Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
26 hits were found for UCGAAUUGUUUUAAUAUUA (16 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_015553 | PIP3-E | 2349 | 2367 | c | u | G | A | A | U | U | G | U | U | U | U | A | A | U | A | U | c | u | 78 | 4 | 15 | ac | false | <90% | 6687 | ||
| NR_002723 | GABPAP | 49359 | 49377 | a | u | a | A | A | U | U | G | U | U | U | U | A | A | U | A | U | U | A | 67 | 3 | 16 | bc | false | <90% | 194142 | ||
| XM_057296 | LRRC58 | 5410 | 5428 | g | u | G | A | A | U | U | G | U | U | U | U | A | A | a | A | U | U | A | 61 | 3 | 12 | c | false | <90% | 8099 | ||
| XM_938862 | LRRC58 | 5411 | 5429 | g | u | G | A | A | U | U | G | U | U | U | U | A | A | a | A | U | U | A | 61 | 3 | 12 | c | false | <90% | 8100 | ||
| NM_177948 | ARMCX3 | 2341 | 2359 | g | a | G | A | A | U | U | G | U | U | U | g | A | A | U | A | U | U | A | 52 | 3 | 9 | false | <90% | 3318 | |||
| NM_177947 | ARMCX3 | 2390 | 2408 | g | a | G | A | A | U | U | G | U | U | U | g | A | A | U | A | U | U | A | 52 | 3 | 9 | false | <90% | 3367 | |||
| NM_016607 | ARMCX3 | 2418 | 2436 | g | a | G | A | A | U | U | G | U | U | U | g | A | A | U | A | U | U | A | 52 | 3 | 9 | false | <90% | 3395 | |||
| NR_003266 | LOC220729 | 7145 | 7163 | a | u | G | g | A | U | U | G | U | U | U | U | A | A | U | A | U | U | A | 49 | 3 | 15 | bc | false | <90% | 15309 | ||
| NR_003264 | SDHALP1 | 7135 | 7153 | a | u | G | g | A | U | U | G | U | U | U | U | A | A | U | A | U | U | A | 49 | 3 | 15 | bc | false | <90% | 30398 | ||
| NR_000034 | TMEM185B | 1729 | 1747 | U | C | G | A | A | U | U | G | U | U | U | U | A | g | U | A | g | g | u | 49 | 4 | 13 | c | false | <90% | 2131 | ||
| NM_001609 | ACADSB | 5846 | 5864 | U | C | G | g | A | U | U | G | U | U | U | U | A | A | U | g | U | U | A | 37 | 2 | 11 | c | false | <90% | 5941 | ||
| NM_024090 | ELOVL6 | 2881 | 2899 | U | C | G | A | A | U | U | a | U | U | U | U | u | A | U | A | U | U | A | 27 | 2 | 7 | false | <90% | 3045 | |||
| NM_152787 | MAP3K7IP3 | 6150 | 6168 | U | u | G | A | A | U | U | a | U | U | U | U | A | A | U | A | U | U | g | 21 | 3 | 10 | bc | false | <90% | 6798 | ||
| NM_018247 | TMEM30A | 2435 | 2453 | a | u | G | A | A | U | U | a | U | U | U | U | A | A | U | A | U | U | c | 19 | 4 | 10 | bc | false | <90% | 4410 | ||
| NM_153235 | TXLNB | 4393 | 4411 | g | g | G | A | A | U | U | a | U | U | U | U | A | A | U | A | U | U | c | 19 | 4 | 10 | bc | false | <90% | 4647 | ||
| NM_052847 | GNG7 | 4081 | 4099 | U | C | G | c | A | g | U | G | U | U | U | U | A | A | U | A | U | U | g | -5 | 3 | 12 | bc | false | <90% | 4175 | ||
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_018981 | DNAJC10 | 3092 | 3110 | a | A | A | U | A | U | U | A | A | A | A | C | g | A | U | U | C | u | u | 79 | 4 | 11 | false | <90% | 4193 | |||
| NM_006017 | PROM1 | 2062 | 2080 | a | A | c | U | A | U | U | A | A | A | A | C | A | A | U | U | C | a | c | 70 | 4 | 14 | c | false | <90% | 3794 | ||
| NM_016156 | MTMR2 | 2401 | 2419 | U | A | A | U | A | U | U | A | A | A | A | C | c | A | U | U | u | u | A | 63 | 3 | 12 | false | <90% | 4493 | |||
| NM_201281 | MTMR2 | 2473 | 2491 | U | A | A | U | A | U | U | A | A | A | A | C | c | A | U | U | u | u | A | 63 | 3 | 12 | false | <90% | 4565 | |||
| NM_201278 | MTMR2 | 2596 | 2614 | U | A | A | U | A | U | U | A | A | A | A | C | c | A | U | U | u | u | A | 63 | 3 | 12 | false | <90% | 4688 | |||
| NM_145176 | SLC2A12 | 2672 | 2690 | a | A | A | U | A | U | U | A | A | A | A | u | A | A | U | U | C | c | A | 61 | 3 | 10 | false | <90% | 5599 | |||
| NM_021114 | SPINK2 | 288 | 306 | U | A | A | U | A | U | U | A | A | A | A | u | c | A | U | U | C | G | A | 55 | 2 | 11 | false | <90% | 591 | |||
| NM_052923 | ZNF452 | 4853 | 4871 | U | A | A | U | A | U | U | A | A | A | A | C | A | u | U | U | g | a | u | 49 | 4 | 13 | c | false | <90% | 4895 | ||
| NM_004725 | BUB3 | 1151 | 1169 | U | g | A | U | A | a | U | A | A | A | A | C | A | A | U | U | C | G | u | 20 | 3 | 12 | bc | false | <90% | 2659 | ||
| NM_152737 | RNF182 | 2113 | 2131 | g | A | A | U | c | U | U | A | u | A | A | C | A | A | U | U | C | G | A | -13 | 3 | 10 | bc | false | <90% | 3317 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 322
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