Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
17 hits were found for UCCUAUGGAAAUCCCUGGU (11 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_012395 | PFTK1 | 2890 | 2908 | U | C | C | U | A | U | G | G | A | A | A | U | a | C | C | U | u | u | g | 58 | 4 | 12 | false | <90% | 4953 | |||
| NM_018367 | PHCA | 3103 | 3121 | U | u | u | U | A | U | G | G | A | A | A | U | C | a | C | U | G | G | U | 49 | 3 | 10 | c | false | <90% | 3471 | ||
| NM_001024210 | S100A13 | 383 | 401 | U | C | C | a | A | U | G | G | A | A | A | U | C | C | a | U | G | G | U | 38 | 2 | 10 | c | false | <90% | 951 | ||
| NM_000138 | FBN1 | 1501 | 1519 | U | C | C | U | A | U | G | G | u | A | A | U | u | C | C | U | G | G | g | 24 | 3 | 8 | false | <90% | 11626 | |||
| NM_016290 | UIMC1 | 1858 | 1876 | a | C | C | U | c | U | G | u | A | A | A | U | C | C | C | U | G | G | U | -15 | 3 | 11 | bc | false | <90% | 2656 | ||
| NM_058188 | C21orf67 | 910 | 928 | U | C | C | U | c | U | G | G | A | c | A | U | C | C | C | U | G | G | g | -39 | 3 | 8 | bc | false | <90% | 1071 | ||
| NM_153823 | GSG1 | 545 | 563 | U | C | C | U | A | U | G | G | u | u | A | U | C | C | C | U | G | G | g | -47 | 3 | 8 | bc | false | <90% | 1942 | ||
| NM_001080555 | GSG1 | 658 | 676 | U | C | C | U | A | U | G | G | u | u | A | U | C | C | C | U | G | G | g | -47 | 3 | 8 | bc | false | <90% | 2055 | ||
| NM_031289 | GSG1 | 669 | 687 | U | C | C | U | A | U | G | G | u | u | A | U | C | C | C | U | G | G | g | -47 | 3 | 8 | bc | false | <90% | 2066 | ||
| NM_001080554 | GSG1 | 782 | 800 | U | C | C | U | A | U | G | G | u | u | A | U | C | C | C | U | G | G | g | -47 | 3 | 8 | bc | false | <90% | 2179 | ||
| NM_014945 | ABLIM3 | 1781 | 1799 | U | C | C | U | A | U | G | c | A | g | A | U | C | C | C | U | G | G | a | -49 | 3 | 8 | bc | false | <90% | 4256 | ||
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_173489 | FLJ40243 | 4899 | 4917 | g | C | C | A | G | G | G | A | U | U | U | C | u | A | U | A | G | G | c | 82 | 3 | 11 | false | <90% | 5255 | |||
| NM_024617 | ZCCHC6 | 4161 | 4179 | u | C | a | A | G | G | G | A | U | U | U | C | C | A | a | A | G | G | A | 53 | 3 | 11 | c | false | <90% | 5648 | ||
| NM_002996 | CX3CL1 | 2525 | 2543 | A | C | C | A | G | G | G | A | U | U | U | C | C | A | U | g | a | u | g | 42 | 4 | 15 | c | false | <90% | 3304 | ||
| NM_144626 | TMEM125 | 1358 | 1376 | A | u | C | A | a | G | G | A | U | U | U | C | C | A | U | A | G | G | g | 32 | 3 | 13 | bc | false | <90% | 1655 | ||
| NM_001885 | CRYAB | 370 | 388 | u | C | C | A | G | G | G | A | g | U | U | C | C | A | c | A | G | G | A | 13 | 3 | 7 | c | false | <90% | 691 | ||
| NM_030766 | BCL2L14 | 916 | 934 | u | C | C | A | G | G | G | u | U | U | U | C | C | A | c | A | G | G | A | 11 | 3 | 6 | c | false | <90% | 2039 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1466
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