Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
38 hits were found for AAGGAACAACAUUGCCAAA (19 guide strand hits and 19 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_014992 | DAAM1 | 4138 | 4156 | A | A | a | G | A | A | C | A | A | C | A | U | U | G | C | C | A | g | A | 77 | 2 | 14 | c | false | <90% | 4256 | ||
NM_182766 | C1orf125 | 3043 | 3061 | A | A | G | G | A | A | C | A | A | C | A | U | U | c | C | C | u | u | u | 49 | 4 | 13 | c | false | <90% | 3186 | ||
NM_144696 | C1orf125 | 3265 | 3283 | A | A | G | G | A | A | C | A | A | C | A | U | U | c | C | C | u | u | u | 49 | 4 | 13 | c | false | <90% | 3408 | ||
NM_145739 | OSBPL6 | 1857 | 1875 | g | A | G | G | A | A | C | A | A | C | A | U | U | G | g | u | A | A | A | 47 | 3 | 13 | c | false | <90% | 3548 | ||
NM_032523 | OSBPL6 | 2103 | 2121 | g | A | G | G | A | A | C | A | A | C | A | U | U | G | g | u | A | A | A | 47 | 3 | 13 | c | false | <90% | 3794 | ||
XM_001126743 | LOC392529 | 435 | 453 | c | A | G | G | g | A | C | A | A | C | A | U | U | G | C | C | A | g | g | 38 | 4 | 12 | c | false | <90% | 513 | ||
XM_001127546 | LOC392529 | 435 | 453 | c | A | G | G | g | A | C | A | A | C | A | U | U | G | C | C | A | g | g | 38 | 4 | 12 | c | false | <90% | 513 | ||
NM_020786 | PDP2 | 201 | 219 | A | A | G | G | A | A | C | A | g | C | A | U | U | G | C | C | A | c | A | 37 | 2 | 8 | c | false | <90% | 3830 | ||
NM_002054 | GCG | 351 | 369 | c | A | G | G | A | A | u | A | A | C | A | U | U | G | C | C | A | A | A | 31 | 2 | 12 | bc | false | <90% | 1128 | ||
NM_015102 | NPHP4 | 2239 | 2257 | g | A | G | G | A | A | C | A | u | C | A | U | g | G | C | C | A | A | A | 27 | 3 | 7 | false | <90% | 5020 | |||
NM_020920 | CHD8 | 2184 | 2202 | c | A | G | G | A | A | C | A | c | C | A | U | U | G | C | a | A | A | A | 11 | 3 | 7 | c | false | <90% | 7525 | ||
NM_175849 | DNMT3B | 3855 | 3873 | A | A | G | G | A | A | C | A | A | C | g | U | U | G | a | C | A | A | g | 9 | 3 | 10 | c | false | <90% | 4104 | ||
NM_175850 | DNMT3B | 4023 | 4041 | A | A | G | G | A | A | C | A | A | C | g | U | U | G | a | C | A | A | g | 9 | 3 | 10 | c | false | <90% | 4267 | ||
NM_175848 | DNMT3B | 4044 | 4062 | A | A | G | G | A | A | C | A | A | C | g | U | U | G | a | C | A | A | g | 9 | 3 | 10 | c | false | <90% | 4293 | ||
NM_006892 | DNMT3B | 4104 | 4122 | A | A | G | G | A | A | C | A | A | C | g | U | U | G | a | C | A | A | g | 9 | 3 | 10 | c | false | <90% | 4353 | ||
NM_007124 | UTRN | 313 | 331 | c | A | G | G | A | A | C | A | u | C | A | c | U | G | C | C | A | A | A | 4 | 3 | 7 | false | <90% | 12436 | |||
NM_019045 | WDR44 | 3354 | 3372 | c | u | a | G | A | A | u | A | A | C | A | U | U | G | C | C | A | A | A | 0 | 4 | 12 | bc | false | <90% | 4154 | ||
NM_177986 | DSG4 | 333 | 351 | g | A | G | G | A | A | C | c | c | C | A | U | U | G | C | C | A | A | A | -24 | 3 | 10 | bc | false | <90% | 3579 | ||
NM_001303 | COX10 | 1038 | 1056 | A | A | G | G | A | u | C | A | g | C | A | U | U | G | C | C | A | A | c | -28 | 3 | 9 | bc | false | <90% | 3031 |
