Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
24 hits were found for ACUGCAGAGAGUGCUGAUA (16 guide strand hits and 8 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_206909 | PSD3 | 8756 | 8774 | c | C | U | G | C | A | G | A | G | A | G | U | G | g | U | G | A | U | A | 78 | 2 | 12 | c | false | <90% | 10091 | ||
NM_015310 | PSD3 | 10352 | 10370 | c | C | U | G | C | A | G | A | G | A | G | U | G | g | U | G | A | U | A | 78 | 2 | 12 | c | false | <90% | 11687 | ||
NM_002649 | PIK3CG | 5289 | 5307 | A | C | U | G | C | A | G | A | G | A | G | U | c | a | U | G | A | U | c | 65 | 3 | 12 | false | <90% | 5379 | |||
NM_025201 | PLEKHQ1 | 933 | 951 | g | C | U | G | C | A | G | A | G | A | G | U | G | C | a | G | A | a | c | 65 | 4 | 13 | c | false | <90% | 3675 | ||
NM_032809 | FAM73B | 2916 | 2934 | c | C | U | G | C | A | G | A | G | A | G | U | c | C | U | G | u | U | A | 64 | 3 | 11 | false | <90% | 3597 | |||
NM_018212 | ENAH | 2556 | 2574 | u | u | U | G | C | A | G | A | G | A | G | U | G | C | U | G | g | U | A | 63 | 3 | 14 | ac | false | <90% | 13109 | ||
NM_001008493 | ENAH | 2619 | 2637 | u | u | U | G | C | A | G | A | G | A | G | U | G | C | U | G | g | U | A | 63 | 3 | 14 | ac | false | <90% | 13172 | ||
NM_015599 | PGM3 | 343 | 361 | u | a | U | G | C | A | G | A | G | A | G | U | G | C | U | u | A | U | u | 55 | 4 | 13 | c | false | <90% | 2013 | ||
NR_003366 | ANKRD20B | 72627 | 72645 | A | C | U | G | C | A | G | A | G | A | G | a | G | C | U | G | u | g | A | 40 | 3 | 11 | false | <90% | 96524 | |||
NM_001018112 | FANCA | 849 | 867 | A | C | U | G | C | A | G | A | G | A | a | U | G | C | U | G | A | U | u | 33 | 2 | 10 | c | false | <90% | 1673 | ||
NM_000135 | FANCA | 849 | 867 | A | C | U | G | C | A | G | A | G | A | a | U | G | C | U | G | A | U | u | 33 | 2 | 10 | c | false | <90% | 5460 | ||
NM_002387 | MCC | 703 | 721 | A | C | U | G | C | A | G | A | G | g | G | U | G | C | U | G | A | c | A | 14 | 2 | 9 | c | false | <90% | 4181 | ||
NM_004781 | VAMP3 | 1631 | 1649 | A | C | U | G | C | A | G | A | G | A | a | U | G | C | U | G | u | U | g | 10 | 3 | 10 | c | false | <90% | 2225 | ||
NM_025228 | TRAF3IP3 | 1088 | 1106 | A | C | U | G | C | A | G | A | a | A | G | U | G | C | U | G | g | a | g | 8 | 4 | 8 | c | false | <90% | 2058 | ||
NM_018028 | SAMD4B | 1347 | 1365 | A | C | U | G | C | A | G | A | a | A | G | U | G | C | U | G | g | c | c | 8 | 4 | 8 | c | false | <90% | 4543 | ||
NM_014680 | KIAA0100 | 4291 | 4309 | A | C | U | G | a | A | G | A | G | A | a | U | G | C | U | G | A | U | c | -17 | 3 | 7 | c | false | <90% | 7456 |
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_018211 | RAVER2 | 707 | 725 | c | A | U | C | A | G | C | A | C | U | C | U | u | U | G | C | A | c | a | 79 | 4 | 11 | false | <90% | 4352 | |||
NM_018941 | CLN8 | 3130 | 3148 | a | g | g | C | A | G | C | A | C | U | C | U | C | U | G | C | A | G | c | 62 | 4 | 15 | bc | false | <90% | 4817 | ||
NM_004924 | ACTN4 | 2889 | 2907 | g | c | a | a | A | G | C | A | C | U | C | U | C | U | G | C | A | G | U | 30 | 4 | 15 | bc | false | <90% | 3893 | ||
NM_172376 | KCNH5 | 941 | 959 | a | A | U | C | A | G | C | A | g | U | C | U | C | U | u | C | A | G | U | 13 | 3 | 7 | c | false | <90% | 2490 | ||
NM_172375 | KCNH5 | 998 | 1016 | a | A | U | C | A | G | C | A | g | U | C | U | C | U | u | C | A | G | U | 13 | 3 | 7 | c | false | <90% | 3118 | ||
NM_139318 | KCNH5 | 998 | 1016 | a | A | U | C | A | G | C | A | g | U | C | U | C | U | u | C | A | G | U | 13 | 3 | 7 | c | false | <90% | 3308 | ||
NM_013448 | BAZ1A | 2120 | 2138 | a | A | U | C | u | G | C | A | C | U | g | U | C | U | G | C | A | G | U | -14 | 3 | 8 | c | false | <90% | 6031 | ||
NM_012229 | NT5C2 | 2002 | 2020 | U | A | U | C | u | G | u | A | C | U | C | U | C | U | G | C | A | G | a | -22 | 3 | 11 | bc | false | <90% | 3364 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3210
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