Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
40 hits were found for ACAUCAAGGAGAAAAUUAU (32 guide strand hits and 8 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_942521 | USP24 | 1814 | 1832 | u | C | u | U | C | A | A | G | G | A | G | A | A | A | A | U | U | c | U | 75 | 3 | 14 | c | false | <90% | 10051 | ||
| XM_371254 | USP24 | 1832 | 1850 | u | C | u | U | C | A | A | G | G | A | G | A | A | A | A | U | U | c | U | 75 | 3 | 14 | c | false | <90% | 10069 | ||
| NM_032242 | PLXNA1 | 1026 | 1044 | c | C | A | U | C | A | A | G | G | A | G | A | A | g | A | U | U | A | a | 73 | 3 | 12 | c | false | <90% | 9040 | ||
| NM_013250 | ZNF215 | 1025 | 1043 | g | C | A | U | C | A | A | G | G | A | G | A | A | A | A | U | g | A | a | 69 | 3 | 15 | ac | false | <90% | 3658 | ||
| XM_001127690 | LOC730303 | 2616 | 2634 | c | u | A | U | C | A | A | G | G | A | G | A | A | A | A | U | a | A | g | 58 | 4 | 14 | ac | false | <90% | 3106 | ||
| XM_001127254 | LOC728194 | 2616 | 2634 | c | u | A | U | C | A | A | G | G | A | G | A | A | A | A | U | a | A | g | 58 | 4 | 14 | ac | false | <90% | 3106 | ||
| NM_173565 | LOC222967 | 2616 | 2634 | c | u | A | U | C | A | A | G | G | A | G | A | A | A | A | U | a | A | g | 58 | 4 | 14 | ac | false | <90% | 3122 | ||
| NM_005791 | MPHOSPH10 | 2010 | 2028 | A | g | A | U | C | A | A | G | G | A | G | A | A | A | A | a | U | A | a | 57 | 3 | 13 | c | false | <90% | 2503 | ||
| NM_015841 | ADAR | 1093 | 1111 | A | g | A | U | C | A | A | G | G | A | G | A | A | A | A | U | c | u | g | 57 | 4 | 14 | ac | false | <90% | 6505 | ||
| NM_001025107 | ADAR | 985 | 1003 | A | g | A | U | C | A | A | G | G | A | G | A | A | A | A | U | c | u | g | 57 | 4 | 14 | ac | false | <90% | 6532 | ||
| NM_015840 | ADAR | 1093 | 1111 | A | g | A | U | C | A | A | G | G | A | G | A | A | A | A | U | c | u | g | 57 | 4 | 14 | ac | false | <90% | 6562 | ||
| NM_001111 | ADAR | 1093 | 1111 | A | g | A | U | C | A | A | G | G | A | G | A | A | A | A | U | c | u | g | 57 | 4 | 14 | ac | false | <90% | 6640 | ||
| NM_001613 | ACTA2 | 685 | 703 | A | C | A | U | C | A | A | G | G | A | G | A | A | A | c | U | g | u | g | 44 | 4 | 14 | c | false | <90% | 1330 | ||
| NM_032230 | C12orf26 | 921 | 939 | A | C | A | U | C | A | A | G | a | A | G | A | A | A | A | U | U | u | g | 32 | 3 | 8 | c | false | <90% | 2085 | ||
| NM_002062 | GLP1R | 3031 | 3049 | A | C | A | U | C | A | A | G | u | A | G | A | A | A | A | U | U | u | c | 32 | 3 | 8 | c | false | <90% | 3071 | ||
| NM_004270 | CRSP9 | 668 | 686 | A | C | A | U | C | A | A | a | G | A | G | A | A | A | A | U | U | c | a | 30 | 3 | 9 | c | false | <90% | 1066 | ||
| NM_152726 | EFHA1 | 313 | 331 | A | C | A | U | g | A | A | G | G | A | G | A | A | u | A | U | U | A | U | 29 | 2 | 8 | c | false | <90% | 1891 | ||
| XR_018506 | LOC648398 | 1022 | 1040 | A | C | A | U | g | A | A | G | G | A | G | A | A | A | A | U | g | A | a | 20 | 3 | 11 | c | false | <90% | 2487 | ||
| NM_178565 | RSPO2 | 2413 | 2431 | u | g | A | U | C | c | A | G | G | A | G | A | A | A | A | U | U | A | g | 18 | 4 | 12 | bc | false | <90% | 2842 | ||
| XM_940940 | LOC651723 | 1814 | 1832 | A | g | A | U | C | A | u | G | G | A | G | A | A | A | A | U | U | A | a | 17 | 3 | 11 | bc | false | <90% | 2739 | ||
