Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
18 hits were found for GUUAAAGGUCUUUGUAUUA (9 guide strand hits and 9 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_001017396 | ZNF2 | 2464 | 2482 | c | U | U | A | c | A | G | G | U | C | U | U | U | G | U | A | U | c | u | 38 | 4 | 12 | c | false | <90% | 3879 | ||
| NM_021088 | ZNF2 | 2536 | 2554 | c | U | U | A | c | A | G | G | U | C | U | U | U | G | U | A | U | c | u | 38 | 4 | 12 | c | false | <90% | 3951 | ||
| NM_015308 | FNBP4 | 3899 | 3917 | u | U | U | A | A | A | G | c | U | C | U | U | U | G | U | A | U | U | u | 30 | 3 | 10 | bc | false | <90% | 3995 | ||
| XM_001132660 | LOC728925 | 466 | 484 | u | U | U | A | A | A | G | a | U | C | U | U | U | G | U | A | U | g | c | 28 | 4 | 9 | c | false | <90% | 842 | ||
| XM_001133567 | LOC731553 | 466 | 484 | u | U | U | A | A | A | G | a | U | C | U | U | U | G | U | A | U | g | c | 28 | 4 | 9 | c | false | <90% | 842 | ||
| NM_144600 | C16orf63 | 1086 | 1104 | a | U | g | A | A | A | G | G | g | C | U | U | U | G | U | A | U | U | A | 18 | 3 | 10 | bc | false | <90% | 2250 | ||
| NM_014098 | PRDX3 | 1149 | 1167 | c | U | U | g | A | A | u | G | U | C | U | U | U | G | U | A | U | U | A | -5 | 3 | 12 | bc | false | <90% | 1537 | ||
| NM_006793 | PRDX3 | 1203 | 1221 | c | U | U | g | A | A | u | G | U | C | U | U | U | G | U | A | U | U | A | -5 | 3 | 12 | bc | false | <90% | 1591 | ||
| NM_014860 | SUPT7L | 1633 | 1651 | a | g | a | A | A | A | G | G | U | u | U | U | U | G | U | A | U | U | A | -15 | 4 | 9 | bc | false | <90% | 4261 | ||
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_006811 | SERINC3 | 2356 | 2374 | a | A | A | U | A | C | A | A | A | G | A | C | u | U | U | U | A | A | g | 82 | 3 | 11 | false | <90% | 2592 | |||
| NM_153020 | RBM24 | 263 | 281 | U | u | A | U | A | C | A | A | A | G | A | C | C | U | U | U | c | g | g | 57 | 4 | 14 | ac | false | <90% | 2369 | ||
| NM_032452 | JPH4 | 4337 | 4355 | a | A | A | U | A | C | A | A | A | G | A | a | a | U | U | U | A | A | C | 53 | 3 | 10 | false | <90% | 4396 | |||
| NM_015196 | KIAA0922 | 2293 | 2311 | U | A | u | U | A | C | A | A | A | G | A | a | C | U | U | U | A | A | a | 41 | 3 | 8 | false | <90% | 4980 | |||
| NM_174908 | CCDC50 | 820 | 838 | c | g | c | U | A | C | A | A | A | G | A | C | C | U | U | g | A | A | C | 40 | 4 | 12 | c | false | <90% | 1926 | ||
| NM_178335 | CCDC50 | 820 | 838 | c | g | c | U | A | C | A | A | A | G | A | C | C | U | U | g | A | A | C | 40 | 4 | 12 | c | false | <90% | 2454 | ||
| NM_006888 | CALM1 | 1524 | 1542 | c | A | A | U | A | a | A | A | A | G | A | C | C | a | U | U | A | A | C | 15 | 3 | 7 | c | false | <90% | 4201 | ||
| NM_018086 | FIGN | 2999 | 3017 | U | A | A | U | A | u | A | A | A | G | A | g | C | U | U | U | A | A | C | 2 | 2 | 7 | false | <90% | 4535 | |||
| NM_033427 | CTTNBP2 | 5148 | 5166 | a | g | A | U | A | C | A | A | A | u | A | C | C | U | U | U | A | A | a | -1 | 4 | 8 | bc | false | <90% | 5980 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1846
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