Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
38 hits were found for UGACUGCAGAGAGUGCUGA (26 guide strand hits and 12 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_001018112 | FANCA | 847 | 865 | g | u | A | C | U | G | C | A | G | A | G | A | a | U | G | C | U | G | A | 76 | 3 | 10 | false | <90% | 1673 | |||
| NM_000135 | FANCA | 847 | 865 | g | u | A | C | U | G | C | A | G | A | G | A | a | U | G | C | U | G | A | 76 | 3 | 10 | false | <90% | 5460 | |||
| NM_004781 | VAMP3 | 1629 | 1647 | c | a | A | C | U | G | C | A | G | A | G | A | a | U | G | C | U | G | u | 71 | 4 | 10 | false | <90% | 2225 | |||
| NR_003366 | ANKRD20B | 72625 | 72643 | g | a | A | C | U | G | C | A | G | A | G | A | G | a | G | C | U | G | u | 62 | 4 | 11 | c | false | <90% | 96524 | ||
| NM_017759 | FLJ20309 | 1300 | 1318 | c | G | A | C | U | G | C | A | G | A | G | A | c | U | G | g | U | G | A | 61 | 3 | 11 | false | <90% | 3765 | |||
| NM_002387 | MCC | 701 | 719 | g | a | A | C | U | G | C | A | G | A | G | g | G | U | G | C | U | G | A | 52 | 3 | 9 | false | <90% | 4181 | |||
| NM_002578 | PAK3 | 1494 | 1512 | U | G | u | C | U | G | C | A | G | A | G | A | G | U | G | C | c | u | g | 49 | 4 | 13 | c | false | <90% | 2516 | ||
| NM_014797 | ZBTB24 | 1895 | 1913 | U | G | A | C | U | G | C | A | G | A | G | A | G | U | u | C | c | c | A | 49 | 3 | 14 | c | false | <90% | 5597 | ||
| XM_936538 | FAT3 | 5714 | 5732 | U | G | A | C | U | G | C | A | G | A | G | A | G | U | c | C | c | G | u | 46 | 3 | 14 | c | false | <90% | 19162 | ||
| XM_926199 | FAT3 | 5714 | 5732 | U | G | A | C | U | G | C | A | G | A | G | A | G | U | c | C | c | G | u | 46 | 3 | 14 | c | false | <90% | 19163 | ||
| NM_025201 | PLEKHQ1 | 931 | 949 | c | u | g | C | U | G | C | A | G | A | G | A | G | U | G | C | a | G | A | 43 | 4 | 13 | c | false | <90% | 3675 | ||
| NM_206909 | PSD3 | 8754 | 8772 | g | c | c | C | U | G | C | A | G | A | G | A | G | U | G | g | U | G | A | 40 | 4 | 12 | c | false | <90% | 10091 | ||
| NM_015310 | PSD3 | 10350 | 10368 | g | c | c | C | U | G | C | A | G | A | G | A | G | U | G | g | U | G | A | 40 | 4 | 12 | c | false | <90% | 11687 | ||
| NM_199053 | FLJ12716 | 3037 | 3055 | a | G | A | C | U | G | g | A | G | A | G | A | G | U | G | C | U | a | g | 24 | 4 | 10 | c | false | <90% | 4442 | ||
| NM_021942 | FLJ12716 | 3037 | 3055 | a | G | A | C | U | G | g | A | G | A | G | A | G | U | G | C | U | a | g | 24 | 4 | 10 | c | false | <90% | 4561 | ||
| NM_025228 | TRAF3IP3 | 1086 | 1104 | U | c | A | C | U | G | C | A | G | A | a | A | G | U | G | C | U | G | g | 22 | 3 | 8 | c | false | <90% | 2058 | ||
| NM_018028 | SAMD4B | 1345 | 1363 | c | u | A | C | U | G | C | A | G | A | a | A | G | U | G | C | U | G | g | 20 | 4 | 8 | c | false | <90% | 4543 | ||
| NM_152850 | PIGO | 2066 | 2084 | U | G | g | C | U | a | C | A | G | A | G | A | G | U | G | C | U | G | g | 12 | 3 | 12 | bc | false | <90% | 2459 | ||
| NM_032634 | PIGO | 3690 | 3708 | U | G | g | C | U | a | C | A | G | A | G | A | G | U | G | C | U | G | g | 12 | 3 | 12 | bc | false | <90% | 4076 | ||
