Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
45 hits were found for AAGGAGUUCCUGAUCUUCU (21 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_198265 | SPO11 | 728 | 746 | A | g | G | G | A | G | U | U | C | C | U | G | A | U | C | U | a | a | a | 57 | 4 | 14 | ac | false | <90% | 1712 | ||
| NM_012444 | SPO11 | 842 | 860 | A | g | G | G | A | G | U | U | C | C | U | G | A | U | C | U | a | a | a | 57 | 4 | 14 | ac | false | <90% | 1826 | ||
| NM_003307 | TRPM2 | 3896 | 3914 | A | c | G | G | A | G | U | U | C | C | U | G | A | U | C | U | a | u | g | 57 | 4 | 14 | ac | false | <90% | 5876 | ||
| NM_019863 | F8 | 569 | 587 | A | A | G | G | A | G | U | U | C | C | U | c | A | U | C | U | c | C | a | 37 | 3 | 11 | false | <90% | 2617 | |||
| NM_000132 | F8 | 7000 | 7018 | A | A | G | G | A | G | U | U | C | C | U | c | A | U | C | U | c | C | a | 37 | 3 | 11 | false | <90% | 9030 | |||
| NM_198955 | MGAT5B | 878 | 896 | A | A | G | G | A | G | U | c | C | C | U | G | A | U | C | U | U | C | a | 32 | 2 | 10 | bc | false | <90% | 4068 | ||
| NM_144677 | MGAT5B | 1056 | 1074 | A | A | G | G | A | G | U | c | C | C | U | G | A | U | C | U | U | C | a | 32 | 2 | 10 | bc | false | <90% | 4246 | ||
| NM_133640 | SURF5 | 481 | 499 | A | A | G | c | A | G | U | U | C | C | U | G | A | U | C | c | U | C | a | 32 | 3 | 11 | c | false | <90% | 1448 | ||
| NM_181491 | SURF5 | 481 | 499 | A | A | G | c | A | G | U | U | C | C | U | G | A | U | C | c | U | C | a | 32 | 3 | 11 | c | false | <90% | 3887 | ||
| NM_001531 | MR1 | 420 | 438 | c | A | G | G | A | u | U | U | C | C | U | G | A | U | C | U | U | C | a | 29 | 3 | 12 | bc | false | <90% | 1263 | ||
| NM_000092 | COL4A4 | 1883 | 1901 | A | A | G | G | A | u | U | U | C | C | U | G | g | U | C | U | U | C | c | 21 | 3 | 6 | false | <90% | 10341 | |||
| NM_004771 | MMP20 | 941 | 959 | A | A | G | G | A | G | c | U | C | C | U | G | c | U | C | U | U | C | a | 18 | 3 | 6 | false | <90% | 1956 | |||
| NM_133378 | TTN | 51436 | 51454 | u | u | a | G | g | G | U | U | C | C | U | G | A | U | C | U | U | C | U | 15 | 4 | 14 | bc | false | <90% | 101519 | ||
| NM_133437 | TTN | 32521 | 32539 | u | u | a | G | g | G | U | U | C | C | U | G | A | U | C | U | U | C | U | 15 | 4 | 14 | bc | false | <90% | 82604 | ||
| NM_133432 | TTN | 32320 | 32338 | u | u | a | G | g | G | U | U | C | C | U | G | A | U | C | U | U | C | U | 15 | 4 | 14 | bc | false | <90% | 82403 | ||
| NM_003319 | TTN | 31945 | 31963 | u | u | a | G | g | G | U | U | C | C | U | G | A | U | C | U | U | C | U | 15 | 4 | 14 | bc | false | <90% | 82028 | ||
| NM_001089 | ABCA3 | 3725 | 3743 | g | A | G | G | A | G | U | U | C | u | U | G | A | U | C | U | U | C | a | 10 | 3 | 8 | bc | false | <90% | 6623 | ||
| NM_001080973 | IL17RD | 5662 | 5680 | A | A | G | u | A | c | U | U | C | C | U | G | A | U | C | U | U | C | c | -5 | 3 | 12 | bc | false | <90% | 8720 | ||
| NM_017563 | IL17RD | 5684 | 5702 | A | A | G | u | A | c | U | U | C | C | U | G | A | U | C | U | U | C | c | -5 | 3 | 12 | bc | false | <90% | 8742 | ||
| NM_022065 | THADA | 5034 | 5052 | A | A | G | G | A | G | U | U | C | u | U | G | A | U | C | U | g | g | a | -13 | 4 | 9 | c | false | <90% | 6134 | ||
| NM_001083953 | THADA | 5246 | 5264 | A | A | G | G | A | G | U | U | C | u | U | G | A | U | C | U | g | g | a | -13 | 4 | 9 | c | false | <90% | 6346 | ||
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_133378 | TTN | 3945 | 3963 | A | G | A | A | G | A | U | C | A | G | G | A | A | u | U | C | C | a | U | 77 | 2 | 13 | c | false | <90% | 101519 | ||
