Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
20 hits were found for GGACAACUUCACUAUGAAA (9 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_014106 | ZNF770 | 609 | 627 | c | a | A | C | A | A | C | U | U | C | A | C | a | A | U | G | A | A | A | 76 | 3 | 10 | false | <90% | 5418 | |||
| NM_007067 | MYST2 | 660 | 678 | c | u | A | C | A | A | C | U | U | C | A | a | U | A | U | G | A | A | g | 47 | 4 | 9 | false | <90% | 3600 | |||
| NM_139165 | RAET1E | 162 | 180 | c | u | u | C | A | A | C | U | U | C | A | C | U | A | U | a | A | A | A | 40 | 4 | 12 | c | false | <90% | 885 | ||
| NM_152618 | BBS12 | 392 | 410 | G | G | A | C | A | A | C | U | U | C | u | C | a | A | U | G | A | A | g | 23 | 3 | 10 | false | <90% | 3260 | |||
| NM_033393 | KIAA1727 | 6247 | 6265 | G | G | A | C | A | A | C | U | U | C | u | C | U | A | U | G | c | A | u | 10 | 3 | 10 | c | false | <90% | 6480 | ||
| NM_003030 | SHOX2 | 1777 | 1795 | u | u | u | C | A | u | C | U | U | C | A | C | U | A | U | G | A | A | A | 3 | 4 | 13 | bc | false | <90% | 2781 | ||
| NM_006884 | SHOX2 | 2131 | 2149 | u | u | u | C | A | u | C | U | U | C | A | C | U | A | U | G | A | A | A | 3 | 4 | 13 | bc | false | <90% | 3135 | ||
| XM_929706 | LOC653781 | 147 | 165 | G | G | A | C | g | A | C | U | c | C | A | C | U | A | U | G | A | A | g | -16 | 3 | 9 | bc | false | <90% | 3826 | ||
| XM_928585 | LOC653269 | 199 | 217 | G | G | A | C | g | A | C | U | c | C | A | C | U | A | U | G | A | A | g | -16 | 3 | 9 | bc | false | <90% | 3989 | ||
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_003870 | IQGAP1 | 5253 | 5271 | U | U | U | C | A | U | A | G | U | G | A | A | a | U | U | G | U | g | u | 81 | 3 | 12 | false | <90% | 7219 | |||
| NM_145102 | ZKSCAN5 | 197 | 215 | U | U | U | C | A | U | A | G | U | G | A | A | G | g | U | G | g | a | a | 49 | 4 | 13 | c | false | <90% | 4234 | ||
| NM_014569 | ZKSCAN5 | 324 | 342 | U | U | U | C | A | U | A | G | U | G | A | A | G | g | U | G | g | a | a | 49 | 4 | 13 | c | false | <90% | 4361 | ||
| NM_002539 | ODC1 | 729 | 747 | U | U | U | g | A | U | A | G | U | G | A | A | G | U | U | G | a | g | u | 32 | 4 | 12 | c | false | <90% | 2062 | ||
| NM_001040110 | NRF1 | 3324 | 3342 | c | g | U | C | A | U | u | G | U | G | A | A | G | U | U | G | U | C | C | 20 | 3 | 12 | bc | false | <90% | 3523 | ||
| NM_005011 | NRF1 | 3341 | 3359 | c | g | U | C | A | U | u | G | U | G | A | A | G | U | U | G | U | C | C | 20 | 3 | 12 | bc | false | <90% | 3540 | ||
| NM_181521 | CMTM4 | 4725 | 4743 | U | U | U | C | c | U | A | G | U | G | A | A | G | U | U | G | c | a | g | 17 | 4 | 11 | c | false | <90% | 8133 | ||
| XM_001127181 | LOC728005 | 485 | 503 | g | U | c | C | A | c | A | G | U | G | A | A | G | U | U | G | U | C | C | 15 | 3 | 13 | bc | false | <90% | 3293 | ||
| XM_001132582 | LOC729092 | 487 | 505 | g | U | c | C | A | c | A | G | U | G | A | A | G | U | U | G | U | C | C | 15 | 3 | 13 | bc | false | <90% | 3295 | ||
| XM_001127140 | LOC728005 | 4497 | 4515 | g | U | c | C | A | c | A | G | U | G | A | A | G | U | U | G | U | C | C | 15 | 3 | 13 | bc | false | <90% | 7115 | ||
| NM_015634 | KIAA1279 | 1352 | 1370 | g | a | c | C | A | U | A | u | U | G | A | A | G | U | U | G | U | C | C | 4 | 4 | 11 | bc | false | <90% | 2542 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 946
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