Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
39 hits were found for GGAUGAUCCUGAUGACUCA (26 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_033272 | KCNH7 | 2933 | 2951 | a | a | A | U | G | A | U | C | C | U | G | A | a | G | A | C | U | C | u | 71 | 4 | 10 | false | <90% | 4225 | |||
NM_031414 | STK31 | 1983 | 2001 | a | G | A | U | G | A | U | C | C | U | G | A | U | G | g | C | U | C | u | 68 | 3 | 13 | c | false | <90% | 3244 | ||
NM_032944 | STK31 | 2365 | 2383 | a | G | A | U | G | A | U | C | C | U | G | A | U | G | g | C | U | C | u | 68 | 3 | 13 | c | false | <90% | 3616 | ||
NM_172112 | EYA2 | 50 | 68 | G | G | g | U | G | A | U | C | C | U | G | A | U | G | A | C | a | g | u | 49 | 4 | 13 | c | false | <90% | 2458 | ||
NM_014079 | KLF15 | 575 | 593 | G | G | g | U | G | A | U | C | C | U | G | A | U | G | A | C | g | u | c | 49 | 4 | 13 | c | false | <90% | 2543 | ||
XM_029101 | KIAA0947 | 4239 | 4257 | a | G | A | U | G | c | U | C | C | U | G | A | U | G | A | C | U | C | A | 34 | 2 | 13 | bc | false | <90% | 8577 | ||
XM_940469 | KIAA0947 | 4548 | 4566 | a | G | A | U | G | c | U | C | C | U | G | A | U | G | A | C | U | C | A | 34 | 2 | 13 | bc | false | <90% | 8886 | ||
NM_002661 | PLCG2 | 3322 | 3340 | G | G | A | a | G | A | U | C | C | U | G | A | U | G | A | C | g | C | u | 34 | 3 | 12 | c | false | <90% | 4263 | ||
XR_018374 | LOC441818 | 357 | 375 | a | G | A | U | G | A | U | u | C | U | G | A | U | G | A | C | U | C | u | 30 | 3 | 10 | bc | false | <90% | 1424 | ||
XR_017309 | LOC441818 | 357 | 375 | a | G | A | U | G | A | U | u | C | U | G | A | U | G | A | C | U | C | u | 30 | 3 | 10 | bc | false | <90% | 1424 | ||
NM_016312 | WBP11 | 1235 | 1253 | a | G | A | U | G | A | U | u | C | U | G | A | U | G | A | C | U | C | u | 30 | 3 | 10 | bc | false | <90% | 2690 | ||
NM_173087 | CAPN3 | 1566 | 1584 | c | G | A | U | G | A | c | C | C | U | G | A | U | G | A | C | U | C | g | 26 | 3 | 11 | bc | false | <90% | 3040 | ||
NM_212465 | CAPN3 | 1635 | 1653 | c | G | A | U | G | A | c | C | C | U | G | A | U | G | A | C | U | C | g | 26 | 3 | 11 | bc | false | <90% | 3223 | ||
NM_024344 | CAPN3 | 1710 | 1728 | c | G | A | U | G | A | c | C | C | U | G | A | U | G | A | C | U | C | g | 26 | 3 | 11 | bc | false | <90% | 3298 | ||
NM_000070 | CAPN3 | 1710 | 1728 | c | G | A | U | G | A | c | C | C | U | G | A | U | G | A | C | U | C | g | 26 | 3 | 11 | bc | false | <90% | 3316 | ||
NM_212467 | CAPN3 | 1913 | 1931 | c | G | A | U | G | A | c | C | C | U | G | A | U | G | A | C | U | C | g | 26 | 3 | 11 | bc | false | <90% | 3501 | ||
NM_212464 | CAPN3 | 1635 | 1653 | c | G | A | U | G | A | c | C | C | U | G | A | U | G | A | C | U | C | g | 26 | 3 | 11 | bc | false | <90% | 3881 | ||
NM_018557 | LRP1B | 11010 | 11028 | u | G | A | U | G | A | a | C | C | U | G | A | U | G | A | C | U | g | u | 24 | 4 | 10 | c | false | <90% | 16557 | ||
NM_021129 | PPA1 | 590 | 608 | G | G | A | U | G | A | U | C | C | U | G | A | U | G | c | a | g | C | c | 20 | 4 | 14 | c | false | <90% | 1316 | ||