| XM_496207 | SLFN14 | 1814 | 1832 | A | g | A | U | C | A | u | G | G | A | G | A | A | A | A | U | U | A | a | 17 | 3 | 11 | bc | false | <90% | 2739 | ||
| XM_940627 | LBA1 | 3008 | 3026 | u | C | A | U | C | A | A | G | a | A | G | A | A | A | A | U | c | A | U | 14 | 3 | 7 | c | false | <90% | 10815 | ||
| XM_047357 | LBA1 | 3008 | 3026 | u | C | A | U | C | A | A | G | a | A | G | A | A | A | A | U | c | A | U | 14 | 3 | 7 | c | false | <90% | 10815 | ||
| NM_015303 | VPS8 | 3468 | 3486 | A | C | A | U | C | A | A | G | G | u | G | A | A | A | A | U | a | c | c | -13 | 4 | 9 | c | false | <90% | 5058 | ||
| NM_001009921 | VPS8 | 3474 | 3492 | A | C | A | U | C | A | A | G | G | u | G | A | A | A | A | U | a | c | c | -13 | 4 | 9 | c | false | <90% | 5064 | ||
| XM_929288 | LOC646359 | 662 | 680 | A | C | A | U | g | A | u | G | G | A | G | A | A | A | A | U | U | A | a | -22 | 3 | 11 | bc | false | <90% | 1514 | ||
| XM_939377 | LOC650291 | 662 | 680 | A | C | A | U | g | A | u | G | G | A | G | A | A | A | A | U | U | A | a | -22 | 3 | 11 | bc | false | <90% | 2033 | ||
| XM_208097 | LOC283523 | 662 | 680 | A | C | A | U | g | A | u | G | G | A | G | A | A | A | A | U | U | A | a | -22 | 3 | 11 | bc | false | <90% | 2034 | ||
| NM_003218 | TERF1 | 719 | 737 | A | C | A | U | g | A | u | G | G | A | G | A | A | A | A | U | U | A | a | -22 | 3 | 11 | bc | false | <90% | 2626 | ||
| NM_017489 | TERF1 | 719 | 737 | A | C | A | U | g | A | u | G | G | A | G | A | A | A | A | U | U | A | a | -22 | 3 | 11 | bc | false | <90% | 2686 | ||
| XM_937430 | LOC648377 | 686 | 704 | A | C | A | U | g | A | g | G | G | A | G | A | A | A | A | U | U | A | a | -22 | 3 | 11 | bc | false | <90% | 2850 | ||
| XM_929253 | LOC646316 | 686 | 704 | A | C | A | U | g | A | g | G | G | A | G | A | A | A | A | U | U | A | a | -22 | 3 | 11 | bc | false | <90% | 2850 | ||
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_020935 | USP37 | 6527 | 6545 | u | U | A | u | U | U | U | U | C | U | C | C | U | U | G | A | U | c | a | 53 | 4 | 13 | c | false | <90% | 8015 | ||
| NM_005233 | EPHA3 | 5349 | 5367 | A | U | A | u | U | U | U | U | C | U | C | C | U | U | G | A | c | c | U | 37 | 3 | 12 | c | false | <90% | 5826 | ||
| NM_025214 | CCDC68 | 1931 | 1949 | c | U | A | A | U | U | U | U | C | U | u | C | U | U | G | A | U | a | g | 29 | 4 | 9 | c | false | <90% | 3997 | ||
| NM_001004057 | GRK4 | 1402 | 1420 | A | g | A | A | U | a | U | U | C | U | C | C | U | U | G | A | U | G | a | 20 | 3 | 12 | bc | false | <90% | 2183 | ||
| NM_001004056 | GRK4 | 1306 | 1324 | A | g | A | A | U | a | U | U | C | U | C | C | U | U | G | A | U | G | a | 20 | 3 | 12 | bc | false | <90% | 2225 | ||
| NM_182982 | GRK4 | 1402 | 1420 | A | g | A | A | U | a | U | U | C | U | C | C | U | U | G | A | U | G | a | 20 | 3 | 12 | bc | false | <90% | 2321 | ||
| NM_003828 | MTMR1 | 567 | 585 | c | g | c | A | U | U | U | U | a | U | C | C | U | U | G | A | U | G | U | 6 | 4 | 10 | bc | false | <90% | 2732 | ||
| NM_198564 | FLJ44290 | 1431 | 1449 | A | U | A | A | U | U | g | g | C | U | C | C | U | U | G | A | U | G | g | -33 | 3 | 10 | bc | false | <90% | 2048 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1753
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