Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
38 hits were found for GAGGAACUACUGUCUUCAC (10 guide strand hits and 28 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_053036 | NPFFR2 | 149 | 167 | u | g | u | G | A | A | C | U | A | C | U | a | U | C | U | U | C | A | C | 33 | 4 | 8 | false | <90% | 1560 | |||
NM_004885 | NPFFR2 | 506 | 524 | u | g | u | G | A | A | C | U | A | C | U | a | U | C | U | U | C | A | C | 33 | 4 | 8 | false | <90% | 1936 | |||
NM_153610 | CMYA5 | 8716 | 8734 | a | A | G | G | A | A | C | c | A | C | U | G | U | C | U | U | C | A | g | 30 | 3 | 10 | bc | false | <90% | 12911 | ||
NM_000876 | IGF2R | 1476 | 1494 | a | A | G | G | A | A | C | U | c | C | U | G | U | a | U | U | C | A | C | 18 | 3 | 7 | c | false | <90% | 9093 | ||
NM_014293 | NPTXR | 5458 | 5476 | a | A | G | G | g | A | C | U | A | C | U | c | U | C | U | U | C | A | C | 12 | 3 | 7 | false | <90% | 5814 | |||
NM_198798 | ANKRD5 | 2361 | 2379 | G | A | G | G | A | A | C | U | g | C | U | G | U | C | a | U | C | A | a | 10 | 3 | 8 | c | false | <90% | 3775 | ||
NM_022096 | ANKRD5 | 2425 | 2443 | G | A | G | G | A | A | C | U | g | C | U | G | U | C | a | U | C | A | a | 10 | 3 | 8 | c | false | <90% | 3839 | ||
NM_171825 | CAMK2A | 3050 | 3068 | u | A | G | G | A | u | C | U | A | C | U | G | U | C | U | g | C | A | C | 8 | 3 | 9 | c | false | <90% | 4803 | ||
NM_015981 | CAMK2A | 3083 | 3101 | u | A | G | G | A | u | C | U | A | C | U | G | U | C | U | g | C | A | C | 8 | 3 | 9 | c | false | <90% | 4836 | ||
NM_001935 | DPP4 | 3024 | 3042 | u | A | G | G | g | A | C | U | u | C | U | G | U | C | U | U | C | A | C | -13 | 3 | 10 | bc | false | <90% | 3913 |
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_018559 | KIAA1704 | 253 | 271 | a | U | G | A | A | G | A | C | A | G | U | A | G | U | U | C | u | U | u | 69 | 3 | 15 | ac | false | <90% | 1431 | ||
NM_025176 | KIAA0980 | 326 | 344 | a | U | G | A | A | G | A | C | A | G | U | A | G | U | U | C | u | U | u | 69 | 3 | 15 | ac | false | <90% | 4979 | ||
NM_018077 | RBM28 | 505 | 523 | u | U | G | A | A | G | A | C | A | G | U | A | u | U | U | g | C | U | C | 61 | 3 | 11 | false | <90% | 2809 | |||
XM_928706 | KIAA0754 | 5988 | 6006 | G | U | G | A | A | G | A | C | A | G | U | A | G | g | U | C | a | a | C | 54 | 3 | 13 | c | false | <90% | 6171 | ||
XM_941912 | KIAA0754 | 6044 | 6062 | G | U | G | A | A | G | A | C | A | G | U | A | G | g | U | C | a | a | C | 54 | 3 | 13 | c | false | <90% | 6227 | ||
NM_002519 | NPAT | 3922 | 3940 | G | U | G | A | A | G | A | C | A | G | U | A | G | U | a | C | a | U | C | 51 | 2 | 14 | c | false | <90% | 5895 | ||
NM_201252 | AFAR3 | 1416 | 1434 | u | U | G | A | A | G | A | C | A | G | g | A | G | U | U | C | C | a | g | 29 | 4 | 9 | c | false | <90% | 2001 | ||
NM_014674 | EDEM1 | 925 | 943 | c | U | a | A | A | G | A | C | A | G | g | A | G | U | U | C | C | U | C | 17 | 3 | 8 | c | false | <90% | 6072 | ||
NM_001083900 | DNAH10 | 6940 | 6958 | c | U | G | A | A | G | A | C | A | a | U | A | G | U | U | C | C | U | C | 15 | 2 | 9 | bc | false | <90% | 13694 | ||
NM_018026 | PACS1 | 2167 | 2185 | G | U | a | A | A | u | A | C | A | G | U | A | G | U | U | C | C | U | u | 12 | 3 | 12 | bc | false | <90% | 4488 | ||
NM_080670 | SLC35A4 | 460 | 478 | u | U | G | u | g | G | A | C | A | G | U | A | G | U | U | C | C | U | C | 9 | 3 | 14 | bc | false | <90% | 2676 | ||
XM_940167 | LOC400652 | 572 | 590 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 741 | ||
XM_927103 | LOC400652 | 572 | 590 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 741 | ||
XR_017289 | LOC643932 | 566 | 584 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 748 | ||
XR_018891 | LOC643932 | 566 | 584 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 752 | ||
XR_019418 | LOC646527 | 694 | 712 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 793 | ||
XR_016632 | LOC646527 | 694 | 712 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 793 | ||
XR_001449 | LOC644972 | 715 | 733 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 867 | ||
XR_017187 | LOC146053 | 721 | 739 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 898 | ||
XR_019637 | LOC146053 | 721 | 739 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 907 | ||
XR_018444 | LOC643981 | 815 | 833 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 914 | ||
XR_016514 | LOC643981 | 815 | 833 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 914 | ||
NM_001006 | RPS3A | 747 | 765 | G | U | G | A | A | G | g | C | A | G | U | A | G | U | U | C | u | g | g | 2 | 4 | 9 | c | false | <90% | 930 | ||
NM_058177 | HDAC9 | 69 | 87 | G | U | G | A | A | G | u | C | A | G | a | A | G | U | U | C | C | U | g | -32 | 3 | 7 | c | false | <90% | 2681 | ||
NM_058176 | HDAC9 | 69 | 87 | G | U | G | A | A | G | u | C | A | G | a | A | G | U | U | C | C | U | g | -32 | 3 | 7 | c | false | <90% | 3149 | ||
NM_014707 | HDAC9 | 178 | 196 | G | U | G | A | A | G | u | C | A | G | a | A | G | U | U | C | C | U | g | -32 | 3 | 7 | c | false | <90% | 4238 | ||
NM_178425 | HDAC9 | 69 | 87 | G | U | G | A | A | G | u | C | A | G | a | A | G | U | U | C | C | U | g | -32 | 3 | 7 | c | false | <90% | 4559 | ||
NM_178423 | HDAC9 | 178 | 196 | G | U | G | A | A | G | u | C | A | G | a | A | G | U | U | C | C | U | g | -32 | 3 | 7 | c | false | <90% | 4659 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1668
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