NM_000031 | ALAD | 268 | 286 | G | G | A | U | G | u | U | C | C | U | G | A | U | G | A | C | a | u | A | 10 | 3 | 10 | c | false | <90% | 3151 | ||
NM_001003945 | ALAD | 434 | 452 | G | G | A | U | G | u | U | C | C | U | G | A | U | G | A | C | a | u | A | 10 | 3 | 10 | c | false | <90% | 3317 | ||
XM_930002 | LOC647016 | 72 | 90 | u | G | A | U | G | A | U | C | C | a | G | A | U | G | A | C | U | u | g | 7 | 4 | 8 | c | false | <90% | 195 | ||
XM_941572 | LOC652199 | 72 | 90 | u | G | A | U | G | A | U | C | C | a | G | A | U | G | A | C | U | u | g | 7 | 4 | 8 | c | false | <90% | 195 | ||
NM_006210 | PEG3 | 3661 | 3679 | G | G | A | U | G | A | c | C | C | U | G | A | U | G | A | C | a | a | A | 7 | 3 | 9 | c | false | <90% | 6371 | ||
NM_005927 | MFAP3 | 1259 | 1277 | G | G | A | U | G | A | c | C | C | U | G | A | U | G | A | C | c | u | g | 2 | 4 | 9 | c | false | <90% | 2914 | ||
NM_015349 | KIAA0240 | 166 | 184 | G | G | A | U | G | A | U | g | a | U | G | A | U | G | A | C | U | C | g | -27 | 3 | 9 | bc | false | <90% | 6520 |
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_014341 | MTCH1 | 1088 | 1106 | g | G | u | G | U | C | A | U | C | A | G | G | A | U | C | A | U | g | C | 75 | 3 | 14 | c | false | <90% | 1890 | ||
NM_181042 | PBRM1 | 2371 | 2389 | U | G | A | G | U | C | A | U | C | A | G | G | A | U | g | A | U | g | a | 67 | 3 | 14 | c | false | <90% | 7448 | ||
NM_018165 | PBRM1 | 2275 | 2293 | U | G | A | G | U | C | A | U | C | A | G | G | A | U | g | A | U | g | a | 67 | 3 | 14 | c | false | <90% | 7508 | ||
NM_018313 | PBRM1 | 2468 | 2486 | U | G | A | G | U | C | A | U | C | A | G | G | A | U | g | A | U | g | a | 67 | 3 | 14 | c | false | <90% | 7545 | ||
NM_015226 | KIAA0350 | 1757 | 1775 | a | G | A | c | U | C | A | U | C | A | G | G | A | U | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 6786 | ||
NM_138967 | SCAMP5 | 512 | 530 | U | u | g | G | U | C | A | U | C | A | G | c | A | U | C | A | U | C | C | 35 | 3 | 8 | false | <90% | 3408 | |||
XR_019076 | LOC390933 | 1320 | 1338 | g | c | A | G | U | C | A | U | C | A | a | G | A | U | C | A | U | C | u | 20 | 4 | 8 | c | false | <90% | 2416 | ||
NM_152716 | FLJ36874 | 825 | 843 | g | c | A | G | U | C | A | U | C | A | a | G | A | U | C | A | U | C | u | 20 | 4 | 8 | c | false | <90% | 3636 | ||
NM_002095 | GTF2E2 | 340 | 358 | U | G | A | G | U | C | A | U | C | A | u | c | A | U | C | A | U | C | g | 0 | 3 | 10 | false | <90% | 1560 | |||
NM_178468 | FAM83C | 3005 | 3023 | U | G | A | G | U | C | A | U | C | A | u | c | A | U | C | A | U | C | a | 0 | 3 | 10 | false | <90% | 3188 | |||
NM_014633 | CTR9 | 1827 | 1845 | a | G | A | u | U | a | A | U | C | A | G | G | A | U | C | A | U | C | C | -2 | 3 | 13 | bc | false | <90% | 4324 | ||
NM_001057 | TACR2 | 161 | 179 | a | u | c | G | U | C | A | U | C | u | G | G | A | U | C | A | U | C | C | -15 | 4 | 9 | bc | false | <90% | 1197 | ||
NM_001059 | TACR3 | 460 | 478 | a | u | c | G | U | C | A | U | C | u | G | G | A | U | C | A | U | C | C | -15 | 4 | 9 | bc | false | <90% | 1755 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1499
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