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_001547 | IFIT2 | 1867 | 1885 | U | U | U | u | G | C | A | A | U | G | U | U | G | U | U | C | C | a | U | 60 | 2 | 13 | c | false | <90% | 3058 | ||
NM_006108 | SPON1 | 4749 | 4767 | U | U | U | u | G | C | A | A | U | G | U | U | G | U | U | C | u | a | a | 32 | 4 | 12 | c | false | <90% | 5400 | ||
NM_182720 | CREM | 524 | 542 | a | U | U | G | G | g | A | A | U | G | U | U | G | U | U | C | C | a | g | 27 | 4 | 11 | c | false | <90% | 1955 | ||
NM_182717 | CREM | 560 | 578 | a | U | U | G | G | g | A | A | U | G | U | U | G | U | U | C | C | a | g | 27 | 4 | 11 | c | false | <90% | 1991 | ||
NM_182721 | CREM | 634 | 652 | a | U | U | G | G | g | A | A | U | G | U | U | G | U | U | C | C | a | g | 27 | 4 | 11 | c | false | <90% | 2065 | ||
NM_182722 | CREM | 677 | 695 | a | U | U | G | G | g | A | A | U | G | U | U | G | U | U | C | C | a | g | 27 | 4 | 11 | c | false | <90% | 2108 | ||
NM_182723 | CREM | 713 | 731 | a | U | U | G | G | g | A | A | U | G | U | U | G | U | U | C | C | a | g | 27 | 4 | 11 | c | false | <90% | 2144 | ||
NM_182853 | CREM | 757 | 775 | a | U | U | G | G | g | A | A | U | G | U | U | G | U | U | C | C | a | g | 27 | 4 | 11 | c | false | <90% | 2188 | ||
NM_183012 | CREM | 899 | 917 | a | U | U | G | G | g | A | A | U | G | U | U | G | U | U | C | C | a | g | 27 | 4 | 11 | c | false | <90% | 2330 | ||
NM_183011 | CREM | 1088 | 1106 | a | U | U | G | G | g | A | A | U | G | U | U | G | U | U | C | C | a | g | 27 | 4 | 11 | c | false | <90% | 2519 | ||
NM_183013 | CREM | 1256 | 1274 | a | U | U | G | G | g | A | A | U | G | U | U | G | U | U | C | C | a | g | 27 | 4 | 11 | c | false | <90% | 2687 | ||
NM_015271 | TRIM2 | 6180 | 6198 | a | U | U | G | G | C | u | A | U | G | U | U | G | U | U | C | C | a | a | 24 | 4 | 10 | c | false | <90% | 6734 | ||
NM_006382 | CDRT1 | 949 | 967 | g | U | U | G | G | C | A | A | U | G | c | U | G | a | U | C | C | U | U | 17 | 3 | 9 | c | false | <90% | 1305 | ||
NM_006766 | MYST3 | 2171 | 2189 | U | U | U | G | G | C | A | A | a | G | U | U | G | U | U | u | C | U | U | 13 | 2 | 8 | c | false | <90% | 7861 | ||
NM_015657 | ABCA12 | 2608 | 2626 | U | U | U | G | G | C | A | A | U | a | U | U | c | U | U | C | C | U | a | 1 | 3 | 9 | false | <90% | 8097 | |||
NM_173076 | ABCA12 | 3623 | 3641 | U | U | U | G | G | C | A | A | U | a | U | U | c | U | U | C | C | U | a | 1 | 3 | 9 | false | <90% | 9112 | |||
NM_022463 | NXN | 2860 | 2878 | g | U | U | G | a | C | A | c | U | G | U | U | G | U | U | C | C | U | U | -15 | 3 | 11 | bc | false | <90% | 3004 | ||
NM_032550 | AFAP1L2 | 3706 | 3724 | a | U | U | G | G | C | A | g | U | G | c | U | G | U | U | C | C | U | U | -25 | 3 | 8 | c | false | <90% | 3985 | ||
NM_001001936 | AFAP1L2 | 3718 | 3736 | a | U | U | G | G | C | A | g | U | G | c | U | G | U | U | C | C | U | U | -25 | 3 | 8 | c | false | <90% | 3997 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2046
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