Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for GAAUCCAUAUGCUGUAUGU (6 guide strand hits and 10 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_138940 | CD200R1 | 752 | 770 | a | A | u | U | C | C | A | U | A | U | G | C | U | u | U | A | U | G | U | 58 | 3 | 10 | c | false | <90% | 956 | ||
| NM_138939 | CD200R1 | 821 | 839 | a | A | u | U | C | C | A | U | A | U | G | C | U | u | U | A | U | G | U | 58 | 3 | 10 | c | false | <90% | 1025 | ||
| NM_004262 | TMPRSS11D | 107 | 125 | G | A | A | U | C | C | A | U | A | U | G | u | a | G | U | A | U | G | U | 55 | 2 | 11 | false | <90% | 2800 | |||
| NM_005177 | ATP6V0A1 | 1801 | 1819 | u | c | A | U | C | C | A | U | A | U | G | C | U | G | U | u | U | G | g | 55 | 4 | 13 | c | false | <90% | 4187 | ||
| NM_002215 | ITIH1 | 533 | 551 | G | A | A | a | C | C | A | U | A | U | G | C | a | G | U | A | U | G | a | 47 | 3 | 8 | false | <90% | 2920 | |||
| NM_002526 | NT5E | 1410 | 1428 | G | A | A | U | C | C | A | U | g | U | G | g | U | G | U | A | U | G | a | 1 | 3 | 8 | false | <90% | 3547 | |||
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_005813 | PRKD3 | 3891 | 3909 | c | u | A | U | A | C | A | G | C | A | U | A | a | G | G | A | U | U | g | 71 | 4 | 10 | false | <90% | 5907 | |||
| NM_014970 | KIFAP3 | 2598 | 2616 | u | g | c | c | A | C | A | G | C | A | U | A | U | G | G | A | U | U | C | 30 | 4 | 15 | bc | false | <90% | 2997 | ||
| NM_001025068 | ARPP-21 | 2077 | 2095 | g | u | A | U | A | C | A | G | u | A | U | A | U | G | G | A | U | U | g | 21 | 4 | 9 | bc | false | <90% | 2409 | ||
| NM_198399 | ARPP-21 | 2068 | 2086 | g | u | A | U | A | C | A | G | u | A | U | A | U | G | G | A | U | U | g | 21 | 4 | 9 | bc | false | <90% | 2413 | ||
| NM_001025069 | ARPP-21 | 2086 | 2104 | g | u | A | U | A | C | A | G | u | A | U | A | U | G | G | A | U | U | g | 21 | 4 | 9 | bc | false | <90% | 2418 | ||
| NM_016226 | VPS29 | 796 | 814 | g | u | u | U | A | C | A | G | u | A | U | A | U | G | G | A | U | U | C | 6 | 4 | 10 | bc | false | <90% | 1089 | ||
| NM_057180 | VPS29 | 808 | 826 | g | u | u | U | A | C | A | G | u | A | U | A | U | G | G | A | U | U | C | 6 | 4 | 10 | bc | false | <90% | 1107 | ||
| NM_003991 | EDNRB | 1548 | 1566 | u | C | A | c | A | C | A | c | C | A | U | A | U | G | G | A | U | U | C | 0 | 3 | 11 | bc | false | <90% | 1578 | ||
| NM_000115 | EDNRB | 3328 | 3346 | u | C | A | c | A | C | A | c | C | A | U | A | U | G | G | A | U | U | C | 0 | 3 | 11 | bc | false | <90% | 4286 | ||
| NM_144711 | KLHL23 | 1697 | 1715 | A | C | A | U | c | C | A | G | a | A | U | A | U | G | G | A | U | U | g | -16 | 3 | 9 | bc | false | <90% | 2211 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1733
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