Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
40 hits were found for ACUAUAAAUUAAAUACAGA (12 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_152588 | TMTC2 | 4229 | 4247 | A | C | U | A | U | A | A | A | U | U | A | A | g | U | A | g | A | G | A | 63 | 2 | 12 | false | <90% | 4855 | |||
NM_016588 | NRN1 | 1982 | 2000 | A | u | U | A | U | A | A | A | U | U | A | A | A | U | u | C | A | G | c | 58 | 3 | 12 | c | false | <90% | 2072 | ||
NM_013339 | ALG6 | 854 | 872 | g | C | U | A | U | A | A | A | U | U | A | u | A | a | A | C | A | G | A | 44 | 3 | 10 | false | <90% | 2003 | |||
NM_002717 | PPP2R2A | 2062 | 2080 | u | u | U | u | U | A | A | A | U | U | A | A | A | U | A | C | A | G | c | 44 | 4 | 14 | bc | false | <90% | 2385 | ||
NM_020810 | TRMT5 | 1107 | 1125 | A | C | U | g | U | A | A | A | U | U | A | A | A | U | A | a | A | G | u | 32 | 3 | 11 | c | false | <90% | 5302 | ||
NM_001004316 | FLJ16641 | 462 | 480 | g | C | U | A | a | A | A | A | U | U | A | A | A | U | A | u | A | G | A | 20 | 3 | 10 | c | false | <90% | 2881 | ||
NM_000397 | CYBB | 2721 | 2739 | g | C | U | A | U | A | A | A | a | U | A | A | A | U | g | C | A | G | A | 13 | 3 | 7 | c | false | <90% | 4266 | ||
NM_152292 | RG9MTD2 | 2220 | 2238 | u | C | U | A | U | A | A | A | U | c | A | A | A | U | A | C | A | c | A | 12 | 3 | 8 | c | false | <90% | 3710 | ||
NM_005664 | MKRN3 | 2689 | 2707 | g | u | a | A | U | A | A | A | g | U | A | A | A | U | A | C | A | G | A | 6 | 4 | 10 | bc | false | <90% | 3107 | ||
NM_033426 | KIAA1737 | 2352 | 2370 | A | C | U | u | U | g | A | A | U | U | A | A | A | U | A | C | A | G | u | -5 | 3 | 12 | bc | false | <90% | 4397 | ||
NM_003410 | ZFX | 5161 | 5179 | c | C | U | A | U | A | A | A | a | U | u | A | A | U | A | C | A | G | A | -23 | 3 | 8 | c | false | <90% | 5811 | ||
NM_013249 | ZNF214 | 2292 | 2310 | A | C | U | A | U | A | A | A | U | a | u | A | A | U | A | C | A | G | u | -49 | 3 | 9 | c | false | <90% | 2628 |
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_006626 | ZBTB6 | 2899 | 2917 | a | C | U | G | U | A | U | U | U | A | A | U | U | U | c | U | A | u | U | 70 | 3 | 13 | c | false | <90% | 4128 | ||
NM_016226 | VPS29 | 1002 | 1020 | c | C | U | G | U | A | U | U | U | A | A | U | U | U | A | a | A | a | a | 64 | 4 | 14 | c | false | <90% | 1089 | ||
NM_057180 | VPS29 | 1014 | 1032 | c | C | U | G | U | A | U | U | U | A | A | U | U | U | A | a | A | a | a | 64 | 4 | 14 | c | false | <90% | 1107 | ||
NM_198273 | LYSMD3 | 3166 | 3184 | U | C | U | G | U | A | U | U | U | A | A | a | U | U | A | U | A | u | a | 58 | 3 | 11 | false | <90% | 4261 | |||
NM_201572 | CACNB2 | 2941 | 2959 | U | C | U | G | U | A | U | U | U | A | A | U | U | a | A | U | u | G | U | 56 | 2 | 13 | c | false | <90% | 3229 | ||
NM_201570 | CACNB2 | 2953 | 2971 | U | C | U | G | U | A | U | U | U | A | A | U | U | a | A | U | u | G | U | 56 | 2 | 13 | c | false | <90% | 3241 | ||
NM_201571 | CACNB2 | 3013 | 3031 | U | C | U | G | U | A | U | U | U | A | A | U | U | a | A | U | u | G | U | 56 | 2 | 13 | c | false | <90% | 3301 | ||
NM_201593 | CACNB2 | 3034 | 3052 | U | C | U | G | U | A | U | U | U | A | A | U | U | a | A | U | u | G | U | 56 | 2 | 13 | c | false | <90% | 3322 | ||
