Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
23 hits were found for GCAAGCUGUCCUUCUUUGA (10 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_001379 | DNMT1 | 1388 | 1406 | a | g | A | A | G | C | U | G | U | C | C | a | U | C | U | U | U | G | A | 52 | 3 | 9 | false | <90% | 5434 | |||
NM_002661 | PLCG2 | 1654 | 1672 | c | C | A | A | G | C | U | G | U | C | C | U | U | C | a | g | U | G | A | 47 | 3 | 13 | c | false | <90% | 4263 | ||
NR_003133 | LOC400759 | 15135 | 15153 | c | a | A | A | G | C | U | G | U | C | C | g | U | C | U | U | U | G | c | 47 | 4 | 9 | false | <90% | 16075 | |||
NM_001005281 | OR6B1 | 191 | 209 | c | C | A | A | c | C | U | G | U | C | C | U | U | C | U | U | g | G | A | 23 | 3 | 11 | c | false | <90% | 936 | ||
NM_001004463 | OR10G7 | 185 | 203 | c | C | A | A | c | C | U | G | U | C | C | U | U | C | a | U | U | G | A | 21 | 3 | 9 | c | false | <90% | 936 | ||
NM_001001953 | OR10G9 | 185 | 203 | c | C | A | A | c | C | U | G | U | C | C | U | U | C | a | U | U | G | A | 21 | 3 | 9 | c | false | <90% | 936 | ||
NM_001004462 | OR10G4 | 185 | 203 | c | C | A | A | c | C | U | G | U | C | C | U | U | C | a | U | U | G | A | 21 | 3 | 9 | c | false | <90% | 936 | ||
NM_130445 | COL18A1 | 1440 | 1458 | a | C | A | A | G | C | U | G | a | C | C | U | U | C | a | U | U | G | A | 13 | 3 | 7 | c | false | <90% | 5398 | ||
NM_030582 | COL18A1 | 1952 | 1970 | a | C | A | A | G | C | U | G | a | C | C | U | U | C | a | U | U | G | A | 13 | 3 | 7 | c | false | <90% | 5910 | ||
NM_002182 | IL1RAP | 1510 | 1528 | a | C | A | A | G | C | U | G | U | g | C | a | U | C | U | U | U | G | A | -18 | 3 | 8 | false | <90% | 4726 |
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_053028 | MYLK | 797 | 815 | U | C | A | A | A | G | A | A | G | G | A | C | A | G | a | U | g | G | g | 46 | 3 | 14 | c | false | <90% | 7492 | ||
NM_053026 | MYLK | 797 | 815 | U | C | A | A | A | G | A | A | G | G | A | C | A | G | a | U | g | G | g | 46 | 3 | 14 | c | false | <90% | 7645 | ||
NM_053027 | MYLK | 797 | 815 | U | C | A | A | A | G | A | A | G | G | A | C | A | G | a | U | g | G | g | 46 | 3 | 14 | c | false | <90% | 7699 | ||
NM_053025 | MYLK | 797 | 815 | U | C | A | A | A | G | A | A | G | G | A | C | A | G | a | U | g | G | g | 46 | 3 | 14 | c | false | <90% | 7852 | ||
NM_015381 | FAM19A5 | 259 | 277 | U | C | A | A | A | G | A | A | G | G | u | C | A | G | C | U | g | G | C | 15 | 2 | 10 | c | false | <90% | 2652 | ||
NM_173598 | KSR2 | 6412 | 6430 | c | g | g | A | A | G | A | A | G | G | c | C | A | G | C | U | U | G | C | 5 | 4 | 8 | c | false | <90% | 16655 | ||
NM_006269 | RP1 | 2206 | 2224 | a | u | c | A | A | G | A | u | G | G | A | C | A | G | C | U | U | G | C | 4 | 4 | 11 | bc | false | <90% | 7100 | ||
NM_024704 | C20orf23 | 3013 | 3031 | a | a | A | A | A | G | A | A | G | a | A | C | A | G | C | U | U | G | C | 3 | 3 | 9 | bc | false | <90% | 5274 | ||
NM_080830 | CST11 | 167 | 185 | U | a | u | g | c | G | A | A | G | G | A | C | A | G | C | U | U | G | C | -19 | 4 | 14 | bc | false | <90% | 448 | ||
NM_130794 | CST11 | 167 | 185 | U | a | u | g | c | G | A | A | G | G | A | C | A | G | C | U | U | G | C | -19 | 4 | 14 | bc | false | <90% | 553 | ||
XM_944654 | LOC648716 | 1573 | 1591 | a | C | A | A | A | G | A | A | a | G | g | C | A | G | C | U | U | G | C | -23 | 3 | 8 | c | false | <90% | 2230 | ||
XM_935966 | LOC641798 | 1573 | 1591 | a | C | A | A | A | G | A | A | a | G | g | C | A | G | C | U | U | G | C | -23 | 3 | 8 | c | false | <90% | 2230 | ||
XM_935369 | LOC646329 | 1573 | 1591 | a | C | A | A | A | G | A | A | a | G | g | C | A | G | C | U | U | G | C | -23 | 3 | 8 | c | false | <90% | 2230 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1587
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