Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for GGAUGGAGCUUGAGAGAAA (16 guide strand hits and 6 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_002180 | IGHMBP2 | 149 | 167 | u | G | c | U | G | G | A | G | C | U | U | G | A | G | A | G | A | g | A | 75 | 3 | 14 | c | false | <90% | 3955 | ||
| NM_020839 | WDR48 | 906 | 924 | a | G | A | U | G | G | A | G | C | U | U | G | A | u | A | G | A | u | c | 70 | 4 | 12 | c | false | <90% | 3705 | ||
| NM_001080454 | LOC341392 | 262 | 280 | a | a | A | U | G | G | A | G | C | U | U | c | A | G | A | G | A | A | c | 47 | 4 | 9 | false | <90% | 1743 | |||
| XM_937749 | LOC341392 | 262 | 280 | a | a | A | U | G | G | A | G | C | U | U | c | A | G | A | G | A | A | c | 47 | 4 | 9 | false | <90% | 1743 | |||
| XR_018145 | LOC126826 | 624 | 642 | a | G | A | U | G | G | A | G | C | U | U | G | A | G | A | a | g | c | A | 45 | 4 | 14 | c | false | <90% | 706 | ||
| NM_173553 | FLJ25801 | 458 | 476 | u | c | g | U | G | G | A | G | C | U | U | G | A | G | A | a | A | A | A | 40 | 4 | 12 | c | false | <90% | 1300 | ||
| NM_017850 | C1orf109 | 1047 | 1065 | G | G | A | U | G | G | A | G | C | U | a | G | A | G | A | G | A | c | A | 36 | 2 | 10 | c | false | <90% | 2376 | ||
| NM_001081 | CUBN | 402 | 420 | u | G | g | U | G | G | A | u | C | U | U | G | A | G | A | G | A | A | A | 16 | 3 | 11 | bc | false | <90% | 11933 | ||
| NM_021146 | ANGPTL7 | 481 | 499 | u | G | A | U | G | G | A | G | C | U | g | G | A | G | A | G | c | A | A | 13 | 3 | 9 | c | false | <90% | 2255 | ||
| NM_058166 | TRIM6 | 656 | 674 | a | G | A | U | G | G | A | G | C | c | U | G | A | G | A | G | A | u | g | 7 | 4 | 8 | c | false | <90% | 3215 | ||
| NM_001003818 | TRIM6 | 850 | 868 | a | G | A | U | G | G | A | G | C | c | U | G | A | G | A | G | A | u | g | 7 | 4 | 8 | c | false | <90% | 3409 | ||
| NM_001003819 | TRIM6-TRIM34 | 850 | 868 | a | G | A | U | G | G | A | G | C | c | U | G | A | G | A | G | A | u | g | 7 | 4 | 8 | c | false | <90% | 3490 | ||
| NM_004934 | CDH18 | 101 | 119 | c | a | g | U | G | G | A | G | a | U | U | G | A | G | A | G | A | A | A | 6 | 4 | 10 | bc | false | <90% | 2944 | ||
| NM_020652 | ZNF286A | 608 | 626 | c | a | u | U | G | a | A | G | C | U | U | G | A | G | A | G | A | A | A | 3 | 4 | 13 | bc | false | <90% | 2515 | ||
| NM_019105 | TNXB | 5057 | 5075 | a | c | c | U | G | G | A | G | C | c | U | G | A | G | A | G | A | A | A | -15 | 4 | 9 | bc | false | <90% | 13268 | ||
| NM_014065 | ASTE1 | 721 | 739 | G | G | A | U | a | G | A | G | C | U | a | G | A | G | A | G | A | A | g | -17 | 3 | 7 | c | false | <90% | 2662 | ||
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_025109 | MYOHD1 | 2349 | 2367 | c | U | U | C | U | C | U | C | A | A | G | C | U | C | C | c | U | g | u | 64 | 4 | 14 | c | false | <90% | 3258 | ||
| NM_001039464 | C1orf175 | 1725 | 1743 | U | c | U | C | U | C | U | C | A | A | G | C | U | C | C | g | U | C | C | 62 | 2 | 13 | c | false | <90% | 4367 | ||
| NR_003135 | CEP170L | 59153 | 59171 | c | c | U | C | U | C | U | C | A | A | G | C | U | C | C | c | U | C | u | 55 | 4 | 13 | c | false | <90% | 90477 | ||
| NM_053042 | KIAA1729 | 6654 | 6672 | U | U | U | C | U | C | a | C | A | A | G | C | U | C | C | A | U | C | C | 33 | 1 | 12 | bc | false | <90% | 6936 | ||
| NM_173851 | SLC30A8 | 4931 | 4949 | U | U | g | C | U | C | U | C | c | A | G | C | U | C | C | A | U | C | C | 20 | 2 | 10 | bc | false | <90% | 5373 | ||
| NM_175861 | TMTC1 | 1770 | 1788 | g | g | g | C | U | C | U | C | c | A | G | C | U | C | C | A | U | C | C | 6 | 4 | 10 | bc | false | <90% | 8821 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2247
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