| NM_021871 | FGA | 111 | 129 | g | G | A | C | U | G | C | A | G | A | u | A | G | U | G | g | U | G | A | 10 | 3 | 9 | c | false | <90% | 2210 | ||
| NM_000508 | FGA | 111 | 129 | g | G | A | C | U | G | C | A | G | A | u | A | G | U | G | g | U | G | A | 10 | 3 | 9 | c | false | <90% | 3655 | ||
| XM_929714 | LOC646762 | 1469 | 1487 | U | G | A | C | U | G | g | A | G | A | G | A | G | a | G | C | U | G | g | 9 | 3 | 6 | c | false | <90% | 4090 | ||
| XM_938418 | LOC646762 | 1469 | 1487 | U | G | A | C | U | G | g | A | G | A | G | A | G | a | G | C | U | G | g | 9 | 3 | 6 | c | false | <90% | 4090 | ||
| XM_935722 | LOC646762 | 1469 | 1487 | U | G | A | C | U | G | g | A | G | A | G | A | G | a | G | C | U | G | g | 9 | 3 | 6 | c | false | <90% | 4090 | ||
| NM_014026 | DCPS | 471 | 489 | a | G | A | C | U | G | C | A | G | A | a | g | G | U | G | C | U | G | A | 2 | 3 | 9 | false | <90% | 1508 | |||
| NR_002723 | GABPAP | 98606 | 98624 | U | G | A | C | U | c | C | A | G | A | a | A | G | U | G | C | U | G | c | -29 | 3 | 7 | c | false | <90% | 194142 | ||
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_004924 | ACTN4 | 2888 | 2906 | a | a | A | G | C | A | C | U | C | U | C | U | G | C | A | G | U | C | c | 81 | 3 | 16 | abc | false | <90% | 3893 | ||
| NM_018941 | CLN8 | 3130 | 3148 | g | C | A | G | C | A | C | U | C | U | C | U | G | C | A | G | c | C | g | 69 | 3 | 15 | ac | false | <90% | 4817 | ||
| NM_006836 | GCN1L1 | 280 | 298 | U | C | u | a | C | A | C | U | C | U | C | U | G | C | A | G | U | C | u | 38 | 3 | 14 | bc | false | <90% | 8699 | ||
| NM_018593 | SLC16A10 | 1634 | 1652 | c | C | A | G | a | A | C | U | C | U | C | U | G | C | u | G | U | C | A | 21 | 3 | 9 | c | false | <90% | 2488 | ||
| XM_938321 | LOC649259 | 529 | 547 | g | C | A | G | C | A | C | U | u | U | C | U | G | g | A | G | U | C | A | 18 | 3 | 7 | c | false | <90% | 864 | ||
| XR_016672 | LOC441238 | 877 | 895 | g | C | A | G | C | A | C | U | u | U | C | U | G | g | A | G | U | C | A | 18 | 3 | 7 | c | false | <90% | 1493 | ||
| NM_005923 | MAP3K5 | 929 | 947 | c | u | c | G | g | A | C | U | C | U | C | U | G | C | A | G | U | C | A | 15 | 4 | 14 | bc | false | <90% | 5215 | ||
| NM_018008 | FEZF2 | 1078 | 1096 | c | C | A | G | C | A | C | g | C | U | C | U | G | C | A | G | g | C | A | 12 | 3 | 8 | c | false | <90% | 1919 | ||
| XM_001126647 | MLKL | 376 | 394 | g | C | A | G | C | A | u | U | C | U | C | U | G | C | A | G | g | C | A | 8 | 3 | 9 | c | false | <90% | 1832 | ||
| NM_152649 | MLKL | 80 | 98 | g | C | A | G | C | A | u | U | C | U | C | U | G | C | A | G | g | C | A | 8 | 3 | 9 | c | false | <90% | 2496 | ||
| NM_014686 | KIAA0355 | 3786 | 3804 | g | C | A | c | C | A | C | U | C | U | a | U | G | C | A | G | U | C | A | 0 | 3 | 8 | c | false | <90% | 6639 | ||
| XR_019099 | LOC651419 | 854 | 872 | U | C | A | G | C | A | C | g | a | U | C | U | G | C | A | G | U | C | c | -27 | 3 | 9 | bc | false | <90% | 1259 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1901
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