Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
29 hits were found for UUAUUAACACUGUUUUGAA (12 guide strand hits and 17 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_001005473 | PLCXD3 | 5638 | 5656 | U | U | A | U | U | A | A | C | A | C | U | u | U | U | U | U | G | u | u | 58 | 3 | 11 | false | <90% | 7739 | |||
| NM_003591 | CUL2 | 1268 | 1286 | U | U | A | U | c | A | A | C | A | C | U | G | U | U | U | U | G | A | A | 48 | 1 | 14 | bc | false | <90% | 2910 | ||
| NM_181839 | PKIA | 1105 | 1123 | U | U | A | U | U | u | A | C | A | C | U | G | U | U | U | U | G | u | A | 34 | 2 | 11 | c | false | <90% | 2055 | ||
| NM_006823 | PKIA | 1234 | 1252 | U | U | A | U | U | u | A | C | A | C | U | G | U | U | U | U | G | u | A | 34 | 2 | 11 | c | false | <90% | 2184 | ||
| NM_001005366 | FBXL10 | 5200 | 5218 | c | a | g | U | a | A | A | C | A | C | U | G | U | U | U | U | G | A | A | 15 | 4 | 14 | bc | false | <90% | 5236 | ||
| NM_032590 | FBXL10 | 5251 | 5269 | c | a | g | U | a | A | A | C | A | C | U | G | U | U | U | U | G | A | A | 15 | 4 | 14 | bc | false | <90% | 5287 | ||
| NM_014979 | SV2C | 1744 | 1762 | U | U | A | U | U | g | A | C | A | C | U | G | U | U | U | U | u | g | A | 10 | 3 | 10 | c | false | <90% | 2362 | ||
| NM_004289 | NFE2L3 | 2467 | 2485 | c | a | g | U | U | A | A | C | g | C | U | G | U | U | U | U | G | A | A | 6 | 4 | 10 | bc | false | <90% | 2864 | ||
| NM_002572 | PAFAH1B2 | 1067 | 1085 | U | U | A | U | U | A | u | C | A | C | U | G | U | U | U | U | c | u | u | 2 | 4 | 9 | c | false | <90% | 1191 | ||
| NM_181733 | COG5 | 3392 | 3410 | c | U | A | U | U | A | A | C | A | u | U | G | U | U | U | U | u | A | A | -8 | 3 | 8 | c | false | <90% | 3541 | ||
| NM_006348 | COG5 | 3455 | 3473 | c | U | A | U | U | A | A | C | A | u | U | G | U | U | U | U | u | A | A | -8 | 3 | 8 | c | false | <90% | 3604 | ||
| NM_005385 | NKTR | 3617 | 3635 | a | U | A | U | a | A | A | C | A | u | U | G | U | U | U | U | G | A | A | -36 | 3 | 9 | bc | false | <90% | 7312 | ||
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_057096 | CYP3A43 | 373 | 391 | a | U | C | A | A | A | A | C | A | G | U | G | U | U | A | g | U | g | A | 69 | 3 | 14 | c | false | <90% | 2001 | ||
| NM_057095 | CYP3A43 | 373 | 391 | a | U | C | A | A | A | A | C | A | G | U | G | U | U | A | g | U | g | A | 69 | 3 | 14 | c | false | <90% | 2164 | ||
| NM_022820 | CYP3A43 | 373 | 391 | a | U | C | A | A | A | A | C | A | G | U | G | U | U | A | g | U | g | A | 69 | 3 | 14 | c | false | <90% | 2167 | ||
| NM_144726 | RNF145 | 2983 | 3001 | a | U | C | A | A | A | A | C | A | G | U | G | U | U | A | A | a | u | u | 66 | 4 | 15 | ac | false | <90% | 3362 | ||
| XM_927593 | ATP10B | 5695 | 5713 | c | U | C | A | A | A | A | C | A | G | U | G | U | U | A | A | a | g | g | 66 | 4 | 15 | ac | false | <90% | 6896 | ||
| XM_940711 | ATP10B | 5695 | 5713 | c | U | C | A | A | A | A | C | A | G | U | G | U | U | A | A | a | g | g | 66 | 4 | 15 | ac | false | <90% | 6896 | ||
| NM_001017420 | ESCO2 | 195 | 213 | a | U | C | A | A | A | A | C | A | G | U | G | a | U | A | A | a | A | A | 64 | 3 | 11 | false | <90% | 3376 | |||
| NM_004543 | NEB | 1545 | 1563 | c | U | C | A | A | A | A | C | A | G | U | G | a | U | A | A | a | A | A | 64 | 3 | 11 | false | <90% | 20632 | |||
| NM_004508 | IDI1 | 1433 | 1451 | U | U | C | A | A | A | A | C | A | G | U | c | U | U | A | A | U | u | A | 63 | 2 | 11 | false | <90% | 2150 | |||
| NM_001018116 | LOC347273 | 2211 | 2229 | U | c | C | A | A | A | A | C | A | G | U | G | U | U | g | A | U | A | g | 58 | 3 | 12 | c | false | <90% | 2640 | ||
| NM_002267 | KPNA3 | 4303 | 4321 | U | U | C | A | A | A | A | C | A | G | U | G | U | U | u | A | a | A | A | 51 | 2 | 14 | c | false | <90% | 4471 | ||
| XM_001126109 | LOC727903 | 111 | 129 | U | U | C | A | A | A | A | C | A | G | c | G | a | U | A | A | U | A | A | 28 | 2 | 10 | false | <90% | 687 | |||
| NM_020346 | SLC17A6 | 3884 | 3902 | a | g | C | A | A | A | A | a | A | G | U | G | U | U | A | A | U | A | A | 24 | 3 | 11 | bc | false | <90% | 3946 | ||
| NM_003151 | STAT4 | 2735 | 2753 | a | a | g | A | A | A | c | C | A | G | U | G | U | U | A | A | U | A | A | 0 | 4 | 12 | bc | false | <90% | 2761 | ||
| XM_943460 | LOC648790 | 374 | 392 | a | U | u | u | u | A | A | C | A | G | U | G | U | U | A | A | U | A | A | -9 | 4 | 14 | bc | false | <90% | 663 | ||
| NM_001018058 | TFEC | 6345 | 6363 | a | a | g | A | A | A | A | C | A | u | U | G | U | U | A | A | U | A | A | -15 | 4 | 9 | bc | false | <90% | 6544 | ||
| NM_012252 | TFEC | 6432 | 6450 | a | a | g | A | A | A | A | C | A | u | U | G | U | U | A | A | U | A | A | -15 | 4 | 9 | bc | false | <90% | 6631 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4587
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