Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
19 hits were found for UUGCCAGGAUGACCGGGUC (6 guide strand hits and 13 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_003105 | SORL1 | 4610 | 4628 | U | U | G | C | C | A | G | G | A | U | G | g | C | C | G | G | G | a | C | 63 | 2 | 11 | false | <90% | 6906 | |||
XM_931978 | LOC644026 | 573 | 591 | U | U | G | C | C | A | G | G | A | U | G | u | C | a | G | G | G | U | C | 46 | 2 | 11 | false | <90% | 1011 | |||
XM_942794 | LOC642232 | 573 | 591 | U | U | G | C | C | A | G | G | A | U | G | u | C | a | G | G | G | U | C | 46 | 2 | 11 | false | <90% | 1011 | |||
NM_031310 | PLVAP | 404 | 422 | g | U | G | C | C | A | G | G | g | U | G | A | C | C | G | G | G | U | C | 37 | 2 | 10 | bc | false | <90% | 2317 | ||
NM_020655 | JPH3 | 3714 | 3732 | U | U | G | C | C | A | G | G | A | U | G | u | C | C | G | a | G | U | g | 35 | 3 | 11 | false | <90% | 3997 | |||
NM_033225 | CSMD1 | 3380 | 3398 | U | U | G | C | C | A | G | G | c | U | c | A | C | C | G | G | G | U | C | -21 | 2 | 8 | c | false | <90% | 11820 |
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_022372 | GBL | 151 | 169 | G | A | C | C | C | G | G | U | C | A | U | C | C | U | G | G | C | c | A | 97 | 1 | 17 | ac | false | <90% | 1655 | ||
XM_939581 | LOC344875 | 3260 | 3278 | u | A | C | C | C | G | G | U | C | A | U | C | C | U | G | G | u | g | A | 71 | 3 | 15 | ac | false | <90% | 3475 | ||
XM_497913 | LOC344875 | 3260 | 3278 | u | A | C | C | C | G | G | U | C | A | U | C | C | U | G | G | u | g | A | 71 | 3 | 15 | ac | false | <90% | 3475 | ||
NM_080625 | C20orf160 | 909 | 927 | a | A | C | C | u | G | G | U | C | A | U | C | C | U | G | G | C | u | g | 38 | 4 | 12 | c | false | <90% | 2566 | ||
NM_012067 | AKR7A3 | 922 | 940 | G | A | C | g | C | G | G | U | C | A | U | C | C | U | G | G | g | c | A | 37 | 3 | 12 | c | false | <90% | 1301 | ||
NM_003689 | AKR7A2 | 951 | 969 | G | A | C | g | C | G | G | U | C | A | U | C | C | U | G | G | g | c | A | 37 | 3 | 12 | c | false | <90% | 1377 | ||
NM_201252 | AFAR3 | 515 | 533 | G | A | C | g | C | G | G | U | C | A | U | C | C | U | G | G | g | c | A | 37 | 3 | 12 | c | false | <90% | 2001 | ||
NM_172369 | C1QC | 315 | 333 | u | A | C | C | C | G | G | c | C | A | U | C | C | U | G | G | g | A | A | 12 | 3 | 8 | c | false | <90% | 1171 | ||
NM_001858 | COL19A1 | 2645 | 2663 | c | A | C | C | C | G | G | U | C | c | U | C | C | U | G | G | C | c | c | 7 | 4 | 8 | c | false | <90% | 8725 | ||
NM_032531 | KIRREL3 | 529 | 547 | G | A | C | C | C | c | G | U | C | A | U | C | C | U | G | G | g | g | g | 5 | 4 | 10 | c | false | <90% | 2495 | ||
NM_001008410 | STEAP3 | 1083 | 1101 | G | A | C | C | u | G | G | U | C | A | a | C | C | U | G | G | C | A | g | -17 | 3 | 7 | c | false | <90% | 3870 | ||
NM_018234 | STEAP3 | 1151 | 1169 | G | A | C | C | u | G | G | U | C | A | a | C | C | U | G | G | C | A | g | -17 | 3 | 7 | c | false | <90% | 3938 | ||
NM_182915 | STEAP3 | 1498 | 1516 | G | A | C | C | u | G | G | U | C | A | a | C | C | U | G | G | C | A | g | -17 | 3 | 7 | c | false | <90% | 4285 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2350
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