Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
32 hits were found for GGAAUCAAGAAUAAAGACU (19 guide strand hits and 13 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_007292 | ACOX1 | 4340 | 4358 | a | u | A | A | U | C | A | A | G | A | A | U | A | A | A | G | A | u | a | 78 | 4 | 15 | ac | false | <90% | 7514 | ||
| NM_004035 | ACOX1 | 4340 | 4358 | a | u | A | A | U | C | A | A | G | A | A | U | A | A | A | G | A | u | a | 78 | 4 | 15 | ac | false | <90% | 7514 | ||
| NM_018222 | PARVA | 3632 | 3650 | G | G | A | A | U | C | A | A | G | A | A | U | A | A | A | u | A | a | a | 66 | 3 | 15 | c | false | <90% | 4091 | ||
| NM_004063 | CDH17 | 3654 | 3672 | c | a | A | A | U | C | A | A | G | A | A | U | A | A | A | c | A | C | U | 60 | 3 | 13 | c | false | <90% | 3697 | ||
| XM_943502 | LOC646576 | 601 | 619 | G | G | A | A | U | C | A | A | G | A | A | U | c | A | A | u | A | C | a | 58 | 3 | 12 | false | <90% | 1368 | |||
| XM_933718 | LOC646576 | 601 | 619 | G | G | A | A | U | C | A | A | G | A | A | U | c | A | A | u | A | C | a | 58 | 3 | 12 | false | <90% | 1368 | |||
| NM_005239 | ETS2 | 209 | 227 | G | G | A | A | U | C | A | A | G | A | A | U | A | u | g | G | A | C | c | 50 | 3 | 13 | c | false | <90% | 3672 | ||
| NM_002221 | ITPKB | 2479 | 2497 | G | G | A | A | U | C | A | A | G | A | A | a | g | A | A | G | A | C | g | 50 | 3 | 11 | false | <90% | 5875 | |||
| NM_001126 | ADSS | 1743 | 1761 | a | a | A | u | U | C | A | A | G | A | A | U | A | A | A | G | A | C | a | 44 | 4 | 14 | bc | false | <90% | 2775 | ||
| NM_001684 | ATP2B4 | 2721 | 2739 | c | c | A | u | U | C | A | A | G | A | A | U | A | A | A | G | A | C | a | 44 | 4 | 14 | bc | false | <90% | 8733 | ||
| NM_001001396 | ATP2B4 | 2721 | 2739 | c | c | A | u | U | C | A | A | G | A | A | U | A | A | A | G | A | C | a | 44 | 4 | 14 | bc | false | <90% | 8911 | ||
| NM_024345 | WDR32 | 2710 | 2728 | G | G | A | A | U | C | A | A | G | A | g | U | A | A | A | G | A | g | g | 31 | 3 | 10 | c | false | <90% | 7932 | ||
| NM_198996 | LIPI | 1587 | 1605 | a | G | A | A | U | C | A | A | a | A | A | U | A | A | A | G | A | a | a | 30 | 4 | 8 | c | false | <90% | 1636 | ||
| NM_005747 | ELA3A | 873 | 891 | u | G | A | A | U | a | A | A | G | A | A | U | A | A | A | G | A | u | c | 27 | 4 | 11 | c | false | <90% | 963 | ||
| NM_007352 | ELA3B | 969 | 987 | u | G | A | A | U | a | A | A | G | A | A | U | A | A | A | G | A | u | c | 27 | 4 | 11 | c | false | <90% | 1055 | ||
| NR_002789 | LOC168474 | 2239 | 2257 | a | u | A | A | U | C | A | A | u | A | A | U | A | A | A | G | A | C | U | 26 | 3 | 10 | bc | false | <90% | 4125 | ||
| NR_002451 | ABCA11 | 302 | 320 | G | a | A | A | U | C | A | u | G | A | A | U | A | A | A | G | A | C | c | 21 | 3 | 10 | bc | false | <90% | 1815 | ||
| NM_015569 | DNM3 | 6625 | 6643 | a | G | A | A | U | g | A | A | G | A | A | U | A | A | A | G | c | C | U | 11 | 3 | 10 | c | false | <90% | 7644 | ||
| NM_016308 | CMPK | 2333 | 2351 | u | G | A | A | g | C | A | A | G | A | g | U | A | A | A | G | A | C | U | -14 | 3 | 8 | c | false | <90% | 2836 | ||
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 | |||||||||||||
| XM_044434 | KIAA1458 | 3244 | 3262 | u | G | U | C | U | U | U | A | U | U | C | U | U | G | A | U | a | C | a | 69 | 3 | 15 | ac | false | <90% | 6472 | ||
| XM_941571 | KIAA1458 | 3244 | 3262 | u | G | U | C | U | U | U | A | U | U | C | U | U | G | A | U | a | C | a | 69 | 3 | 15 | ac | false | <90% | 6472 | ||
| NM_006805 | HNRPA0 | 1809 | 1827 | A | u | U | C | U | U | U | A | U | U | C | U | U | G | A | U | g | u | g | 57 | 4 | 14 | ac | false | <90% | 2983 | ||
| NM_005065 | SEL1L | 1822 | 1840 | A | G | c | C | U | U | U | A | U | U | C | U | U | G | A | U | c | a | g | 49 | 4 | 13 | c | false | <90% | 7885 | ||
| NM_003417 | ZNF264 | 4830 | 4848 | u | G | U | C | U | c | U | A | U | U | C | U | U | G | A | U | U | u | C | 32 | 3 | 11 | c | false | <90% | 12171 | ||
| NM_153456 | HS6ST3 | 5315 | 5333 | u | G | U | C | U | U | U | A | U | U | a | U | U | G | A | U | U | g | u | 29 | 4 | 9 | c | false | <90% | 7817 | ||
| XM_376679 | FLJ25778 | 6202 | 6220 | u | c | U | C | U | U | U | A | g | U | C | U | U | G | A | U | U | C | C | 26 | 3 | 10 | bc | false | <90% | 8672 | ||
| XM_379933 | FLJ25778 | 6202 | 6220 | u | c | U | C | U | U | U | A | g | U | C | U | U | G | A | U | U | C | C | 26 | 3 | 10 | bc | false | <90% | 8672 | ||
| XM_939098 | FLJ25778 | 6202 | 6220 | u | c | U | C | U | U | U | A | g | U | C | U | U | G | A | U | U | C | C | 26 | 3 | 10 | bc | false | <90% | 8672 | ||
| NR_002723 | GABPAP | 96806 | 96824 | c | u | U | C | U | U | U | A | U | U | a | U | U | G | A | U | U | C | u | 20 | 4 | 8 | c | false | <90% | 194142 | ||
| NM_030664 | PTER | 2473 | 2491 | A | G | U | C | a | U | U | A | U | U | C | U | U | G | A | U | g | a | a | 17 | 4 | 11 | c | false | <90% | 3755 | ||
| NM_001001484 | PTER | 2528 | 2546 | A | G | U | C | a | U | U | A | U | U | C | U | U | G | A | U | g | a | a | 17 | 4 | 11 | c | false | <90% | 3810 | ||
| NM_022828 | YTHDC2 | 2154 | 2172 | A | G | U | C | U | U | U | A | U | g | C | U | U | c | A | U | U | C | a | -7 | 3 | 9 | c | false | <90% | 6301 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1794
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