Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
41 hits were found for GAACAAACCCAAGGAAAUU (28 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 | |||||||||||||
XM_933286 | LOC645946 | 94 | 112 | G | A | A | C | A | A | A | C | C | C | A | A | G | G | c | A | A | g | a | 67 | 3 | 14 | c | false | <90% | 825 | ||
XM_944541 | LOC645946 | 94 | 112 | G | A | A | C | A | A | A | C | C | C | A | A | G | G | c | A | A | g | a | 67 | 3 | 14 | c | false | <90% | 825 | ||
NM_012219 | MRAS | 2765 | 2783 | a | A | A | g | A | A | A | C | C | C | A | A | G | G | A | A | A | g | U | 58 | 3 | 13 | c | false | <90% | 4454 | ||
NM_015601 | HERC4 | 1156 | 1174 | a | A | A | u | A | A | A | C | C | C | A | A | G | G | A | A | A | g | U | 58 | 3 | 13 | c | false | <90% | 4507 | ||
NM_022079 | HERC4 | 1156 | 1174 | a | A | A | u | A | A | A | C | C | C | A | A | G | G | A | A | A | g | U | 58 | 3 | 13 | c | false | <90% | 4531 | ||
XM_001133395 | LOC731379 | 232 | 250 | G | u | A | g | A | A | A | C | C | C | A | A | G | G | A | A | A | U | g | 46 | 3 | 14 | bc | false | <90% | 411 | ||
XM_001134101 | LOC729898 | 232 | 250 | G | u | A | g | A | A | A | C | C | C | A | A | G | G | A | A | A | U | g | 46 | 3 | 14 | bc | false | <90% | 411 | ||
NM_007212 | RNF2 | 1196 | 1214 | G | A | A | C | A | A | A | C | C | C | A | u | G | G | A | A | c | U | U | 42 | 2 | 11 | false | <90% | 3551 | |||
XM_938953 | LOC389072 | 1439 | 1457 | G | A | A | C | A | A | A | C | C | C | A | A | G | G | A | u | c | a | a | 42 | 4 | 15 | c | false | <90% | 2315 | ||
NM_001080475 | LOC389072 | 1439 | 1457 | G | A | A | C | A | A | A | C | C | C | A | A | G | G | A | u | c | a | a | 42 | 4 | 15 | c | false | <90% | 2315 | ||
NM_207345 | CLEC9A | 1586 | 1604 | G | A | A | C | A | A | A | C | g | C | A | A | G | G | A | A | A | U | a | 34 | 2 | 9 | bc | false | <90% | 1673 | ||
NM_138700 | TRIM40 | 25 | 43 | u | A | A | C | A | A | A | C | a | C | A | A | G | G | A | A | A | c | c | 30 | 4 | 8 | c | false | <90% | 997 | ||
NM_001011666 | CREB5 | 6464 | 6482 | a | A | A | C | A | A | A | C | a | C | A | A | a | G | A | A | A | U | U | 27 | 3 | 7 | false | <90% | 7772 | |||
NM_182899 | CREB5 | 6880 | 6898 | a | A | A | C | A | A | A | C | a | C | A | A | a | G | A | A | A | U | U | 27 | 3 | 7 | false | <90% | 8188 | |||
NM_004904 | CREB5 | 6905 | 6923 | a | A | A | C | A | A | A | C | a | C | A | A | a | G | A | A | A | U | U | 27 | 3 | 7 | false | <90% | 8213 | |||
NM_182898 | CREB5 | 7224 | 7242 | a | A | A | C | A | A | A | C | a | C | A | A | a | G | A | A | A | U | U | 27 | 3 | 7 | false | <90% | 8532 | |||
NM_001004334 | GPR179 | 2094 | 2112 | c | c | A | C | A | A | A | a | C | C | A | A | G | G | A | A | A | U | g | 19 | 4 | 10 | bc | false | <90% | 7980 | ||
NM_177531 | PKHD1L1 | 1980 | 1998 | G | A | A | C | A | A | A | C | C | a | A | A | G | G | A | A | A | a | c | 9 | 3 | 9 | c | false | <90% | 14017 | ||
XM_931961 | LOC643983 | 43 | 61 | c | g | c | C | A | A | A | C | a | C | A | A | G | G | A | A | A | U | U | 6 | 4 | 10 | bc | false | <90% | 597 | ||
XR_016340 | KRT223P | 768 | 786 | G | A | A | C | A | A | c | C | C | C | A | A | G | G | A | A | g | a | a | 2 | 4 | 9 | c | false | <90% | 1301 | ||
