Automatic recommendation
Not OK - siRNA is not specific
22 hits were found for UUUCCCUGACGGCUGCCGA (12 guide strand hits and 10 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_004265 | FADS2 | 1966 | 1984 | U | c | U | C | C | C | U | G | A | C | G | G | C | U | G | C | C | a | u | 80 | 3 | 15 | ac | false | <90% | 3149 | ||
NM_181519 | SYT15 | 579 | 597 | c | U | U | C | C | C | c | G | A | C | G | G | C | U | G | C | C | u | g | 24 | 4 | 10 | c | false | <90% | 1536 | ||
NM_031912 | SYT15 | 579 | 597 | c | U | U | C | C | C | c | G | A | C | G | G | C | U | G | C | C | u | g | 24 | 4 | 10 | c | false | <90% | 4862 | ||
NM_152475 | ZNF417 | 2952 | 2970 | c | U | U | C | C | C | U | G | A | g | G | G | C | U | G | C | C | u | A | 12 | 3 | 8 | c | false | <90% | 4703 | ||
NM_032828 | ZNF587 | 4523 | 4541 | c | U | U | C | C | C | U | G | A | g | G | G | C | U | G | C | C | u | A | 12 | 3 | 8 | c | false | <90% | 6845 | ||
XM_001125813 | LOC730446 | 1628 | 1646 | U | g | a | C | C | C | U | G | A | g | G | G | C | U | G | C | C | G | A | -13 | 3 | 9 | bc | false | <90% | 2364 | ||
XR_019188 | LOC401676 | 206 | 224 | U | U | U | C | C | C | a | G | g | C | G | G | C | U | G | C | C | G | A | -26 | 2 | 10 | bc | false | <90% | 869 | ||
XR_016830 | LOC401676 | 206 | 224 | U | U | U | C | C | C | a | G | g | C | G | G | C | U | G | C | C | G | A | -26 | 2 | 10 | bc | false | <90% | 869 | ||
XR_015827 | LOC729212 | 481 | 499 | U | U | U | C | C | C | a | G | g | C | G | G | C | U | G | C | C | G | A | -26 | 2 | 10 | bc | false | <90% | 1136 | ||
XR_015880 | LOC731461 | 481 | 499 | U | U | U | C | C | C | a | G | g | C | G | G | C | U | G | C | C | G | A | -26 | 2 | 10 | bc | false | <90% | 1136 | ||
XR_018503 | LOC402342 | 2599 | 2617 | U | U | U | C | C | C | a | G | g | C | G | G | C | U | G | C | C | G | A | -26 | 2 | 10 | bc | false | <90% | 3247 | ||
XR_016922 | LOC402342 | 2599 | 2617 | U | U | U | C | C | C | a | G | g | C | G | G | C | U | G | C | C | G | A | -26 | 2 | 10 | bc | false | <90% | 3247 |
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_001134364 | FOXK2 | 1615 | 1633 | c | C | G | G | C | A | G | C | C | G | U | a | A | G | G | G | A | A | A | 64 | 2 | 10 | false | <90% | 4750 | |||
XM_001134363 | FOXK2 | 1672 | 1690 | c | C | G | G | C | A | G | C | C | G | U | a | A | G | G | G | A | A | A | 64 | 2 | 10 | false | <90% | 4807 | |||
NM_004514 | FOXK2 | 2121 | 2139 | c | C | G | G | C | A | G | C | C | G | U | a | A | G | G | G | A | A | A | 64 | 2 | 10 | false | <90% | 5262 | |||
XM_001133186 | LOC731345 | 2061 | 2079 | g | a | c | G | C | A | G | C | C | G | U | C | A | G | G | u | A | A | A | 40 | 4 | 12 | c | false | <90% | 2186 | ||
XM_001134172 | LOC730034 | 2061 | 2079 | g | a | c | G | C | A | G | C | C | G | U | C | A | G | G | u | A | A | A | 40 | 4 | 12 | c | false | <90% | 2186 | ||
NM_019842 | KCNQ5 | 229 | 247 | U | C | G | G | C | A | G | C | C | G | c | C | A | G | G | G | g | c | g | 7 | 4 | 10 | c | false | <90% | 3325 | ||
XM_001129501 | LOC729154 | 937 | 955 | g | C | G | G | C | A | G | C | C | u | U | C | g | G | G | G | A | A | A | 4 | 3 | 8 | false | <90% | 1502 | |||
XM_001129311 | LOC731349 | 937 | 955 | g | C | G | G | C | A | G | C | C | u | U | C | g | G | G | G | A | A | A | 4 | 3 | 8 | false | <90% | 1502 | |||
NM_033197 | C20orf114 | 1627 | 1645 | a | u | G | G | C | A | G | C | C | a | U | C | A | G | G | G | A | A | g | -1 | 4 | 8 | bc | false | <90% | 1734 | ||
NM_004577 | PSPH | 2039 | 2057 | U | C | G | G | C | A | G | C | C | u | U | C | A | G | u | G | A | A | u | -12 | 3 | 9 | c | false | <90% | 2142 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4618
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