Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
34 hits were found for CAGUGAUAAAGGUAAAGAA (16 guide strand hits and 18 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_031407 | HUWE1 | 8112 | 8130 | a | A | c | U | G | A | U | A | A | A | G | G | c | A | A | A | G | A | A | 68 | 3 | 9 | false | <90% | 13671 | |||
| NM_012414 | RAB3GAP2 | 391 | 409 | u | A | G | U | G | A | U | A | A | A | G | G | a | A | A | g | G | A | A | 61 | 3 | 11 | false | <90% | 5129 | |||
| NM_145036 | CCDC46 | 1882 | 1900 | a | c | u | U | G | A | U | A | A | A | G | G | a | A | A | A | G | A | A | 56 | 4 | 9 | false | <90% | 3511 | |||
| NM_170721 | MSI2 | 1249 | 1267 | C | A | G | U | G | A | U | A | A | A | G | G | U | g | A | A | c | A | c | 51 | 3 | 13 | c | false | <90% | 2151 | ||
| NM_015578 | LSM14A | 2859 | 2877 | u | A | G | U | G | A | U | A | A | A | G | a | U | A | u | A | G | A | A | 39 | 3 | 10 | false | <90% | 3389 | |||
| NM_033044 | MACF1 | 4517 | 4535 | a | A | G | U | G | A | a | A | A | A | G | G | g | A | A | A | G | A | A | 21 | 3 | 6 | false | <90% | 19271 | |||
| NM_145695 | DGKB | 1184 | 1202 | C | A | G | U | G | A | a | A | A | A | G | G | a | A | A | A | G | A | g | 18 | 3 | 6 | false | <90% | 3172 | |||
| NM_004080 | DGKB | 1184 | 1202 | C | A | G | U | G | A | a | A | A | A | G | G | a | A | A | A | G | A | g | 18 | 3 | 6 | false | <90% | 3926 | |||
| NM_014258 | SYCP2 | 556 | 574 | C | A | G | U | G | A | U | g | A | A | G | G | U | A | A | A | a | A | A | 14 | 2 | 8 | c | false | <90% | 5497 | ||
| NM_144777 | SCEL | 861 | 879 | a | A | G | U | G | A | c | A | A | A | G | G | U | g | A | A | G | A | A | 12 | 3 | 6 | c | false | <90% | 2441 | ||
| NM_174910 | TCTE3 | 285 | 303 | u | g | c | U | G | A | U | A | u | A | G | G | U | A | A | A | G | A | A | 6 | 4 | 10 | bc | false | <90% | 747 | ||
| NM_015360 | SKIV2L2 | 2198 | 2216 | g | u | u | U | G | g | U | A | A | A | G | G | U | A | A | A | G | A | A | 3 | 4 | 13 | bc | false | <90% | 3582 | ||
| XM_940791 | LOC651610 | 5595 | 5613 | g | A | G | U | G | A | a | A | A | A | a | G | U | A | A | A | G | A | A | -29 | 3 | 8 | c | false | <90% | 8799 | ||
| NM_138292 | ATM | 2182 | 2200 | g | A | G | U | G | A | a | A | A | A | a | G | U | A | A | A | G | A | A | -29 | 3 | 8 | c | false | <90% | 8977 | ||
| NM_000051 | ATM | 6352 | 6370 | g | A | G | U | G | A | a | A | A | A | a | G | U | A | A | A | G | A | A | -29 | 3 | 8 | c | false | <90% | 13147 | ||
| NM_198476 | C19orf54 | 2372 | 2390 | C | A | G | U | G | A | U | c | A | g | G | G | U | A | A | A | G | A | g | -49 | 3 | 8 | bc | false | <90% | 2672 | ||
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_031889 | ENAM | 4214 | 4232 | c | U | C | U | U | U | A | C | C | U | U | U | A | U | C | A | u | U | u | 69 | 3 | 15 | ac | false | <90% | 5674 | ||
