Automatic recommendation
Not OK - siRNA is not specific
47 hits were found for GCAGAAGCUUUCCAGAAAU (23 guide strand hits and 24 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_000833 | GRIN2A | 1702 | 1720 | G | a | A | G | A | A | G | C | U | U | U | C | C | A | G | A | A | c | U | 85 | 2 | 15 | ac | false | <90% | 6293 | ||
NM_152628 | MGC39715 | 890 | 908 | u | u | A | G | A | A | G | C | U | U | U | C | C | A | G | A | A | A | g | 81 | 3 | 16 | abc | false | <90% | 2444 | ||
NM_206840 | NVL | 2454 | 2472 | G | a | A | G | A | A | G | C | U | U | U | C | a | A | G | A | A | A | g | 73 | 3 | 10 | false | <90% | 2847 | |||
NM_002533 | NVL | 2528 | 2546 | G | a | A | G | A | A | G | C | U | U | U | C | a | A | G | A | A | A | g | 73 | 3 | 10 | false | <90% | 2921 | |||
NM_201430 | RTN3 | 569 | 587 | u | C | A | G | A | A | G | C | U | U | U | C | C | A | u | A | A | u | U | 70 | 3 | 13 | c | false | <90% | 2542 | ||
NM_006054 | RTN3 | 569 | 587 | u | C | A | G | A | A | G | C | U | U | U | C | C | A | u | A | A | u | U | 70 | 3 | 13 | c | false | <90% | 2583 | ||
NM_201429 | RTN3 | 626 | 644 | u | C | A | G | A | A | G | C | U | U | U | C | C | A | u | A | A | u | U | 70 | 3 | 13 | c | false | <90% | 2668 | ||
NM_201428 | RTN3 | 2900 | 2918 | u | C | A | G | A | A | G | C | U | U | U | C | C | A | u | A | A | u | U | 70 | 3 | 13 | c | false | <90% | 4942 | ||
NM_001036 | RYR3 | 3992 | 4010 | a | g | u | G | A | A | G | C | U | U | U | C | C | A | G | A | A | A | a | 62 | 4 | 15 | bc | false | <90% | 15563 | ||
NM_001077242 | DEPDC7 | 946 | 964 | G | C | A | G | A | A | G | C | U | U | U | C | C | u | G | A | g | c | a | 49 | 4 | 13 | c | false | <90% | 1774 | ||
NM_139160 | DEPDC7 | 1185 | 1203 | G | C | A | G | A | A | G | C | U | U | U | C | C | u | G | A | g | c | a | 49 | 4 | 13 | c | false | <90% | 2013 | ||
NM_005562 | LAMC2 | 3461 | 3479 | G | C | A | G | A | A | G | C | U | U | U | C | C | c | G | A | g | c | c | 49 | 4 | 13 | c | false | <90% | 5175 | ||
NM_001031712 | TRMT11 | 1318 | 1336 | G | C | A | G | A | A | G | C | U | U | U | C | C | A | G | u | c | A | c | 45 | 3 | 15 | c | false | <90% | 1967 | ||
NM_002035 | FVT1 | 696 | 714 | G | C | A | G | A | A | G | C | U | U | U | g | C | A | G | A | u | g | g | 35 | 4 | 11 | false | <90% | 2272 | |||
NM_001004439 | ITGA11 | 838 | 856 | u | C | A | G | A | g | G | C | U | U | U | C | C | A | G | A | A | g | g | 27 | 4 | 11 | c | false | <90% | 5035 | ||
XM_001132805 | LOC731351 | 341 | 359 | u | a | A | G | A | A | G | g | U | U | U | C | C | A | G | A | A | A | a | 19 | 4 | 10 | bc | false | <90% | 1047 | ||
XM_001130997 | LOC728442 | 388 | 406 | u | a | A | G | A | A | G | g | U | U | U | C | C | A | G | A | A | A | a | 19 | 4 | 10 | bc | false | <90% | 1094 | ||
NM_001031689 | PLAA | 262 | 280 | a | C | A | G | g | A | G | C | U | U | U | a | C | A | G | A | A | A | U | 12 | 3 | 7 | false | <90% | 2719 | |||
NM_004253 | PLAA | 9 | 27 | a | C | A | G | g | A | G | C | U | U | U | a | C | A | G | A | A | A | U | 12 | 3 | 7 | false | <90% | 3237 | |||
NM_178828 | C9orf79 | 3915 | 3933 | G | C | A | G | A | u | G | C | U | U | U | C | C | A | G | A | g | c | U | 10 | 3 | 10 | c | false | <90% | 4445 | ||
NM_153265 | EML3 | 809 | 827 | G | C | A | G | A | A | G | C | U | c | U | C | C | A | G | g | A | A | g | -13 | 3 | 9 | c | false | <90% | 3265 | ||
NM_004475 | FLOT2 | 1156 | 1174 | G | C | A | G | A | A | G | C | c | U | a | C | C | A | G | A | A | A | U | -21 | 2 | 8 | c | false | <90% | 2659 | ||
NM_001195 | BFSP1 | 1814 | 1832 | G | C | A | G | A | A | G | C | c | U | g | C | C | A | G | A | A | A | a | -26 | 3 | 8 | c | false | <90% | 2176 |
