Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
34 hits were found for UUUGGAGAGUGGCAGGUGG (13 guide strand hits and 21 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_182811 | PLCG1 | 4708 | 4726 | a | g | a | G | G | A | G | A | G | U | G | G | C | A | G | G | U | G | G | 67 | 3 | 16 | bc | false | <90% | 5202 | ||
NM_002660 | PLCG1 | 4711 | 4729 | a | g | a | G | G | A | G | A | G | U | G | G | C | A | G | G | U | G | G | 67 | 3 | 16 | bc | false | <90% | 5205 | ||
NM_004958 | FRAP1 | 5339 | 5357 | c | U | U | G | G | A | G | A | G | U | G | G | C | A | G | c | U | G | a | 66 | 3 | 14 | c | false | <90% | 8680 | ||
XR_017421 | LOC400129 | 1092 | 1110 | c | a | a | G | G | A | G | A | G | U | G | G | C | A | G | G | a | G | G | 43 | 4 | 13 | c | false | <90% | 1300 | ||
XR_019239 | LOC400129 | 1092 | 1110 | c | a | a | G | G | A | G | A | G | U | G | G | C | A | G | G | a | G | G | 43 | 4 | 13 | c | false | <90% | 1300 | ||
NM_022044 | SDF2L1 | 770 | 788 | g | a | U | G | G | A | G | g | G | U | G | G | C | A | G | G | U | G | G | 24 | 3 | 11 | bc | false | <90% | 876 | ||
XM_295058 | LOC339760 | 452 | 470 | U | g | U | G | G | g | G | A | G | U | G | G | C | A | G | G | U | G | a | 20 | 3 | 12 | bc | false | <90% | 1365 | ||
XM_944576 | LOC651281 | 788 | 806 | U | g | U | G | G | g | G | A | G | U | G | G | C | A | G | G | U | G | a | 20 | 3 | 12 | bc | false | <90% | 1974 | ||
XR_017539 | LOC647305 | 364 | 382 | U | U | U | G | a | g | G | A | G | U | G | G | C | A | G | G | U | G | G | -14 | 2 | 13 | bc | false | <90% | 773 | ||
XR_019398 | LOC647305 | 364 | 382 | U | U | U | G | a | g | G | A | G | U | G | G | C | A | G | G | U | G | G | -14 | 2 | 13 | bc | false | <90% | 783 | ||
XM_001131744 | LOC732060 | 1165 | 1183 | a | U | U | G | G | u | G | A | c | U | G | G | C | A | G | G | U | G | G | -25 | 3 | 10 | bc | false | <90% | 1692 | ||
XM_001126476 | LOC728073 | 1165 | 1183 | a | U | U | G | G | u | G | A | c | U | G | G | C | A | G | G | U | G | G | -25 | 3 | 10 | bc | false | <90% | 1694 | ||
NM_015215 | CAMTA1 | 5877 | 5895 | U | U | U | G | c | A | G | A | G | g | G | G | C | A | G | G | U | G | u | -39 | 3 | 8 | bc | false | <90% | 8457 |
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 | |||||||||||||
XM_001127301 | LOC727992 | 203 | 221 | u | C | A | C | C | U | G | C | C | A | C | U | C | U | a | g | A | A | A | 47 | 3 | 13 | c | false | <90% | 348 | ||
XM_001132525 | LOC731142 | 203 | 221 | u | C | A | C | C | U | G | C | C | A | C | U | C | U | a | g | A | A | A | 47 | 3 | 13 | c | false | <90% | 348 | ||
XR_016078 | LOC732203 | 1874 | 1892 | C | C | A | C | u | U | G | C | C | A | C | U | C | U | C | C | A | g | u | 40 | 3 | 12 | c | false | <90% | 3055 | ||
