Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
24 hits were found for GGUGACUAUGGUGAUGCUG (12 guide strand hits and 12 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_001129 | AEBP1 | 1203 | 1221 | c | c | U | G | A | C | U | A | U | G | G | U | G | A | U | G | g | U | u | 58 | 4 | 14 | ac | false | <90% | 4125 | ||
XR_017088 | LOC441774 | 380 | 398 | G | G | U | G | A | C | U | A | U | G | G | g | G | A | U | G | a | a | G | 40 | 3 | 11 | false | <90% | 803 | |||
XR_018247 | LOC441774 | 380 | 398 | G | G | U | G | A | C | U | A | U | G | G | g | G | A | U | G | a | a | G | 40 | 3 | 11 | false | <90% | 803 | |||
NM_019841 | TRPV5 | 1575 | 1593 | G | G | U | G | A | C | c | A | U | G | G | U | G | A | U | G | C | g | G | 31 | 2 | 10 | c | false | <90% | 2486 | ||
XM_001126541 | TRPV6 | 1281 | 1299 | G | G | U | G | A | C | c | A | U | G | G | U | G | A | U | G | C | g | G | 31 | 2 | 10 | c | false | <90% | 2650 | ||
NM_018646 | TRPV6 | 1527 | 1545 | G | G | U | G | A | C | c | A | U | G | G | U | G | A | U | G | C | g | G | 31 | 2 | 10 | c | false | <90% | 2918 | ||
NM_014550 | CARD10 | 3149 | 3167 | G | G | U | G | u | C | U | A | U | G | G | U | G | A | a | G | C | U | G | 23 | 2 | 9 | c | false | <90% | 3912 | ||
NM_080878 | ITLN2 | 725 | 743 | u | a | U | G | A | C | U | u | U | G | G | U | G | A | U | G | C | U | a | 19 | 4 | 10 | bc | false | <90% | 1150 | ||
NM_015255 | UBR2 | 445 | 463 | u | G | U | G | A | C | U | g | U | G | G | U | G | A | U | a | C | U | G | 9 | 3 | 7 | c | false | <90% | 5268 | ||
NM_016321 | RHCG | 81 | 99 | G | G | U | G | A | u | U | A | U | G | G | U | G | A | U | u | C | U | c | 5 | 3 | 9 | c | false | <90% | 1952 | ||
NM_015185 | ARHGEF9 | 3115 | 3133 | u | c | a | G | A | C | U | A | U | G | a | U | G | A | U | G | C | U | G | 5 | 4 | 8 | c | false | <90% | 5413 | ||
XR_019641 | LOC651995 | 280 | 298 | G | G | U | G | A | C | a | c | U | G | G | U | G | A | U | G | C | U | G | -28 | 2 | 11 | bc | false | <90% | 1127 |
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_174918 | C19orf59 | 460 | 478 | g | A | G | C | A | U | C | A | C | C | A | U | g | G | U | C | A | g | g | 79 | 4 | 11 | false | <90% | 1326 | |||
NM_006869 | CENTA1 | 1151 | 1169 | u | g | G | C | A | U | C | A | C | C | A | U | c | G | U | C | A | C | g | 71 | 4 | 10 | false | <90% | 2378 | |||
NM_144664 | FAM76B | 841 | 859 | C | A | c | C | A | U | C | A | C | C | A | U | c | G | U | C | A | C | a | 65 | 3 | 9 | false | <90% | 3958 | |||
XM_001131758 | INDOL1 | 847 | 865 | u | c | a | C | A | U | C | A | C | C | A | U | g | G | U | C | A | C | C | 56 | 4 | 9 | false | <90% | 1029 | |||
XM_001127080 | INDOL1 | 847 | 865 | u | c | a | C | A | U | C | A | C | C | A | U | g | G | U | C | A | C | C | 56 | 4 | 9 | false | <90% | 1029 | |||
NM_012455 | PSD4 | 570 | 588 | C | A | G | C | A | U | C | A | C | C | A | g | g | G | U | C | A | C | C | 55 | 2 | 11 | false | <90% | 5039 | |||
XR_019369 | LOC652524 | 284 | 302 | a | A | G | C | A | U | C | A | C | C | A | c | u | G | U | C | A | C | C | 53 | 3 | 10 | false | <90% | 1529 | |||
XR_017099 | LOC126811 | 284 | 302 | a | A | G | C | A | U | C | A | C | C | A | c | u | G | U | C | A | C | C | 53 | 3 | 10 | false | <90% | 1529 | |||
NM_020826 | SYT13 | 2292 | 2310 | C | A | G | C | A | U | C | A | C | C | A | a | A | G | U | g | A | C | u | 35 | 3 | 11 | false | <90% | 5108 | |||
NM_015665 | AAAS | 666 | 684 | C | A | G | C | A | g | C | A | C | C | A | U | A | G | U | C | c | C | C | 13 | 2 | 10 | c | false | <90% | 1816 | ||
NM_033543 | CEACAM21 | 493 | 511 | C | A | G | C | A | g | C | A | C | C | A | c | A | G | U | C | A | C | a | -2 | 3 | 6 | false | <90% | 1352 | |||
XM_001129009 | LOC728222 | 325 | 343 | u | A | G | a | A | U | C | A | C | u | A | U | A | G | U | C | A | C | C | -21 | 3 | 9 | bc | false | <90% | 545 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1704
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