426 | c | G | G | A | A | U | C | C | A | U | g | U | G | g | U | G | U | A | U | 17 | 3 | 9 | c | false | <90% | 3547 | ||
| XM_001133644 | LOC732436 | 199 | 217 | a | G | G | A | A | U | C | C | A | g | A | U | G | C | U | G | U | g | g | 7 | 4 | 8 | c | false | <90% | 405 | ||
| XM_001133214 | LOC732390 | 21 | 39 | a | G | G | A | A | U | C | C | A | g | A | U | G | C | U | G | U | g | g | 7 | 4 | 8 | c | false | <90% | 1604 | ||
| NM_005577 | LPA | 352 | 370 | a | G | G | A | A | U | C | C | A | g | A | U | G | C | U | G | U | g | g | 7 | 4 | 8 | c | false | <90% | 6489 | ||
| NM_005577 | LPA | 694 | 712 | a | G | G | A | A | U | C | C | A | g | A | U | G | C | U | G | U | g | g | 7 | 4 | 8 | c | false | <90% | 6489 | ||
| NM_005577 | LPA | 1036 | 1054 | a | G | G | A | A | U | C | C | A | g | A | U | G | C | U | G | U | g | g | 7 | 4 | 8 | c | false | <90% | 6489 | ||
| NM_005577 | LPA | 1378 | 1396 | a | G | G | A | A | U | C | C | A | g | A | U | G | C | U | G | U | g | g | 7 | 4 | 8 | c | false | <90% | 6489 | ||
| NM_005577 | LPA | 1720 | 1738 | a | G | G | A | A | U | C | C | A | g | A | U | G | C | U | G | U | g | g | 7 | 4 | 8 | c | false | <90% | 6489 | ||
| NM_005577 | LPA | 2062 | 2080 | a | G | G | A | A | U | C | C | A | g | A | U | G | C | U | G | U | g | g | 7 | 4 | 8 | c | false | <90% | 6489 | ||
| NM_005577 | LPA | 2404 | 2422 | a | G | G | A | A | U | C | C | A | g | A | U | G | C | U | G | U | g | g | 7 | 4 | 8 | c | false | <90% | 6489 | ||
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_014970 | KIFAP3 | 2597 | 2615 | c | c | A | C | A | G | C | A | U | A | U | G | G | A | U | U | C | C | g | 81 | 3 | 16 | abc | false | <90% | 2997 | ||
| NM_133492 | ASAH3 | 299 | 317 | c | U | A | u | A | G | C | A | U | A | U | G | G | A | U | g | C | C | C | 35 | 3 | 11 | c | false | <90% | 795 | ||
| NM_016226 | VPS29 | 794 | 812 | u | U | A | C | A | G | u | A | U | A | U | G | G | A | U | U | C | u | a | 24 | 4 | 10 | c | false | <90% | 1089 | ||
| NM_057180 | VPS29 | 806 | 824 | u | U | A | C | A | G | u | A | U | A | U | G | G | A | U | U | C | u | a | 24 | 4 | 10 | c | false | <90% | 1107 | ||
| NM_005813 | PRKD3 | 3889 | 3907 | A | U | A | C | A | G | C | A | U | A | a | G | G | A | U | U | g | u | C | 12 | 3 | 10 | c | false | <90% | 5907 | ||
| NM_001025068 | ARPP-21 | 2075 | 2093 | A | U | A | C | A | G | u | A | U | A | U | G | G | A | U | U | g | u | a | 2 | 4 | 9 | c | false | <90% | 2409 | ||
| NM_198399 | ARPP-21 | 2066 | 2084 | A | U | A | C | A | G | u | A | U | A | U | G | G | A | U | U | g | u | a | 2 | 4 | 9 | c | false | <90% | 2413 | ||
| NM_001025069 | ARPP-21 | 2084 | 2102 | A | U | A | C | A | G | u | A | U | A | U | G | G | A | U | U | g | u | a | 2 | 4 | 9 | c | false | <90% | 2418 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1256
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