XR_017637 | LOC646555 | 1903 | 1921 | C | C | A | C | u | U | G | C | C | A | C | U | C | U | C | C | A | g | u | 40 | 3 | 12 | c | false | <90% | 4161 | ||
NM_145294 | WDR90 | 4945 | 4963 | C | C | A | C | C | U | G | C | C | A | C | c | C | U | C | C | c | u | c | 35 | 4 | 11 | false | <90% | 5541 | |||
NM_152363 | ANKRD41 | 1106 | 1124 | g | C | A | C | C | U | G | C | C | A | g | U | C | U | C | C | A | c | u | 29 | 4 | 9 | c | false | <90% | 2893 | ||
XM_939337 | RBM20 | 184 | 202 | u | C | A | C | C | U | G | C | C | A | g | U | C | U | C | C | A | g | c | 29 | 4 | 9 | c | false | <90% | 7108 | ||
XM_291671 | RBM20 | 184 | 202 | u | C | A | C | C | U | G | C | C | A | g | U | C | U | C | C | A | g | c | 29 | 4 | 9 | c | false | <90% | 7108 | ||
NM_153029 | N4BP1 | 5832 | 5850 | u | C | A | C | C | U | c | C | C | A | C | U | C | U | C | C | A | c | u | 24 | 4 | 10 | c | false | <90% | 7121 | ||
NM_172130 | KCNAB2 | 1766 | 1784 | C | C | A | C | C | U | c | C | C | A | C | U | u | U | C | C | A | A | g | 18 | 3 | 6 | false | <90% | 3129 | |||
NM_003636 | KCNAB2 | 1808 | 1826 | C | C | A | C | C | U | c | C | C | A | C | U | u | U | C | C | A | A | g | 18 | 3 | 6 | false | <90% | 3171 | |||
NM_006465 | ARID3B | 1901 | 1919 | C | C | A | C | u | U | G | C | C | A | C | U | C | U | C | C | u | g | u | 17 | 4 | 11 | c | false | <90% | 4253 | ||
XM_942072 | CPN2 | 852 | 870 | g | C | A | C | C | U | G | C | C | g | C | U | C | U | C | C | A | u | c | 7 | 4 | 8 | c | false | <90% | 3028 | ||
NM_001080513 | CPN2 | 852 | 870 | g | C | A | C | C | U | G | C | C | g | C | U | C | U | C | C | A | u | c | 7 | 4 | 8 | c | false | <90% | 3028 | ||
NM_153442 | GPR26 | 6927 | 6945 | u | u | g | C | C | U | G | u | C | A | C | U | C | U | C | C | A | A | A | 4 | 4 | 11 | bc | false | <90% | 7512 | ||
NM_014238 | KSR1 | 2418 | 2436 | u | C | A | g | C | U | G | C | C | A | u | U | C | U | C | C | A | A | A | 0 | 3 | 8 | c | false | <90% | 4552 | ||
NM_018028 | SAMD4B | 3448 | 3466 | C | C | A | C | C | U | G | C | C | u | C | U | C | c | C | C | A | A | g | -7 | 3 | 9 | c | false | <90% | 4543 | ||
NM_001002837 | PIB5PA | 2014 | 2032 | C | C | A | C | C | U | G | C | C | u | C | U | C | U | C | C | u | g | c | -13 | 4 | 9 | c | false | <90% | 2238 | ||
NM_014422 | PIB5PA | 2192 | 2210 | C | C | A | C | C | U | G | C | C | u | C | U | C | U | C | C | u | g | c | -13 | 4 | 9 | c | false | <90% | 2416 | ||
NM_004599 | SREBF2 | 3434 | 3452 | C | C | A | C | C | U | G | C | C | c | C | U | C | U | C | C | u | u | c | -13 | 4 | 9 | c | false | <90% | 4325 | ||
NM_001001661 | ZNF425 | 495 | 513 | C | C | A | C | C | U | u | C | C | A | g | U | C | U | C | C | A | A | g | -32 | 3 | 7 | c | false | <90% | 3184 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3376
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