| NM_133437 | TTN | 3807 | 3825 | A | G | A | A | G | A | U | C | A | G | G | A | A | u | U | C | C | a | U | 77 | 2 | 13 | c | false | <90% | 82604 | ||
| NM_133432 | TTN | 3807 | 3825 | A | G | A | A | G | A | U | C | A | G | G | A | A | u | U | C | C | a | U | 77 | 2 | 13 | c | false | <90% | 82403 | ||
| NM_003319 | TTN | 3807 | 3825 | A | G | A | A | G | A | U | C | A | G | G | A | A | u | U | C | C | a | U | 77 | 2 | 13 | c | false | <90% | 82028 | ||
| NM_133379 | TTN | 3945 | 3963 | A | G | A | A | G | A | U | C | A | G | G | A | A | u | U | C | C | a | U | 77 | 2 | 13 | c | false | <90% | 17306 | ||
| NM_005459 | GUCA1C | 491 | 509 | A | a | A | A | G | A | U | C | A | G | G | A | u | C | U | C | C | U | g | 73 | 3 | 10 | false | <90% | 860 | |||
| NM_170774 | RASSF2 | 2457 | 2475 | g | c | A | A | G | A | U | C | A | G | G | A | g | C | U | C | C | U | g | 71 | 4 | 10 | false | <90% | 5307 | |||
| NM_014737 | RASSF2 | 2599 | 2617 | g | c | A | A | G | A | U | C | A | G | G | A | g | C | U | C | C | U | g | 71 | 4 | 10 | false | <90% | 5426 | |||
| NM_003316 | TTC3 | 193 | 211 | g | G | A | A | G | A | U | C | A | G | G | A | A | a | U | g | C | U | U | 52 | 3 | 12 | c | false | <90% | 9021 | ||
| NM_024056 | TMEM106C | 447 | 465 | u | G | A | A | a | A | U | C | A | G | G | A | A | C | U | C | C | a | a | 38 | 4 | 12 | c | false | <90% | 1449 | ||
| NM_001002912 | C1orf173 | 841 | 859 | u | G | A | A | G | u | U | C | A | G | G | A | A | C | U | C | C | a | U | 32 | 3 | 11 | c | false | <90% | 7165 | ||
| NM_013255 | MKLN1 | 9544 | 9562 | u | G | A | A | G | A | U | g | A | G | G | A | c | C | U | C | C | U | U | 25 | 3 | 6 | false | <90% | 11157 | |||
| NM_017774 | CDKAL1 | 1362 | 1380 | c | c | A | A | G | A | c | C | A | G | G | A | A | C | U | C | C | U | g | 15 | 4 | 11 | bc | false | <90% | 2408 | ||
| NM_015065 | EXPH5 | 922 | 940 | c | u | A | A | G | A | c | C | A | G | G | A | A | C | U | C | C | U | a | 15 | 4 | 11 | bc | false | <90% | 6655 | ||
| NM_004003 | CRAT | 792 | 810 | A | G | A | A | G | A | U | C | u | G | G | A | A | C | U | C | a | U | c | 11 | 3 | 8 | c | false | <90% | 2600 | ||
| NM_000755 | CRAT | 996 | 1014 | A | G | A | A | G | A | U | C | u | G | G | A | A | C | U | C | a | U | c | 11 | 3 | 8 | c | false | <90% | 2804 | ||
| NM_001077706 | LFDH | 619 | 637 | A | G | A | A | G | A | U | g | A | G | G | A | A | C | U | a | C | U | g | 6 | 3 | 7 | c | false | <90% | 4261 | ||
| XR_015587 | LOC730833 | 3043 | 3061 | A | G | A | c | a | A | U | C | A | G | G | A | A | C | U | C | C | U | c | 6 | 3 | 13 | bc | false | <90% | 11255 | ||
| NM_002016 | FLG | 3043 | 3061 | A | G | A | c | a | A | U | C | A | G | G | A | A | C | U | C | C | U | c | 6 | 3 | 13 | bc | false | <90% | 12747 | ||
| NM_017773 | LAX1 | 2320 | 2338 | A | G | A | A | G | A | a | C | A | G | G | A | A | C | U | C | u | c | a | 2 | 4 | 9 | c | false | <90% | 3246 | ||
| XM_939377 | LOC650291 | 916 | 934 | A | G | A | A | G | A | g | u | A | G | G | A | A | C | U | C | C | U | c | -33 | 3 | 10 | bc | false | <90% | 2033 | ||
| XM_208097 | LOC283523 | 916 | 934 | A | G | A | A | G | A | g | u | A | G | G | A | A | C | U | C | C | U | c | -33 | 3 | 10 | bc | false | <90% | 2034 | ||
| NM_003218 | TERF1 | 973 | 991 | A | G | A | A | G | A | g | u | A | G | G | A | A | C | U | C | C | U | c | -33 | 3 | 10 | bc | false | <90% | 2626 | ||
| NM_017489 | TERF1 | 1033 | 1051 | A | G | A | A | G | A | g | u | A | G | G | A | A | C | U | C | C | U | c | -33 | 3 | 10 | bc | false | <90% | 2686 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1965
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