Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
31 hits were found for GACCACAGCAGAGAUUUAU (14 guide strand hits and 17 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_020987 | ANK3 | 10386 | 10404 | c | A | C | C | A | C | A | G | C | A | G | A | G | u | U | U | U | c | U | 75 | 3 | 12 | c | false | <90% | 14771 | ||
NM_152263 | TPM3 | 2238 | 2256 | u | u | a | C | A | C | A | G | C | A | G | A | G | A | U | U | U | c | U | 64 | 4 | 14 | c | false | <90% | 7116 | ||
NM_001115 | ADCY8 | 4368 | 4386 | c | A | C | C | A | C | A | G | C | A | G | A | G | g | a | U | U | A | U | 53 | 3 | 12 | c | false | <90% | 6005 | ||
NM_014805 | EPM2AIP1 | 4054 | 4072 | a | u | u | C | A | C | A | G | C | A | G | A | G | c | U | U | U | A | U | 47 | 4 | 10 | c | false | <90% | 5567 | ||
NM_021982 | SEC24A | 3724 | 3742 | G | A | C | C | A | C | A | G | C | A | G | A | G | A | a | U | c | A | a | 46 | 3 | 14 | c | false | <90% | 6387 | ||
NM_032427 | MAML2 | 4586 | 4604 | G | A | C | C | A | C | A | G | C | A | G | u | G | A | c | U | U | A | g | 36 | 3 | 11 | false | <90% | 5428 | |||
NM_016302 | CRBN | 427 | 445 | a | A | C | a | A | C | A | G | C | A | G | A | G | A | U | a | U | A | U | 35 | 3 | 11 | c | false | <90% | 2231 | ||
NM_016841 | MAPT | 3763 | 3781 | G | A | C | C | A | C | A | G | C | A | G | g | G | A | U | U | g | g | g | 35 | 4 | 11 | false | <90% | 5464 | |||
NM_016834 | MAPT | 3856 | 3874 | G | A | C | C | A | C | A | G | C | A | G | g | G | A | U | U | g | g | g | 35 | 4 | 11 | false | <90% | 5557 | |||
NM_005910 | MAPT | 4030 | 4048 | G | A | C | C | A | C | A | G | C | A | G | g | G | A | U | U | g | g | g | 35 | 4 | 11 | false | <90% | 5731 | |||
NM_016835 | MAPT | 4981 | 4999 | G | A | C | C | A | C | A | G | C | A | G | g | G | A | U | U | g | g | g | 35 | 4 | 11 | false | <90% | 6682 | |||
NM_001340 | CYLC2 | 1199 | 1217 | G | A | a | C | u | C | A | G | C | A | G | A | G | A | U | U | U | A | U | 28 | 2 | 14 | bc | false | <90% | 2119 | ||
NM_005742 | PDIA6 | 2014 | 2032 | c | A | C | C | A | C | A | a | C | A | G | A | G | A | U | U | U | u | a | 28 | 4 | 9 | c | false | <90% | 2344 | ||
NM_152774 | MGC42090 | 1184 | 1202 | G | A | C | C | A | C | A | G | C | u | G | A | u | A | U | U | U | A | a | 1 | 3 | 9 | false | <90% | 3992 |
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_031854 | KRTAP4-12 | 647 | 665 | c | U | A | A | A | U | C | U | C | U | G | C | U | G | U | G | a | a | C | 71 | 3 | 15 | ac | false | <90% | 1077 | ||
NM_018245 | OGDHL | 2620 | 2638 | c | U | A | A | A | U | C | U | C | U | G | C | U | G | a | G | G | c | a | 65 | 4 | 13 | c | false | <90% | 3682 | ||
NM_004473 | FOXE1 | 2299 | 2317 | A | g | A | A | A | U | C | U | C | U | G | C | U | c | U | G | G | U | u | 64 | 3 | 11 | c | false | <90% | 3473 | ||
NM_138389 | FAM114A1 | 580 | 598 | g | c | A | A | A | U | C | U | C | U | G | C | U | G | U | c | G | U | C | 60 | 3 | 13 | c | false | <90% | 2129 | ||
XM_001132321 | LOC730079 | 304 | 322 | A | g | A | A | A | U | C | U | C | U | G | C | U | G | U | G | c | a | g | 57 | 4 | 14 | ac | false | <90% | 384 | ||
NM_016252 | BIRC6 | 854 | 872 | g | U | A | u | A | U | C | U | C | U | G | C | U | G | U | G | G | a | u | 53 | 4 | 13 | c | false | <90% | 16079 | ||
NM_018042 | SLFN12 | 210 | 228 | A | U | A | A | A | U | C | U | C | U | G | C | U | u | U | u | G | U | u | 49 | 3 | 13 | c | false | <90% | 2430 | ||
NM_144583 | ATP6V1C2 | 1681 | 1699 | u | a | A | A | A | U | C | U | C | U | G | u | U | G | U | G | G | U | g | 47 | 4 | 9 | false | <90% | 3112 | |||
NM_001039362 | ATP6V1C2 | 1819 | 1837 | u | a | A | A | A | U | C | U | C | U | G | u | U | G | U | G | G | U | g | 47 | 4 | 9 | false | <90% | 3250 | |||
NM_004438 | EPHA4 | 2768 | 2786 | u | g | A | A | u | U | C | U | C | U | G | C | U | G | U | G | G | U | a | 30 | 4 | 13 | bc | false | <90% | 6364 | ||
XM_001128660 | LOC728866 | 2725 | 2743 | c | c | A | A | A | U | C | U | a | U | G | C | U | G | U | G | G | U | u | 21 | 4 | 9 | bc | false | <90% | 3167 | ||
NM_032121 | DKFZp564K142 | 3443 | 3461 | c | c | A | A | A | U | C | U | a | U | G | C | U | G | U | G | G | U | u | 21 | 4 | 9 | bc | false | <90% | 3898 | ||
NM_001010861 | PAP2D | 3936 | 3954 | A | U | A | A | u | U | C | U | C | U | G | C | U | G | U | G | u | a | u | 17 | 4 | 11 | c | false | <90% | 4008 | ||
NM_001037317 | PAP2D | 3951 | 3969 | A | U | A | A | u | U | C | U | C | U | G | C | U | G | U | G | u | a | u | 17 | 4 | 11 | c | false | <90% | 4023 | ||
NM_052917 | GALNT13 | 4606 | 4624 | A | c | c | A | A | U | C | U | C | U | u | C | U | G | U | G | G | U | C | 7 | 3 | 8 | c | false | <90% | 5674 | ||
NM_178172 | LOC338328 | 2254 | 2272 | A | U | A | A | A | U | u | U | C | U | G | C | U | G | U | G | u | U | g | 5 | 3 | 9 | c | false | <90% | 2281 | ||
NM_002652 | PIP | 536 | 554 | u | g | g | A | A | U | u | U | C | U | G | C | U | G | U | G | G | U | C | 0 | 4 | 12 | bc | false | <90% | 591 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1730
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