Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
31 hits were found for GCGAUCCAGAUUUGUUUUG (15 guide strand hits and 16 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_012431 | SEMA3E | 5761 | 5779 | G | a | G | A | U | C | C | A | G | A | U | U | U | G | U | U | a | a | c | 57 | 4 | 14 | ac | false | <90% | 6474 | ||
| XM_939079 | LOC649993 | 184 | 202 | a | u | G | A | U | C | C | A | G | A | U | U | U | G | g | U | U | U | c | 56 | 4 | 12 | c | false | <90% | 453 | ||
| XR_019450 | LOC651804 | 185 | 203 | u | g | G | A | U | C | C | A | G | A | U | U | U | G | g | U | U | U | c | 56 | 4 | 12 | c | false | <90% | 1258 | ||
| XR_019521 | LOC652580 | 184 | 202 | a | g | G | A | U | C | C | A | G | A | U | U | U | G | g | U | U | U | c | 56 | 4 | 12 | c | false | <90% | 1268 | ||
| XR_019564 | LOC652706 | 184 | 202 | a | g | G | A | U | C | C | A | G | A | U | U | U | G | g | U | U | U | c | 56 | 4 | 12 | c | false | <90% | 1269 | ||
| NM_032485 | MCM8 | 2126 | 2144 | a | C | u | A | U | C | C | A | G | A | U | U | U | G | a | U | U | U | G | 53 | 3 | 11 | c | false | <90% | 3704 | ||
| NM_182802 | MCM8 | 2132 | 2150 | a | C | u | A | U | C | C | A | G | A | U | U | U | G | a | U | U | U | G | 53 | 3 | 11 | c | false | <90% | 3710 | ||
| NR_003135 | CEP170L | 53033 | 53051 | a | a | u | A | U | C | C | A | G | A | U | U | U | a | U | U | U | U | G | 47 | 4 | 10 | c | false | <90% | 90477 | ||
| NM_001025232 | CLLU1OS | 585 | 603 | a | g | G | u | U | C | C | A | G | A | U | U | U | G | U | U | U | U | u | 44 | 4 | 14 | bc | false | <90% | 686 | ||
| XR_019124 | LOC649408 | 622 | 640 | a | u | G | g | U | C | C | A | G | A | U | U | U | G | U | U | U | U | c | 44 | 4 | 14 | bc | false | <90% | 1910 | ||
| NM_152701 | ABCA13 | 4041 | 4059 | a | u | G | A | U | C | g | A | G | A | U | U | U | G | U | U | U | U | c | 15 | 4 | 11 | bc | false | <90% | 17208 | ||
| NM_173602 | DIP2B | 537 | 555 | G | C | G | A | U | C | C | A | c | A | U | U | U | G | U | U | c | a | G | 13 | 3 | 8 | c | false | <90% | 8715 | ||
| NM_006306 | SMC1A | 7384 | 7402 | a | g | a | A | U | u | C | A | G | A | U | U | U | G | U | U | U | U | G | 3 | 4 | 13 | bc | false | <90% | 9725 | ||
| NM_001094 | ACCN1 | 2542 | 2560 | c | C | G | A | U | g | g | A | G | A | U | U | U | G | U | U | U | U | G | -31 | 3 | 12 | bc | false | <90% | 2747 | ||
| NM_183377 | ACCN1 | 3294 | 3312 | c | C | G | A | U | g | g | A | G | A | U | U | U | G | U | U | U | U | G | -31 | 3 | 12 | bc | false | <90% | 3470 | ||
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_014033 | METTL7A | 2757 | 2775 | a | A | A | A | A | C | A | A | A | U | C | U | G | a | A | U | C | u | a | 70 | 4 | 12 | c | false | <90% | 3390 | ||
| XM_495886 | RNF169 | 808 | 826 | g | A | A | A | A | C | A | A | A | U | C | U | G | G | A | a | C | G | u | 66 | 3 | 14 | c | false | <90% | 8900 | ||
| XM_940188 | RNF169 | 808 | 826 | g | A | A | A | A | C | A | A | A | U | C | U | G | G | A | a | C | G | u | 66 | 3 | 14 | c | false | <90% | 8900 | ||
| XR_016317 | LOC392508 | 1364 | 1382 | C | A | g | A | A | C | A | A | A | U | C | U | G | G | A | U | g | a | g | 49 | 4 | 13 | c | false | <90% | 1886 | ||
| XR_018360 | LOC392508 | 1364 | 1382 | C | A | g | A | A | C | A | A | A | U | C | U | G | G | A | U | g | a | g | 49 | 4 | 13 | c | false | <90% | 1886 | ||
| NM_019042 | PUS7 | 2597 | 2615 | C | A | A | A | A | C | A | A | A | U | C | U | G | G | A | c | u | a | u | 42 | 4 | 15 | c | false | <90% | 3484 | ||
| NM_057167 | COL6A3 | 9084 | 9102 | g | A | A | A | A | C | A | A | A | U | u | U | G | G | A | U | C | a | C | 34 | 3 | 9 | c | false | <90% | 9944 | ||
| NM_057166 | COL6A3 | 9099 | 9117 | g | A | A | A | A | C | A | A | A | U | u | U | G | G | A | U | C | a | C | 34 | 3 | 9 | c | false | <90% | 9959 | ||
| NM_057165 | COL6A3 | 9102 | 9120 | g | A | A | A | A | C | A | A | A | U | u | U | G | G | A | U | C | a | C | 34 | 3 | 9 | c | false | <90% | 9962 | ||
| NM_057164 | COL6A3 | 9201 | 9219 | g | A | A | A | A | C | A | A | A | U | u | U | G | G | A | U | C | a | C | 34 | 3 | 9 | c | false | <90% | 10061 | ||
| NM_004369 | COL6A3 | 9702 | 9720 | g | A | A | A | A | C | A | A | A | U | u | U | G | G | A | U | C | a | C | 34 | 3 | 9 | c | false | <90% | 10562 | ||
| NM_020877 | DNAH2 | 10014 | 10032 | u | c | A | A | c | C | A | A | A | U | C | U | G | G | A | U | C | G | g | 30 | 4 | 13 | bc | false | <90% | 13505 | ||
| NM_002336 | LRP6 | 698 | 716 | C | A | A | A | u | C | A | A | A | U | C | U | G | G | A | U | g | G | a | 20 | 3 | 11 | c | false | <90% | 5301 | ||
| NM_020127 | TUFT1 | 2843 | 2861 | C | A | A | A | A | C | A | A | A | U | g | U | G | G | A | U | u | a | a | 7 | 4 | 10 | c | false | <90% | 3125 | ||
| NM_001186 | BACH1 | 5051 | 5069 | C | A | A | A | A | C | A | A | A | U | g | U | G | G | A | U | a | c | a | 7 | 4 | 10 | c | false | <90% | 5642 | ||
| NM_206866 | BACH1 | 5179 | 5197 | C | A | A | A | A | C | A | A | A | U | g | U | G | G | A | U | a | c | a | 7 | 4 | 10 | c | false | <90% | 5770 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 264
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