NM_201597 | CACNB2 | 3085 | 3103 | U | C | U | G | U | A | U | U | U | A | A | U | U | a | A | U | u | G | U | 56 | 2 | 13 | c | false | <90% | 3373 | ||
NM_201590 | CACNB2 | 3087 | 3105 | U | C | U | G | U | A | U | U | U | A | A | U | U | a | A | U | u | G | U | 56 | 2 | 13 | c | false | <90% | 3375 | ||
NM_201596 | CACNB2 | 3157 | 3175 | U | C | U | G | U | A | U | U | U | A | A | U | U | a | A | U | u | G | U | 56 | 2 | 13 | c | false | <90% | 3445 | ||
NM_000724 | CACNB2 | 3433 | 3451 | U | C | U | G | U | A | U | U | U | A | A | U | U | a | A | U | u | G | U | 56 | 2 | 13 | c | false | <90% | 3721 | ||
NM_006143 | GPR19 | 1007 | 1025 | U | C | U | G | U | A | U | U | c | A | A | U | U | U | A | U | A | a | U | 37 | 2 | 8 | c | false | <90% | 1409 | ||
NM_001005786 | DAZ2 | 1591 | 1609 | U | C | U | G | U | g | U | U | U | A | A | U | a | U | A | U | A | G | U | 26 | 2 | 6 | false | <90% | 3198 | |||
NM_020420 | DAZ4 | 1665 | 1683 | U | C | U | G | U | g | U | U | U | A | A | U | a | U | A | U | A | G | U | 26 | 2 | 6 | false | <90% | 3271 | |||
NM_020364 | DAZ3 | 1787 | 1805 | U | C | U | G | U | g | U | U | U | A | A | U | a | U | A | U | A | G | U | 26 | 2 | 6 | false | <90% | 3391 | |||
NM_001005785 | DAZ2 | 2153 | 2171 | U | C | U | G | U | g | U | U | U | A | A | U | a | U | A | U | A | G | U | 26 | 2 | 6 | false | <90% | 3756 | |||
NM_020363 | DAZ2 | 2155 | 2173 | U | C | U | G | U | g | U | U | U | A | A | U | a | U | A | U | A | G | U | 26 | 2 | 6 | false | <90% | 3759 | |||
NM_001005375 | DAZ4 | 2215 | 2233 | U | C | U | G | U | g | U | U | U | A | A | U | a | U | A | U | A | G | U | 26 | 2 | 6 | false | <90% | 3821 | |||
NM_004081 | DAZ1 | 2232 | 2250 | U | C | U | G | U | g | U | U | U | A | A | U | a | U | A | U | A | G | U | 26 | 2 | 6 | false | <90% | 3836 | |||
NM_177966 | 2'-PDE | 3551 | 3569 | U | C | U | G | c | A | U | U | U | A | A | U | U | a | A | U | A | G | c | 24 | 3 | 8 | c | false | <90% | 3923 | ||
NM_006353 | HMGN4 | 1829 | 1847 | U | u | U | G | U | A | U | U | g | A | A | U | U | U | A | U | A | G | a | 23 | 3 | 9 | bc | false | <90% | 1980 | ||
NM_001004058 | OR8K5 | 603 | 621 | U | C | U | G | U | A | U | U | U | A | A | U | U | U | g | a | u | c | U | 23 | 4 | 14 | c | false | <90% | 924 | ||
NM_001083900 | DNAH10 | 7826 | 7844 | U | C | U | G | c | A | U | U | U | A | A | U | U | U | A | U | u | c | c | 17 | 4 | 11 | c | false | <90% | 13694 | ||
NM_020962 | NOPE | 6341 | 6359 | U | C | U | G | U | A | U | U | U | A | g | U | U | U | A | U | g | c | U | 12 | 3 | 10 | c | false | <90% | 6485 | ||
NM_018051 | WDR60 | 3469 | 3487 | U | C | U | G | U | A | U | a | U | A | A | U | U | U | A | U | u | u | U | 11 | 3 | 8 | c | false | <90% | 3784 | ||
NM_133493 | CD109 | 6656 | 6674 | a | a | a | G | U | A | U | a | U | A | A | U | U | U | A | U | A | G | U | 4 | 4 | 11 | bc | false | <90% | 9447 | ||
NM_152466 | C17orf69 | 934 | 952 | g | C | U | G | U | A | U | g | a | A | A | U | U | U | A | U | A | G | U | -24 | 3 | 10 | bc | false | <90% | 1219 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1780
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