Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
25 hits were found for AGUUCCUCUAACUUCUUUC (10 guide strand hits and 15 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 | |||||||||||||
NR_003281 | GMCL1L | 917 | 935 | g | G | U | U | C | C | U | C | U | A | A | C | U | U | a | U | U | U | g | 68 | 3 | 13 | c | false | <90% | 2923 | ||
NM_020859 | SHROOM3 | 112 | 130 | u | G | U | U | C | C | U | C | U | A | A | C | U | U | C | c | U | U | a | 66 | 3 | 14 | c | false | <90% | 11020 | ||
NM_152449 | LYSMD4 | 2750 | 2768 | g | G | U | U | C | C | U | C | U | A | A | C | a | U | C | U | g | U | C | 64 | 3 | 11 | false | <90% | 2929 | |||
NM_058163 | TSR2 | 1232 | 1250 | g | u | c | U | C | C | U | C | U | A | A | C | c | U | C | U | U | U | C | 56 | 4 | 9 | false | <90% | 1353 | |||
NM_182648 | BAZ1A | 5775 | 5793 | u | a | U | U | C | C | U | C | U | A | A | C | U | U | C | c | U | U | a | 55 | 4 | 13 | c | false | <90% | 5935 | ||
NM_013448 | BAZ1A | 5871 | 5889 | u | a | U | U | C | C | U | C | U | A | A | C | U | U | C | c | U | U | a | 55 | 4 | 13 | c | false | <90% | 6031 | ||
NM_016231 | NLK | 578 | 596 | A | G | a | U | C | C | U | C | U | A | A | C | U | U | g | U | U | U | g | 50 | 3 | 11 | c | false | <90% | 4059 | ||
NM_016390 | C9orf114 | 1674 | 1692 | c | u | g | U | C | C | U | C | U | A | A | C | U | U | C | U | g | U | C | 43 | 4 | 13 | c | false | <90% | 1891 | ||
NM_004319 | ASTN1 | 6547 | 6565 | A | G | U | U | C | C | U | C | U | A | c | C | U | U | C | U | U | U | a | 33 | 2 | 10 | c | false | <90% | 7331 | ||
NM_006933 | SLC5A3 | 4795 | 4813 | g | G | U | c | C | C | U | C | U | A | c | C | U | U | C | U | U | U | C | 0 | 3 | 8 | c | false | <90% | 11400 |
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_015059 | TLN2 | 6965 | 6983 | c | u | A | A | G | A | A | G | U | U | A | G | A | G | c | A | A | C | U | 61 | 3 | 12 | c | false | <90% | 8500 | ||
NM_182762 | 7A5 | 2399 | 2417 | u | A | A | A | G | A | A | G | U | U | A | a | A | G | G | A | A | g | a | 56 | 4 | 10 | false | <90% | 3188 | |||
NM_018179 | ATF7IP | 1261 | 1279 | a | A | A | A | G | A | A | G | g | U | A | G | A | G | G | A | A | g | a | 30 | 4 | 8 | c | false | <90% | 4661 | ||
NM_001039938 | INTS6 | 1337 | 1355 | u | A | A | A | G | A | u | G | U | U | A | G | A | G | G | A | A | a | U | 29 | 3 | 10 | c | false | <90% | 2494 | ||
NM_031267 | CDC2L5 | 340 | 358 | a | g | A | A | G | A | A | G | U | U | g | G | A | G | G | A | A | C | g | 20 | 4 | 8 | c | false | <90% | 5216 | ||
NM_003718 | CDC2L5 | 340 | 358 | a | g | A | A | G | A | A | G | U | U | g | G | A | G | G | A | A | C | g | 20 | 4 | 8 | c | false | <90% | 5396 | ||
NM_133378 | TTN | 49641 | 49659 | u | A | A | A | G | A | A | G | U | g | A | G | A | G | G | A | A | C | a | 10 | 3 | 8 | bc | false | <90% | 101519 | ||
NM_133437 | TTN | 30726 | 30744 | u | A | A | A | G | A | A | G | U | g | A | G | A | G | G | A | A | C | a | 10 | 3 | 8 | bc | false | <90% | 82604 | ||
NM_133432 | TTN | 30525 | 30543 | u | A | A | A | G | A | A | G | U | g | A | G | A | G | G | A | A | C | a | 10 | 3 | 8 | bc | false | <90% | 82403 | ||
NM_003319 | TTN | 30150 | 30168 | u | A | A | A | G | A | A | G | U | g | A | G | A | G | G | A | A | C | a | 10 | 3 | 8 | bc | false | <90% | 82028 | ||
NM_173527 | REM2 | 189 | 207 | u | A | A | A | G | A | A | G | U | c | A | G | A | G | a | A | A | C | U | -9 | 3 | 8 | c | false | <90% | 1885 | ||
XR_019238 | LOC652192 | 782 | 800 | G | A | A | A | G | A | A | c | U | g | A | G | A | G | G | A | A | C | U | -44 | 2 | 9 | bc | false | <90% | 1282 | ||
XR_017412 | LOC151825 | 782 | 800 | G | A | A | A | G | A | A | c | U | g | A | G | A | G | G | A | A | C | U | -44 | 2 | 9 | bc | false | <90% | 1282 | ||
NM_006766 | MYST3 | 1049 | 1067 | a | A | A | A | G | A | A | G | c | c | A | G | A | G | G | A | A | C | U | -44 | 3 | 9 | bc | false | <90% | 7861 | ||
NM_152586 | USP54 | 2004 | 2022 | G | A | A | A | G | c | A | G | U | g | A | G | A | G | G | A | A | C | a | -51 | 3 | 8 | bc | false | <90% | 6202 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2384
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