Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
16 hits were found for AGAGAUAUGAAGACACAAC (7 guide strand hits and 9 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_019591 | ZNF26 | 1422 | 1440 | u | u | c | a | A | U | A | U | G | A | A | G | A | C | A | C | A | A | C | 30 | 4 | 15 | bc | false | <90% | 3083 | ||
| NM_003126 | SPTA1 | 435 | 453 | A | G | A | G | c | U | A | U | G | A | A | G | A | C | c | C | A | A | C | 23 | 2 | 9 | c | false | <90% | 8017 | ||
| NM_005406 | ROCK1 | 1111 | 1129 | g | c | A | G | A | U | A | U | a | A | A | G | A | C | A | C | A | A | u | 21 | 4 | 9 | bc | false | <90% | 6650 | ||
| NM_004901 | ENTPD4 | 1172 | 1190 | A | G | A | G | A | U | A | c | G | A | A | G | A | C | A | g | A | A | u | 6 | 3 | 7 | c | false | <90% | 2329 | ||
| NM_194431 | RNASE4 | 721 | 739 | A | G | A | G | A | U | A | U | G | g | A | G | A | C | A | u | A | A | a | -13 | 3 | 9 | c | false | <90% | 1361 | ||
| NM_002937 | RNASE4 | 1165 | 1183 | A | G | A | G | A | U | A | U | G | g | A | G | A | C | A | u | A | A | a | -13 | 3 | 9 | c | false | <90% | 1805 | ||
| NM_194430 | RNASE4 | 1269 | 1287 | A | G | A | G | A | U | A | U | G | g | A | G | A | C | A | u | A | A | a | -13 | 3 | 9 | c | false | <90% | 1909 | ||
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_932717 | LOC643224 | 1468 | 1486 | u | U | U | G | U | G | U | C | U | U | C | A | c | A | U | C | U | C | c | 82 | 3 | 11 | false | <90% | 1494 | |||
| XR_015203 | LOC730613 | 1649 | 1667 | u | U | U | G | U | G | U | C | U | U | C | A | c | A | U | C | U | C | c | 82 | 3 | 11 | false | <90% | 1726 | |||
| XR_015241 | LOC728247 | 1649 | 1667 | u | U | U | G | U | G | U | C | U | U | C | A | c | A | U | C | U | C | c | 82 | 3 | 11 | false | <90% | 1726 | |||
| NM_001039768 | LCAP | 1069 | 1087 | u | c | U | G | U | G | U | C | U | U | C | A | U | A | U | C | U | C | a | 81 | 3 | 16 | abc | false | <90% | 1391 | ||
| XM_001131046 | TUBB6 | 1643 | 1661 | c | g | U | G | U | G | U | C | U | U | C | A | U | c | U | C | U | C | U | 67 | 3 | 11 | c | false | <90% | 1698 | ||
| NM_175921 | LOC285636 | 4268 | 4286 | u | U | U | G | U | G | U | C | U | U | C | A | a | A | U | u | U | C | U | 61 | 3 | 11 | false | <90% | 5250 | |||
| XR_018219 | LOC647997 | 26 | 44 | c | U | U | G | U | G | U | C | U | U | C | u | g | A | U | C | U | C | U | 53 | 3 | 10 | false | <90% | 2773 | |||
| XR_016964 | LOC391697 | 26 | 44 | c | U | U | G | U | G | U | C | U | U | C | u | g | A | U | C | U | C | U | 53 | 3 | 10 | false | <90% | 2773 | |||
| NM_133493 | CD109 | 8792 | 8810 | G | U | U | G | U | G | U | u | U | U | C | A | U | g | U | C | U | C | a | 13 | 3 | 7 | c | false | <90% | 9447 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1871
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)
Motif found in sense strand
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