XR_018285 | KRT223P | 768 | 786 | G | A | A | C | A | A | c | C | C | C | A | A | G | G | A | A | g | a | a | 2 | 4 | 9 | c | false | <90% | 1301 | ||
XR_016854 | LOC645204 | 249 | 267 | G | A | A | g | A | A | A | C | u | C | A | A | G | G | A | A | A | U | a | -1 | 3 | 9 | bc | false | <90% | 2292 | ||
XR_018753 | LOC645204 | 249 | 267 | G | A | A | g | A | A | A | C | u | C | A | A | G | G | A | A | A | U | a | -1 | 3 | 9 | bc | false | <90% | 2292 | ||
NM_020242 | KIF15 | 1184 | 1202 | G | A | A | g | A | c | A | C | C | C | A | A | G | G | A | A | A | U | g | -5 | 3 | 12 | bc | false | <90% | 4775 | ||
NM_030960 | SPACA1 | 1018 | 1036 | u | A | A | C | A | A | A | C | C | a | A | A | G | G | A | u | A | U | U | -10 | 3 | 8 | c | false | <90% | 1501 | ||
NM_138780 | SYTL5 | 1693 | 1711 | G | A | A | C | A | A | c | u | C | C | A | A | G | G | A | A | A | U | a | -33 | 3 | 10 | bc | false | <90% | 2193 | ||
XM_943660 | LOC645323 | 194 | 212 | c | A | A | C | c | A | A | C | C | a | A | A | G | G | A | A | A | U | U | -36 | 3 | 9 | bc | false | <90% | 1115 | ||
XM_932810 | LOC645323 | 194 | 212 | c | A | A | C | c | A | A | C | C | a | A | A | G | G | A | A | A | U | U | -36 | 3 | 9 | bc | false | <90% | 1115 |
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_172037 | RDH10 | 777 | 795 | A | A | g | U | U | C | C | U | U | G | G | G | a | U | U | G | U | U | C | 70 | 2 | 9 | false | <90% | 2751 | |||
XM_937933 | LOC646561 | 1796 | 1814 | g | u | U | U | U | C | C | U | U | G | G | G | U | c | U | G | U | U | g | 62 | 4 | 11 | c | false | <90% | 2845 | ||
XM_929496 | LOC646561 | 1798 | 1816 | g | u | U | U | U | C | C | U | U | G | G | G | U | c | U | G | U | U | g | 62 | 4 | 11 | c | false | <90% | 2847 | ||
XR_017975 | C14orf139 | 1646 | 1664 | A | A | U | U | U | C | C | U | U | G | G | G | c | U | g | G | U | U | u | 59 | 3 | 12 | false | <90% | 2824 | |||
XR_017875 | C14orf139 | 1646 | 1664 | A | A | U | U | U | C | C | U | U | G | G | G | c | U | g | G | U | U | u | 59 | 3 | 12 | false | <90% | 2825 | |||
NM_032164 | ZNF394 | 93 | 111 | g | A | g | U | U | C | C | U | U | G | G | G | U | U | U | G | c | U | C | 54 | 3 | 13 | c | false | <90% | 2259 | ||
NM_006147 | IRF6 | 2137 | 2155 | u | u | U | U | U | C | C | U | U | G | G | u | U | U | U | G | U | U | a | 47 | 4 | 9 | false | <90% | 2171 | |||
NM_017758 | ALKBH5 | 1539 | 1557 | u | u | U | U | U | C | C | U | U | G | G | u | U | U | U | G | U | U | g | 47 | 4 | 9 | false | <90% | 2992 | |||
NM_025000 | C2orf37 | 2395 | 2413 | u | u | c | U | U | C | C | U | U | G | G | u | U | U | U | G | U | U | C | 33 | 4 | 8 | false | <90% | 5744 | |||
NM_000676 | ADORA2B | 889 | 907 | A | A | U | U | U | C | u | U | U | G | G | G | U | g | U | G | U | U | C | 14 | 2 | 6 | c | false | <90% | 1885 | ||
NM_014363 | SACS | 3560 | 3578 | A | A | U | U | U | C | C | a | U | G | G | G | U | U | U | G | g | a | C | 11 | 3 | 8 | c | false | <90% | 14805 | ||
NM_194282 | LIN54 | 2867 | 2885 | A | A | U | U | U | g | C | U | U | G | G | G | U | U | U | c | U | U | a | 5 | 3 | 9 | c | false | <90% | 5772 | ||
NM_003417 | ZNF264 | 140 | 158 | c | c | c | U | U | C | C | g | U | G | G | G | U | U | U | G | U | U | C | 4 | 4 | 11 | bc | false | <90% | 12171 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2859
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