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_004776 | B4GALT5 | 2484 | 2502 | g | U | U | U | C | U | G | G | A | A | A | G | a | U | U | C | U | u | u | 79 | 4 | 11 | false | <90% | 4646 | |||
NM_199512 | CCDC80 | 2151 | 2169 | A | U | a | U | C | U | G | G | A | A | A | G | u | U | U | C | U | G | C | 70 | 2 | 9 | false | <90% | 3981 | |||
NM_199511 | CCDC80 | 2748 | 2766 | A | U | a | U | C | U | G | G | A | A | A | G | u | U | U | C | U | G | C | 70 | 2 | 9 | false | <90% | 4578 | |||
NM_003235 | TG | 5497 | 5515 | A | U | c | U | C | U | G | G | A | A | A | G | a | U | U | C | U | G | a | 65 | 3 | 9 | false | <90% | 8453 | |||
NM_001980 | STX2 | 3265 | 3283 | A | U | U | U | C | U | G | G | A | A | A | G | a | U | U | u | U | G | g | 58 | 3 | 12 | false | <90% | 3343 | |||
NM_194356 | STX2 | 3391 | 3409 | A | U | U | U | C | U | G | G | A | A | A | G | a | U | U | u | U | G | g | 58 | 3 | 12 | false | <90% | 3469 | |||
NM_002245 | KCNK1 | 968 | 986 | A | g | U | U | C | U | G | G | A | A | A | c | C | U | U | C | U | G | u | 49 | 3 | 9 | false | <90% | 1901 | |||
NM_025144 | ALPK1 | 451 | 469 | g | U | c | U | C | U | G | G | A | A | A | a | C | U | U | C | U | G | C | 44 | 3 | 8 | false | <90% | 4281 | |||
NM_005453 | ZBTB22 | 895 | 913 | A | c | a | U | C | U | G | G | A | A | A | G | C | U | g | C | U | G | C | 44 | 3 | 11 | c | false | <90% | 2647 | ||
NM_000132 | F8 | 541 | 559 | c | c | U | a | C | U | G | G | A | A | A | G | C | U | U | C | U | G | a | 44 | 4 | 14 | bc | false | <90% | 9030 | ||
NM_000220 | KCNJ1 | 727 | 745 | A | U | U | U | a | U | G | G | A | A | A | G | C | U | U | C | U | G | a | 43 | 2 | 13 | bc | false | <90% | 2332 | ||
NM_153764 | KCNJ1 | 841 | 859 | A | U | U | U | a | U | G | G | A | A | A | G | C | U | U | C | U | G | a | 43 | 2 | 13 | bc | false | <90% | 2446 | ||
NM_153765 | KCNJ1 | 974 | 992 | A | U | U | U | a | U | G | G | A | A | A | G | C | U | U | C | U | G | a | 43 | 2 | 13 | bc | false | <90% | 2579 | ||
NM_153766 | KCNJ1 | 1011 | 1029 | A | U | U | U | a | U | G | G | A | A | A | G | C | U | U | C | U | G | a | 43 | 2 | 13 | bc | false | <90% | 2616 | ||
NM_153767 | KCNJ1 | 1144 | 1162 | A | U | U | U | a | U | G | G | A | A | A | G | C | U | U | C | U | G | a | 43 | 2 | 13 | bc | false | <90% | 2749 | ||
NM_000322 | PRPH2 | 2304 | 2322 | A | U | U | U | C | U | G | G | A | A | u | G | C | U | U | C | U | G | C | 38 | 1 | 10 | c | false | <90% | 2975 | ||
NM_031276 | TEX11 | 2300 | 2318 | A | U | U | a | C | U | G | G | A | A | A | G | C | U | U | C | c | u | g | 32 | 4 | 12 | c | false | <90% | 3029 | ||
NM_001003811 | TEX11 | 2422 | 2440 | A | U | U | a | C | U | G | G | A | A | A | G | C | U | U | C | c | u | g | 32 | 4 | 12 | c | false | <90% | 3151 | ||
NM_014299 | BRD4 | 4017 | 4035 | c | U | U | U | C | U | G | G | g | A | A | G | a | U | U | C | U | G | C | 27 | 3 | 7 | false | <90% | 4635 | |||
NM_015267 | CUTL2 | 5795 | 5813 | g | U | U | U | C | U | G | G | A | A | g | G | C | a | U | C | U | G | C | 17 | 3 | 9 | c | false | <90% | 6841 | ||
NM_000046 | ARSB | 3653 | 3671 | A | U | U | U | C | U | G | G | A | A | c | G | C | U | g | C | U | G | a | 9 | 3 | 10 | c | false | <90% | 6089 | ||
NM_024915 | GRHL2 | 2939 | 2957 | c | U | U | U | C | U | G | G | A | g | A | G | C | c | U | C | U | G | C | -4 | 3 | 8 | c | false | <90% | 4792 | ||
NM_194251 | GPR151 | 662 | 680 | A | U | U | U | C | U | G | G | A | g | A | G | C | U | U | a | U | G | a | -13 | 3 | 9 | c | false | <90% | 1260 | ||
NM_020546 | ADCY2 | 2008 | 2026 | u | U | U | g | C | U | G | G | A | c | A | G | C | U | U | C | U | G | C | -21 | 3 | 9 | bc | false | <90% | 6553 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2840
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