Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
27 hits were found for GGGACUUGAUACACAGAAU (19 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 | |||||||||||||
XR_018729 | LOC646954 | 681 | 699 | a | G | a | A | C | U | U | G | A | U | A | C | A | C | u | G | A | A | U | 53 | 3 | 11 | c | false | <90% | 1006 | ||
XR_017253 | LOC646954 | 681 | 699 | a | G | a | A | C | U | U | G | A | U | A | C | A | C | u | G | A | A | U | 53 | 3 | 11 | c | false | <90% | 1006 | ||
NM_006826 | YWHAQ | 722 | 740 | u | G | a | A | C | U | U | G | A | U | A | C | A | C | u | G | A | A | U | 53 | 3 | 11 | c | false | <90% | 2166 | ||
XM_497652 | LOC441872 | 129 | 147 | G | G | G | A | C | U | U | G | A | U | A | C | A | C | u | G | c | u | g | 44 | 4 | 14 | c | false | <90% | 390 | ||
XM_938420 | PRAMEF17 | 285 | 303 | G | G | G | A | C | U | U | G | A | U | A | C | A | C | u | G | c | u | g | 44 | 4 | 14 | c | false | <90% | 1461 | ||
XR_017926 | LOC391004 | 285 | 303 | G | G | G | A | C | U | U | G | A | U | A | C | A | C | u | G | c | u | g | 44 | 4 | 14 | c | false | <90% | 1461 | ||
XR_016939 | LOC645382 | 297 | 315 | G | G | G | A | C | U | U | G | A | U | A | C | A | C | u | G | g | u | g | 44 | 4 | 14 | c | false | <90% | 1473 | ||
XR_016946 | LOC645399 | 297 | 315 | G | G | G | A | C | U | U | G | A | U | A | C | A | C | u | G | g | u | g | 44 | 4 | 14 | c | false | <90% | 1473 | ||
NM_001039361 | PRAMEF10 | 322 | 340 | G | G | G | A | C | U | U | G | A | U | A | C | A | C | u | G | g | u | g | 44 | 4 | 14 | c | false | <90% | 1518 | ||
NM_001045480 | PRAMEF16 | 279 | 297 | G | G | G | A | C | U | U | G | A | U | A | C | A | C | u | G | c | u | g | 44 | 4 | 14 | c | false | <90% | 1587 | ||
NR_003088 | ABCC13 | 344 | 362 | G | G | c | g | C | U | U | G | A | U | A | C | A | C | A | G | A | A | a | 38 | 3 | 14 | bc | false | <90% | 826 | ||
NR_003087 | ABCC13 | 344 | 362 | G | G | c | g | C | U | U | G | A | U | A | C | A | C | A | G | A | A | a | 38 | 3 | 14 | bc | false | <90% | 2839 | ||
NM_022749 | RAI16 | 2051 | 2069 | G | G | G | A | C | U | U | G | A | U | g | C | A | g | A | G | A | A | U | 19 | 2 | 10 | c | false | <90% | 3759 | ||
NM_183387 | EML5 | 558 | 576 | u | G | G | A | C | U | U | G | A | U | u | C | A | a | A | G | A | A | U | 17 | 3 | 9 | c | false | <90% | 7091 | ||
NM_015490 | SEC31B | 266 | 284 | u | G | G | A | C | U | U | G | A | a | A | C | A | C | A | G | A | g | g | 7 | 4 | 8 | c | false | <90% | 4631 | ||
NM_207482 | FLJ44048 | 4633 | 4651 | a | u | u | A | C | U | U | c | A | U | A | C | A | C | A | G | A | A | U | 4 | 4 | 11 | bc | false | <90% | 5088 | ||
NM_145888 | KLK10 | 1939 | 1957 | G | G | G | A | g | U | U | a | A | U | A | C | A | C | A | G | A | A | U | -13 | 2 | 11 | bc | false | <90% | 2985 | ||
NM_001077500 | KLK10 | 1978 | 1996 | G | G | G | A | g | U | U | a | A | U | A | C | A | C | A | G | A | A | U | -13 | 2 | 11 | bc | false | <90% | 3024 | ||
NM_002776 | KLK10 | 2077 | 2095 | G | G | G | A | g | U | U | a | A | U | A | C | A | C | A | G | A | A | U | -13 | 2 | 11 | bc | false | <90% | 3123 |
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_030627 | CPEB4 | 2180 | 2198 | c | c | U | u | U | G | U | G | U | A | U | C | A | A | G | U | C | C | C | 49 | 3 | 15 | bc | false | <90% | 6930 | ||
NM_001253 | CDC5L | 2815 | 2833 | A | U | U | C | U | G | U | G | U | A | U | a | A | A | G | a | C | C | u | 35 | 3 | 11 | false | <90% | 3012 | |||
XM_001126142 | LOC730509 | 59 | 77 | u | U | U | C | U | G | U | G | U | A | g | C | A | A | G | U | C | u | C | 34 | 3 | 9 | c | false | <90% | 663 | ||
NM_001003810 | HNRPD | 1292 | 1310 | A | U | U | u | U | u | U | G | U | A | U | C | A | A | G | U | C | C | C | 0 | 2 | 13 | bc | false | <90% | 2053 | ||
NM_002138 | HNRPD | 1349 | 1367 | A | U | U | u | U | u | U | G | U | A | U | C | A | A | G | U | C | C | C | 0 | 2 | 13 | bc | false | <90% | 2110 | ||
NM_031369 | HNRPD | 1439 | 1457 | A | U | U | u | U | u | U | G | U | A | U | C | A | A | G | U | C | C | C | 0 | 2 | 13 | bc | false | <90% | 2200 | ||
NM_031370 | HNRPD | 1496 | 1514 | A | U | U | u | U | u | U | G | U | A | U | C | A | A | G | U | C | C | C | 0 | 2 | 13 | bc | false | <90% | 2257 | ||
NM_144713 | FAM82A | 308 | 326 | A | U | U | a | U | c | U | G | U | A | U | C | A | A | G | U | C | C | a | -5 | 3 | 12 | bc | false | <90% | 1985 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1850
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