Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
24 hits were found for UGGUUUUGGGGGCCAAGUC (19 guide strand hits and 5 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_133336 | WHSC1 | 154 | 172 | U | G | u | U | U | U | U | G | G | G | G | G | C | C | A | A | G | U | a | 75 | 2 | 15 | bc | false | <90% | 3619 | ||
NM_003685 | KHSRP | 402 | 420 | U | G | G | U | U | U | U | G | G | G | G | G | C | C | A | A | a | a | g | 68 | 3 | 16 | ac | false | <90% | 3009 | ||
NM_152557 | ZNF746 | 3348 | 3366 | U | G | G | g | U | U | U | G | G | G | G | G | C | C | A | A | G | U | g | 58 | 2 | 14 | bc | false | <90% | 3706 | ||
NM_023923 | PHACTR4 | 5932 | 5950 | a | c | a | U | U | U | U | G | G | G | G | G | u | C | A | A | G | U | C | 56 | 4 | 9 | false | <90% | 6208 | |||
NM_001048183 | PHACTR4 | 5949 | 5967 | a | c | a | U | U | U | U | G | G | G | G | G | u | C | A | A | G | U | C | 56 | 4 | 9 | false | <90% | 6225 | |||
XR_019288 | LOC649828 | 708 | 726 | g | G | G | U | U | U | U | G | G | G | G | c | C | C | g | A | G | U | C | 39 | 3 | 10 | false | <90% | 1307 | |||
NM_002452 | NUDT1 | 146 | 164 | U | G | G | c | U | U | U | G | G | G | G | G | C | a | A | A | G | U | g | 38 | 3 | 9 | c | false | <90% | 692 | ||
NM_198953 | NUDT1 | 182 | 200 | U | G | G | c | U | U | U | G | G | G | G | G | C | a | A | A | G | U | g | 38 | 3 | 9 | c | false | <90% | 728 | ||
NM_198950 | NUDT1 | 194 | 212 | U | G | G | c | U | U | U | G | G | G | G | G | C | a | A | A | G | U | g | 38 | 3 | 9 | c | false | <90% | 740 | ||
NM_198948 | NUDT1 | 197 | 215 | U | G | G | c | U | U | U | G | G | G | G | G | C | a | A | A | G | U | g | 38 | 3 | 9 | c | false | <90% | 743 | ||
NM_198954 | NUDT1 | 255 | 273 | U | G | G | c | U | U | U | G | G | G | G | G | C | a | A | A | G | U | g | 38 | 3 | 9 | c | false | <90% | 801 | ||
NM_198952 | NUDT1 | 267 | 285 | U | G | G | c | U | U | U | G | G | G | G | G | C | a | A | A | G | U | g | 38 | 3 | 9 | c | false | <90% | 813 | ||
NM_198949 | NUDT1 | 270 | 288 | U | G | G | c | U | U | U | G | G | G | G | G | C | a | A | A | G | U | g | 38 | 3 | 9 | c | false | <90% | 816 | ||
XM_001131984 | C14orf25 | 274 | 292 | U | G | G | g | U | U | U | G | G | G | G | u | C | C | A | A | G | U | C | 29 | 2 | 7 | false | <90% | 1899 | |||
XM_001129346 | C14orf25 | 274 | 292 | U | G | G | g | U | U | U | G | G | G | G | u | C | C | A | A | G | U | C | 29 | 2 | 7 | false | <90% | 1899 | |||
NM_014598 | SOCS7 | 1321 | 1339 | U | G | G | U | a | U | U | G | G | G | G | G | C | C | A | A | u | g | a | 17 | 4 | 11 | c | false | <90% | 2162 | ||
XM_936572 | SOCS7 | 1222 | 1240 | U | G | G | U | a | U | U | G | G | G | G | G | C | C | A | A | u | g | a | 17 | 4 | 11 | c | false | <90% | 2206 | ||
XM_001127362 | KIAA0574 | 1355 | 1373 | g | G | G | U | U | U | U | G | G | u | G | G | C | C | A | A | G | U | u | 10 | 3 | 8 | bc | false | <90% | 4593 | ||
NM_145804 | ABTB2 | 3544 | 3562 | U | G | G | U | U | U | U | a | G | G | G | G | C | C | A | A | a | g | u | 6 | 4 | 8 | c | false | <90% | 4149 |
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_181521 | CMTM4 | 2746 | 2764 | u | A | C | U | U | G | G | C | C | C | C | C | A | A | A | A | a | a | g | 66 | 4 | 15 | ac | false | <90% | 8133 | ||
XM_001133722 | LOC731797 | 167 | 185 | c | c | C | U | U | G | G | C | C | C | C | C | A | c | A | A | C | C | c | 62 | 4 | 11 | c | false | <90% | 1278 | ||
NM_016407 | C20orf43 | 792 | 810 | a | A | C | U | U | G | G | C | u | C | C | C | A | A | A | A | g | C | A | 14 | 3 | 7 | c | false | <90% | 1638 | ||
NM_001045476 | LOC401551 | 1188 | 1206 | c | A | C | c | U | G | G | u | C | C | C | C | A | A | A | A | C | C | A | 0 | 3 | 11 | bc | false | <90% | 1252 | ||
NM_024536 | CHPF | 2553 | 2571 | c | A | C | U | U | c | u | C | C | C | C | C | A | A | A | A | C | C | A | -31 | 3 | 12 | bc | false | <90% | 2956 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 5222
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