Automatic recommendation
Not OK - siRNA is not specific
29 hits were found for CAUAGAAGCAGAACCUCCA (22 guide strand hits and 7 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 | |||||||||||||
| XR_016297 | LOC402222 | 38 | 56 | u | u | U | A | G | A | A | G | C | A | G | A | A | C | C | U | C | a | A | 83 | 3 | 15 | ac | false | <90% | 1966 | ||
| XR_019180 | LOC649933 | 38 | 56 | u | u | U | A | G | A | A | G | C | A | G | A | A | C | C | U | C | a | A | 83 | 3 | 15 | ac | false | <90% | 1967 | ||
| NM_152320 | ZNF641 | 762 | 780 | a | c | U | A | G | A | A | G | C | A | G | A | A | C | C | U | C | C | c | 81 | 3 | 16 | abc | false | <90% | 2326 | ||
| XR_019392 | LOC651053 | 38 | 56 | u | c | a | A | G | A | A | G | C | A | G | A | A | C | C | U | C | a | A | 64 | 4 | 14 | c | false | <90% | 1987 | ||
| NM_020939 | CPNE5 | 327 | 345 | a | g | g | A | G | A | A | G | C | A | G | A | A | C | C | U | C | C | g | 62 | 4 | 15 | bc | false | <90% | 3339 | ||
| XR_016647 | LOC392343 | 932 | 950 | C | A | g | A | G | A | A | G | C | A | G | A | A | C | u | U | C | C | A | 55 | 2 | 11 | c | false | <90% | 1398 | ||
| NR_003370 | LOC730092 | 5794 | 5812 | g | u | a | A | G | A | A | G | C | A | G | A | A | C | u | U | C | C | A | 42 | 4 | 11 | c | false | <90% | 26557 | ||
| NM_015202 | KIAA0556 | 3052 | 3070 | C | A | U | A | a | A | A | G | C | A | G | A | c | C | C | U | C | C | c | 33 | 3 | 7 | false | <90% | 6618 | |||
| NM_133650 | SYNE1 | 2052 | 2070 | g | g | a | u | G | A | A | G | C | A | G | A | A | C | C | U | C | C | A | 30 | 4 | 15 | bc | false | <90% | 3801 | ||
| NM_015293 | SYNE1 | 8993 | 9011 | g | g | a | u | G | A | A | G | C | A | G | A | A | C | C | U | C | C | A | 30 | 4 | 15 | bc | false | <90% | 10742 | ||
| NM_033071 | SYNE1 | 25594 | 25612 | g | g | a | u | G | A | A | G | C | A | G | A | A | C | C | U | C | C | A | 30 | 4 | 15 | bc | false | <90% | 27435 | ||
| NM_182961 | SYNE1 | 25903 | 25921 | g | g | a | u | G | A | A | G | C | A | G | A | A | C | C | U | C | C | A | 30 | 4 | 15 | bc | false | <90% | 27652 | ||
| NM_182543 | NSUN6 | 1335 | 1353 | C | A | c | A | G | A | A | G | g | A | G | A | A | C | C | U | C | C | A | 20 | 2 | 10 | bc | false | <90% | 2246 | ||
| NM_021132 | PPP3CB | 377 | 395 | g | A | U | A | G | A | A | G | u | A | G | A | A | g | C | U | C | C | A | 18 | 3 | 7 | c | false | <90% | 3079 | ||
| NM_001080113 | PP8961 | 278 | 296 | C | A | c | A | G | c | A | G | C | A | G | A | A | C | C | U | C | C | u | 12 | 3 | 12 | bc | false | <90% | 2596 | ||
| NM_020382 | SETD8 | 438 | 456 | u | g | a | A | G | c | A | G | C | A | G | A | A | C | C | U | C | C | A | 3 | 4 | 13 | bc | false | <90% | 2765 | ||
| XR_018348 | LOC647597 | 669 | 687 | u | g | a | A | G | c | A | G | C | A | G | A | A | C | C | U | C | C | A | 3 | 4 | 13 | bc | false | <90% | 2983 | ||
| NM_017600 | GOLGA2L1 | 1954 | 1972 | a | u | g | A | G | A | u | G | C | A | G | A | A | C | C | U | C | C | A | 0 | 4 | 12 | bc | false | <90% | 2279 | ||
| NM_015186 | VPS13A | 2009 | 2027 | C | A | U | A | G | A | A | G | C | u | G | A | A | C | C | U | u | u | A | -8 | 3 | 9 | c | false | <90% | 10052 | ||
| NM_001018038 | VPS13A | 2009 | 2027 | C | A | U | A | G | A | A | G | C | u | G | A | A | C | C | U | u | u | A | -8 | 3 | 9 | c | false | <90% | 10135 | ||
| NM_001018037 | VPS13A | 2009 | 2027 | C | A | U | A | G | A | A | G | C | u | G | A | A | C | C | U | u | u | A | -8 | 3 | 9 | c | false | <90% | 11145 | ||
| NM_033305 | VPS13A | 2009 | 2027 | C | A | U | A | G | A | A | G | C | u | G | A | A | C | C | U | u | u | A | -8 | 3 | 9 | c | false | <90% | 11262 | ||
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_198156 | VHL | 1289 | 1307 | U | a | G | A | G | G | U | U | C | U | G | C | c | U | C | U | A | U | u | 73 | 3 | 10 | false | <90% | 2845 | |||
| NM_000551 | VHL | 1412 | 1430 | U | a | G | A | G | G | U | U | C | U | G | C | c | U | C | U | A | U | u | 73 | 3 | 10 | false | <90% | 2968 | |||
| NM_030649 | CENTB5 | 858 | 876 | c | G | G | A | G | G | U | U | C | U | G | C | U | U | C | g | A | g | G | 69 | 3 | 14 | c | false | <90% | 2280 | ||
| NM_021652 | SMA4 | 11 | 29 | a | G | c | A | G | G | U | U | C | U | G | C | U | U | C | U | u | U | G | 54 | 3 | 13 | c | false | <90% | 1296 | ||
| XM_001124748 | LOC730390 | 11 | 29 | a | G | c | A | G | G | U | U | C | U | G | C | U | U | C | U | u | U | G | 54 | 3 | 13 | c | false | <90% | 1298 | ||
| NM_024915 | GRHL2 | 3583 | 3601 | U | G | G | A | G | G | g | U | C | U | G | C | U | U | C | U | A | g | c | 26 | 3 | 10 | c | false | <90% | 4792 | ||
| NM_024636 | STEAP4 | 703 | 721 | U | G | G | A | G | G | U | U | C | c | c | C | U | U | C | U | A | U | u | -49 | 3 | 9 | c | false | <90% | 4454 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1877
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