Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
26 hits were found for UCUUCUCGAGGACUGGGGA (4 guide strand hits and 22 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_002271 | RANBP5 | 3442 | 3460 | a | C | U | U | C | U | g | G | A | G | G | A | C | U | G | u | G | G | A | 5 | 3 | 8 | c | false | <90% | 6019 | ||
NM_031917 | ANGPTL6 | 1233 | 1251 | U | C | U | c | C | U | g | G | A | G | G | A | C | U | G | G | G | G | g | -8 | 3 | 11 | bc | false | <90% | 1857 | ||
NM_001010855 | C17orf38 | 64 | 82 | g | C | U | U | C | U | C | u | g | G | G | A | C | U | G | G | G | G | A | -24 | 3 | 10 | bc | false | <90% | 3061 | ||
NM_014848 | SV2B | 1113 | 1131 | U | C | U | U | C | U | g | G | A | u | G | A | C | U | G | G | G | G | g | -54 | 3 | 8 | bc | false | <90% | 5311 |
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_945855 | USP22 | 338 | 356 | U | C | C | C | C | A | G | U | C | C | U | C | u | g | G | A | A | G | A | 70 | 2 | 12 | false | <90% | 6418 | |||
XM_042698 | USP22 | 338 | 356 | U | C | C | C | C | A | G | U | C | C | U | C | u | g | G | A | A | G | A | 70 | 2 | 12 | false | <90% | 6496 | |||
NM_052909 | KIAA1909 | 10548 | 10566 | g | C | C | C | C | A | G | U | C | C | U | C | G | A | G | A | g | c | c | 66 | 4 | 15 | ac | false | <90% | 11507 | ||
NM_139017 | IL31RA | 932 | 950 | g | C | C | C | C | A | G | U | C | C | U | a | G | A | G | A | A | a | A | 61 | 3 | 10 | false | <90% | 2393 | |||
NM_001037343 | CDKL5 | 1668 | 1686 | U | C | C | C | C | A | G | U | C | C | U | C | u | A | G | g | A | G | u | 58 | 3 | 12 | false | <90% | 3430 | |||
NM_003159 | CDKL5 | 1672 | 1690 | U | C | C | C | C | A | G | U | C | C | U | C | u | A | G | g | A | G | u | 58 | 3 | 12 | false | <90% | 3434 | |||
NM_182539 | MGC33600 | 1043 | 1061 | c | a | C | C | C | A | G | U | C | C | U | C | G | A | G | g | A | G | c | 55 | 4 | 13 | c | false | <90% | 1662 | ||
NM_001008783 | SLC35D3 | 1403 | 1421 | U | a | C | C | C | A | G | U | C | C | U | u | G | A | G | A | A | G | g | 49 | 3 | 9 | false | <90% | 2371 | |||
XM_001131392 | LOC731957 | 491 | 509 | a | C | C | C | a | A | G | U | C | C | U | C | G | A | G | A | A | G | g | 41 | 3 | 13 | bc | false | <90% | 735 | ||
NM_001079804 | GAA | 239 | 257 | U | C | C | C | C | A | G | U | C | C | U | g | G | A | G | g | A | G | A | 40 | 2 | 11 | false | <90% | 3517 | |||
NM_001079803 | GAA | 319 | 337 | U | C | C | C | C | A | G | U | C | C | U | g | G | A | G | g | A | G | A | 40 | 2 | 11 | false | <90% | 3597 | |||
NM_000152 | GAA | 504 | 522 | U | C | C | C | C | A | G | U | C | C | U | g | G | A | G | g | A | G | A | 40 | 2 | 11 | false | <90% | 3782 | |||
XM_001125678 | LOC730434 | 129 | 147 | U | C | C | C | C | A | G | U | C | C | U | u | G | A | G | c | A | G | g | 35 | 3 | 11 | false | <90% | 827 | |||
XM_001125691 | LOC727768 | 129 | 147 | U | C | C | C | C | A | G | U | C | C | U | u | G | A | G | c | A | G | g | 35 | 3 | 11 | false | <90% | 1642 | |||
XR_016522 | LOC643806 | 471 | 489 | a | C | C | a | C | A | G | U | C | C | U | g | G | A | G | A | A | G | A | 27 | 3 | 7 | false | <90% | 698 | |||
XM_001129341 | LOC731605 | 2487 | 2505 | c | u | C | C | C | A | G | U | u | C | U | C | G | A | G | A | A | G | A | 26 | 3 | 10 | bc | false | <90% | 2821 | ||
NM_001077441 | BCLAF1 | 2016 | 2034 | c | u | C | C | C | A | G | U | u | C | U | C | G | A | G | A | A | G | A | 26 | 3 | 10 | bc | false | <90% | 6758 | ||
NM_001077440 | BCLAF1 | 2529 | 2547 | c | u | C | C | C | A | G | U | u | C | U | C | G | A | G | A | A | G | A | 26 | 3 | 10 | bc | false | <90% | 7124 | ||
NM_014739 | BCLAF1 | 2535 | 2553 | c | u | C | C | C | A | G | U | u | C | U | C | G | A | G | A | A | G | A | 26 | 3 | 10 | bc | false | <90% | 7277 | ||
NM_020699 | GATAD2B | 5161 | 5179 | U | C | C | C | C | A | c | U | C | C | U | C | c | A | G | A | A | G | g | 18 | 3 | 6 | false | <90% | 5348 | |||
NM_022648 | TNS1 | 615 | 633 | a | C | C | C | C | A | G | c | C | C | U | g | G | A | G | A | A | G | A | 2 | 3 | 7 | false | <90% | 7261 | |||
NM_005558 | LAD1 | 764 | 782 | U | C | C | C | C | A | G | U | C | u | U | g | G | A | G | A | A | G | u | -21 | 3 | 9 | false | <90% | 2869 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3367
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