Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
21 hits were found for GAUGGCUUGGAAGCUUUGG (10 guide strand hits and 11 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_182506 | MAGEB10 | 1390 | 1408 | G | A | U | G | G | C | U | U | G | G | A | A | u | u | U | U | U | G | a | 65 | 3 | 12 | false | <90% | 1567 | |||
| NM_014588 | VSX1 | 990 | 1008 | a | A | U | G | G | C | U | U | G | G | A | A | G | a | U | g | U | G | G | 52 | 3 | 12 | c | false | <90% | 1956 | ||
| NM_024567 | HMBOX1 | 533 | 551 | c | A | U | G | c | C | U | U | G | G | A | A | a | C | U | U | U | G | G | 36 | 3 | 7 | false | <90% | 2427 | |||
| XM_929433 | LOC644006 | 1785 | 1803 | c | u | g | G | G | C | U | U | G | G | A | u | G | C | U | U | U | G | G | 33 | 4 | 8 | false | <90% | 2759 | |||
| XM_939111 | LOC650020 | 1788 | 1806 | c | u | g | G | G | C | U | U | G | G | A | u | G | C | U | U | U | G | G | 33 | 4 | 8 | false | <90% | 2762 | |||
| NM_006218 | PIK3CA | 1477 | 1495 | a | A | U | G | G | C | U | U | u | G | A | A | u | C | U | U | U | G | G | 27 | 3 | 7 | false | <90% | 3724 | |||
| NM_000132 | F8 | 1180 | 1198 | G | A | U | G | G | C | a | U | G | G | A | A | G | C | U | U | a | u | G | 7 | 3 | 9 | c | false | <90% | 9030 | ||
| NM_005406 | ROCK1 | 1035 | 1053 | G | A | U | G | G | a | U | U | G | G | A | u | G | C | U | U | U | G | G | 2 | 2 | 7 | false | <90% | 6650 | |||
| NM_175940 | DUOX1 | 2078 | 2096 | G | g | a | G | G | C | a | U | G | G | A | A | G | C | U | U | U | G | G | 2 | 3 | 12 | bc | false | <90% | 5501 | ||
| NM_017434 | DUOX1 | 2270 | 2288 | G | g | a | G | G | C | a | U | G | G | A | A | G | C | U | U | U | G | G | 2 | 3 | 12 | bc | false | <90% | 5693 | ||
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_018999 | KIAA1128 | 3279 | 3297 | u | C | A | A | A | G | C | U | U | C | C | A | g | G | C | C | A | a | g | 79 | 4 | 11 | false | <90% | 7676 | |||
| NM_001001411 | ZNF676 | 1516 | 1534 | g | C | A | A | A | G | C | U | U | C | C | A | A | c | u | C | A | U | C | 53 | 3 | 12 | c | false | <90% | 2934 | ||
| NM_182490 | ZNF227 | 1804 | 1822 | u | C | A | A | A | G | C | U | U | C | a | A | A | c | C | C | A | U | C | 17 | 3 | 9 | c | false | <90% | 3075 | ||
| XM_001130675 | LOC729570 | 197 | 215 | C | g | g | A | g | G | C | U | U | C | C | A | A | G | C | C | A | U | C | 17 | 3 | 14 | bc | false | <90% | 1356 | ||
| NM_017863 | CXorf48 | 254 | 272 | C | C | c | A | A | G | C | U | c | C | C | A | A | G | C | C | A | U | u | 15 | 3 | 9 | bc | false | <90% | 2188 | ||
| NM_001005409 | SF3A1 | 1121 | 1139 | C | C | A | A | A | G | C | c | U | C | C | A | A | G | C | C | c | U | u | 9 | 3 | 8 | c | false | <90% | 4941 | ||
| NM_005877 | SF3A1 | 1316 | 1334 | C | C | A | A | A | G | C | c | U | C | C | A | A | G | C | C | c | U | u | 9 | 3 | 8 | c | false | <90% | 5136 | ||
| NM_176817 | TAS2R38 | 352 | 370 | C | C | A | c | A | G | C | U | a | C | C | A | A | G | C | C | A | U | C | 3 | 2 | 10 | bc | false | <90% | 1143 | ||
| NM_152387 | KCTD18 | 1834 | 1852 | C | C | A | A | A | G | C | U | U | u | C | A | A | c | C | C | A | U | u | -7 | 3 | 9 | c | false | <90% | 2959 | ||
| NM_032584 | ZNF347 | 2151 | 2169 | u | C | A | A | A | G | C | U | U | g | C | A | A | G | g | C | A | U | C | -9 | 3 | 8 | c | false | <90% | 3502 | ||
| NM_032584 | ZNF347 | 2560 | 2578 | u | C | A | A | A | c | C | U | U | g | C | A | A | G | C | C | A | U | C | -48 | 3 | 9 | bc | false | <90% | 3502 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1875
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