| NM_024644 | C14orf169 | 2124 | 2142 | a | c | a | U | U | U | A | C | C | U | U | U | A | U | C | A | C | U | G | 67 | 3 | 16 | bc | false | <90% | 2463 | ||
| NM_016123 | IRAK4 | 1512 | 1530 | U | U | C | U | U | U | A | C | C | U | U | U | A | a | C | A | a | g | G | 54 | 3 | 13 | c | false | <90% | 2817 | ||
| NM_019590 | KIAA1217 | 1214 | 1232 | a | U | C | c | U | U | A | C | C | U | U | U | A | U | C | A | C | g | a | 53 | 4 | 13 | c | false | <90% | 7385 | ||
| NR_003135 | CEP170L | 42304 | 42322 | U | U | u | U | U | U | A | C | C | U | U | U | A | U | C | A | g | a | a | 49 | 4 | 13 | c | false | <90% | 90477 | ||
| NM_001039937 | INTS6 | 3638 | 3656 | a | c | C | U | U | U | u | C | C | U | U | U | A | U | C | A | C | U | a | 15 | 4 | 11 | bc | false | <90% | 6973 | ||
| NM_012141 | INTS6 | 4130 | 4148 | a | c | C | U | U | U | u | C | C | U | U | U | A | U | C | A | C | U | a | 15 | 4 | 11 | bc | false | <90% | 7465 | ||
| NM_032160 | DSEL | 957 | 975 | U | U | u | U | U | U | A | C | C | U | g | U | A | U | C | A | C | U | u | 14 | 3 | 7 | c | false | <90% | 9281 | ||
| NM_001942 | DSG1 | 4153 | 4171 | g | U | C | U | U | U | c | C | C | U | U | U | A | c | C | A | C | U | G | 12 | 3 | 6 | c | false | <90% | 5447 | ||
| NM_000075 | CDK4 | 1207 | 1225 | a | U | C | U | U | U | g | C | C | U | U | U | A | U | C | u | C | U | G | 5 | 3 | 8 | c | false | <90% | 1474 | ||
| NM_006391 | IPO7 | 551 | 569 | U | U | C | U | U | U | g | C | C | U | U | U | A | U | C | A | g | c | u | 2 | 4 | 9 | c | false | <90% | 3557 | ||
| NM_024986 | FLJ12331 | 953 | 971 | U | U | C | U | U | c | A | u | C | U | U | U | A | U | C | A | C | U | c | -30 | 3 | 10 | bc | false | <90% | 2057 | ||
| XR_015163 | LOC730488 | 766 | 784 | U | U | C | U | U | U | u | C | C | a | U | U | A | U | C | A | C | U | G | -49 | 2 | 9 | bc | false | <90% | 2273 | ||
| XR_015304 | LOC728144 | 766 | 784 | U | U | C | U | U | U | u | C | C | a | U | U | A | U | C | A | C | U | G | -49 | 2 | 9 | bc | false | <90% | 2273 | ||
| XR_016763 | LOC399774 | 791 | 809 | U | U | C | U | U | U | u | C | C | a | U | U | A | U | C | A | C | U | G | -49 | 2 | 9 | bc | false | <90% | 2281 | ||
| XR_018540 | LOC399774 | 791 | 809 | U | U | C | U | U | U | u | C | C | a | U | U | A | U | C | A | C | U | G | -49 | 2 | 9 | bc | false | <90% | 2281 | ||
| NM_004705 | PRKRIR | 776 | 794 | U | U | C | U | U | U | u | C | C | a | U | U | A | U | C | A | C | U | G | -49 | 2 | 9 | bc | false | <90% | 3202 | ||
| XR_016912 | LOC644363 | 888 | 906 | g | U | C | U | U | U | u | C | C | a | U | U | A | U | C | A | C | U | G | -51 | 3 | 9 | bc | false | <90% | 3306 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2378
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