Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
25 hits were found for CAUGGAGAGCACAACAUCA (18 guide strand hits and 7 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_002771 | PRSS3 | 230 | 248 | C | u | g | G | G | A | G | A | G | C | A | C | A | A | C | A | U | C | A | 69 | 2 | 16 | bc | false | <90% | 807 | ||
| NM_002769 | PRSS1 | 223 | 241 | C | u | g | G | G | A | G | A | G | C | A | C | A | A | C | A | U | C | g | 64 | 3 | 15 | bc | false | <90% | 800 | ||
| NM_002770 | PRSS2 | 223 | 241 | C | u | g | G | G | A | G | A | G | C | A | C | A | A | C | A | U | C | g | 64 | 3 | 15 | bc | false | <90% | 802 | ||
| NM_197962 | GLRX2 | 164 | 182 | g | A | U | G | G | A | G | A | G | C | A | a | u | A | C | A | U | C | A | 53 | 3 | 10 | false | <90% | 735 | |||
| NM_016066 | GLRX2 | 599 | 617 | g | A | U | G | G | A | G | A | G | C | A | a | u | A | C | A | U | C | A | 53 | 3 | 10 | false | <90% | 1170 | |||
| XR_015972 | LOC731540 | 1532 | 1550 | u | A | U | G | G | A | a | A | G | C | A | C | A | A | C | A | U | a | u | 24 | 4 | 10 | c | false | <90% | 1854 | ||
| XR_015968 | LOC729404 | 1532 | 1550 | u | A | U | G | G | A | a | A | G | C | A | C | A | A | C | A | U | a | u | 24 | 4 | 10 | c | false | <90% | 1854 | ||
| XR_015540 | LOC730942 | 1753 | 1771 | u | A | U | G | G | A | a | A | G | C | A | C | A | A | C | A | U | a | u | 24 | 4 | 10 | c | false | <90% | 2424 | ||
| XR_015401 | LOC728291 | 1753 | 1771 | u | A | U | G | G | A | a | A | G | C | A | C | A | A | C | A | U | a | u | 24 | 4 | 10 | c | false | <90% | 2424 | ||
| XR_019055 | LOC650978 | 1349 | 1367 | u | A | U | G | G | A | a | A | G | C | A | C | A | A | C | A | U | a | u | 24 | 4 | 10 | c | false | <90% | 2785 | ||
| XR_016174 | LOC642513 | 1349 | 1367 | u | A | U | G | G | A | a | A | G | C | A | C | A | A | C | A | U | a | u | 24 | 4 | 10 | c | false | <90% | 2785 | ||
| NM_017634 | KCTD9 | 1696 | 1714 | u | A | U | G | G | A | a | A | G | C | A | C | A | A | C | A | U | a | u | 24 | 4 | 10 | c | false | <90% | 3353 | ||
| NM_001007536 | AKR1CL1 | 1753 | 1771 | u | c | U | G | G | A | G | A | G | C | c | C | A | A | C | A | U | C | c | 20 | 4 | 8 | c | false | <90% | 2182 | ||
| NM_016094 | COMMD2 | 516 | 534 | a | A | U | G | G | A | G | A | u | C | A | C | A | A | C | A | c | C | A | 14 | 3 | 7 | c | false | <90% | 1441 | ||
| NM_030772 | GJA10 | 1467 | 1485 | g | A | U | G | G | A | G | A | G | a | A | C | A | A | C | A | U | g | A | 12 | 3 | 8 | c | false | <90% | 2331 | ||
| NM_152558 | IQCE | 1240 | 1258 | g | A | U | G | G | A | G | A | G | C | u | C | A | A | a | A | U | C | A | 11 | 3 | 9 | c | false | <90% | 3032 | ||
| NM_001447 | FAT2 | 3935 | 3953 | g | c | U | G | G | A | G | A | G | u | A | C | A | A | C | A | U | C | c | -1 | 4 | 8 | bc | false | <90% | 14536 | ||
| NM_015073 | SIPA1L3 | 200 | 218 | C | A | U | G | G | c | G | A | G | g | A | C | A | A | C | A | U | C | c | -51 | 3 | 8 | bc | false | <90% | 7984 | ||
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_000959 | PTGFR | 4254 | 4272 | g | u | A | U | G | U | U | G | U | G | C | U | C | U | u | C | A | U | a | 56 | 4 | 12 | c | false | <90% | 5360 | ||
| NM_001039585 | PTGFR | 4325 | 4343 | g | u | A | U | G | U | U | G | U | G | C | U | C | U | u | C | A | U | a | 56 | 4 | 12 | c | false | <90% | 5431 | ||
| NM_015079 | TBC1D2B | 1806 | 1824 | a | G | A | U | G | a | U | G | U | G | C | U | C | U | C | C | A | g | a | 27 | 4 | 11 | c | false | <90% | 5876 | ||
| NM_002312 | LIG4 | 43 | 61 | U | G | A | U | G | c | U | G | U | G | C | U | C | U | u | C | A | U | c | 7 | 3 | 8 | c | false | <90% | 4115 | ||
| NM_006825 | CKAP4 | 1337 | 1355 | g | G | A | U | G | g | g | G | U | G | C | U | C | U | C | C | A | U | G | -31 | 3 | 12 | bc | false | <90% | 2913 | ||
| NM_173054 | RELN | 10572 | 10590 | U | G | A | U | G | U | g | u | U | G | C | U | C | U | C | C | A | U | u | -33 | 3 | 10 | bc | false | <90% | 11558 | ||
| NM_005045 | RELN | 10578 | 10596 | U | G | A | U | G | U | g | u | U | G | C | U | C | U | C | C | A | U | u | -33 | 3 | 10 | bc | false | <90% | 11564 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2457
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