Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for CUCACGCGGUUGAAGGAGA (8 guide strand hits and 9 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_032227 | TMEM164 | 7 | 25 | g | c | C | A | C | G | C | G | G | U | U | G | c | A | G | G | A | G | u | 71 | 4 | 10 | false | <90% | 1339 | |||
| NM_007223 | GPR176 | 470 | 488 | g | a | C | c | C | G | C | G | G | U | U | G | A | A | G | G | A | G | g | 44 | 4 | 14 | bc | false | <90% | 2816 | ||
| XR_018422 | LOC648766 | 1678 | 1696 | C | U | a | A | C | a | C | G | G | U | U | G | A | A | G | G | A | G | u | 12 | 3 | 12 | bc | false | <90% | 4259 | ||
| XR_017049 | LOC284167 | 2576 | 2594 | C | U | C | A | C | G | g | G | G | U | U | G | A | A | G | a | A | G | c | 2 | 3 | 8 | c | false | <90% | 3728 | ||
| XR_019047 | LOC651054 | 2576 | 2594 | C | U | C | A | C | G | g | G | G | U | U | G | A | A | G | a | A | G | c | 2 | 3 | 8 | c | false | <90% | 3728 | ||
| NM_005035 | POLRMT | 2598 | 2616 | C | U | C | A | C | G | g | G | G | U | U | G | A | A | G | a | A | G | c | 2 | 3 | 8 | c | false | <90% | 3800 | ||
| XR_017191 | LOC646737 | 173 | 191 | C | U | C | A | g | G | u | G | G | U | U | G | A | A | G | G | A | G | A | -17 | 2 | 12 | bc | false | <90% | 626 | ||
| NM_000961 | PTGIS | 214 | 232 | C | U | C | A | C | G | a | G | G | a | U | G | A | A | G | G | A | G | A | -49 | 2 | 9 | bc | false | <90% | 5603 | ||
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_001080457 | LRRC4B | 664 | 682 | a | C | g | C | C | U | U | C | A | A | C | C | G | C | G | U | G | c | c | 70 | 4 | 14 | c | false | <90% | 2958 | ||
| XM_936789 | LRRC4B | 664 | 682 | a | C | g | C | C | U | U | C | A | A | C | C | G | C | G | U | G | c | c | 70 | 4 | 14 | c | false | <90% | 2958 | ||
| NM_014858 | TMCC2 | 881 | 899 | c | C | g | C | C | U | U | C | A | A | C | C | G | C | G | U | G | c | u | 70 | 4 | 14 | c | false | <90% | 3792 | ||
| NM_021231 | C19orf29 | 1984 | 2002 | g | C | U | u | C | U | U | C | A | A | C | C | G | C | G | U | G | c | a | 53 | 4 | 13 | c | false | <90% | 2689 | ||
| NM_001080543 | C19orf29 | 1984 | 2002 | g | C | U | u | C | U | U | C | A | A | C | C | G | C | G | U | G | c | a | 53 | 4 | 13 | c | false | <90% | 3625 | ||
| NM_000173 | GP1BA | 443 | 461 | U | C | U | C | C | U | U | C | A | A | C | C | G | g | c | U | G | A | c | 50 | 3 | 13 | c | false | <90% | 2427 | ||
| XM_376062 | KIAA1155 | 2370 | 2388 | c | C | U | C | C | U | U | C | A | u | C | C | u | C | G | U | G | A | G | 4 | 3 | 8 | false | <90% | 6208 | |||
| XM_945908 | KIAA1155 | 2455 | 2473 | c | C | U | C | C | U | U | C | A | u | C | C | u | C | G | U | G | A | G | 4 | 3 | 8 | false | <90% | 6300 | |||
| NM_005104 | BRD2 | 871 | 889 | g | C | U | u | C | U | U | C | A | c | C | C | G | C | G | U | G | A | G | -21 | 3 | 9 | bc | false | <90% | 4693 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1197
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