Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
28 hits were found for UGUUUGGAAAGGGGAGCAU (15 guide strand hits and 13 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_020737 | LRFN2 | 3071 | 3089 | U | G | U | U | U | G | G | A | A | A | G | G | c | G | A | G | a | c | U | 63 | 3 | 12 | false | <90% | 3144 | |||
| NM_033396 | TNKS1BP1 | 3787 | 3805 | U | G | U | U | U | G | G | A | A | A | G | u | G | G | A | G | g | g | U | 40 | 3 | 11 | false | <90% | 5822 | |||
| XM_944015 | LOC388002 | 66 | 84 | g | G | U | U | g | G | G | A | A | A | G | G | G | G | A | G | C | u | c | 38 | 4 | 12 | c | false | <90% | 637 | ||
| XM_373600 | LOC388002 | 66 | 84 | g | G | U | U | g | G | G | A | A | A | G | G | G | G | A | G | C | u | c | 38 | 4 | 12 | c | false | <90% | 637 | ||
| XM_001129325 | LOC731354 | 142 | 160 | U | a | U | U | U | G | G | A | A | A | u | G | G | G | A | G | C | A | c | 22 | 3 | 8 | c | false | <90% | 423 | ||
| NM_002737 | PRKCA | 1075 | 1093 | U | G | U | U | g | G | G | A | A | A | G | G | G | G | A | G | u | u | U | 22 | 3 | 11 | c | false | <90% | 8787 | ||
| XM_936538 | FAT3 | 18353 | 18371 | U | G | U | U | U | G | G | A | A | A | u | G | G | a | A | G | C | A | g | 14 | 3 | 10 | c | false | <90% | 19162 | ||
| XM_926199 | FAT3 | 18354 | 18372 | U | G | U | U | U | G | G | A | A | A | u | G | G | a | A | G | C | A | g | 14 | 3 | 10 | c | false | <90% | 19163 | ||
| NM_020238 | INCENP | 3556 | 3574 | U | G | U | U | U | G | u | A | A | A | G | G | G | G | A | G | u | u | U | 7 | 3 | 9 | c | false | <90% | 4134 | ||
| NM_001040694 | INCENP | 3568 | 3586 | U | G | U | U | U | G | u | A | A | A | G | G | G | G | A | G | u | u | U | 7 | 3 | 9 | c | false | <90% | 4146 | ||
| NM_001901 | CTGF | 2086 | 2104 | U | G | U | U | U | G | c | A | A | A | G | G | G | G | A | G | g | c | a | 2 | 4 | 9 | c | false | <90% | 2358 | ||
| NM_001419 | ELAVL1 | 3775 | 3793 | U | G | U | U | U | G | c | A | A | A | G | G | G | G | A | G | a | u | c | 2 | 4 | 9 | c | false | <90% | 6075 | ||
| XM_001131895 | LOC729961 | 712 | 730 | U | G | U | U | U | G | G | A | c | A | G | u | G | G | A | G | C | A | a | 1 | 3 | 8 | false | <90% | 753 | |||
| XM_001131530 | LOC731993 | 712 | 730 | U | G | U | U | U | G | G | A | c | A | G | u | G | G | A | G | C | A | a | 1 | 3 | 8 | false | <90% | 753 | |||
| NM_005786 | TSHZ1 | 425 | 443 | U | G | U | U | U | G | G | A | A | g | G | u | G | G | A | G | C | A | g | -21 | 3 | 9 | false | <90% | 4982 | |||
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_024420 | PLA2G4A | 2007 | 2025 | A | a | G | C | U | C | C | C | C | U | U | U | C | C | A | A | A | g | A | 85 | 2 | 15 | ac | false | <90% | 2940 | ||
| NM_001077498 | C17orf63 | 2559 | 2577 | A | g | a | C | U | C | C | C | C | U | U | U | C | C | A | A | A | C | c | 64 | 3 | 15 | bc | false | <90% | 4163 | ||
| NM_018182 | C17orf63 | 2593 | 2611 | A | g | a | C | U | C | C | C | C | U | U | U | C | C | A | A | A | C | c | 64 | 3 | 15 | bc | false | <90% | 4197 | ||
| NM_020796 | SEMA6A | 3756 | 3774 | u | U | G | C | U | C | C | C | C | U | U | U | C | C | A | c | A | u | c | 64 | 4 | 14 | c | false | <90% | 6860 | ||
| NM_014690 | FAM131B | 676 | 694 | A | U | G | C | U | C | C | C | C | U | U | c | C | C | A | A | A | a | A | 63 | 2 | 11 | false | <90% | 5859 | |||
| NM_144595 | SLAIN1 | 605 | 623 | A | U | G | u | U | C | C | C | C | U | U | U | C | C | A | A | A | g | A | 60 | 2 | 13 | c | false | <90% | 2310 | ||
| NM_001040153 | SLAIN1 | 669 | 687 | A | U | G | u | U | C | C | C | C | U | U | U | C | C | A | A | A | g | A | 60 | 2 | 13 | c | false | <90% | 2374 | ||
| NM_030918 | SNX27 | 4306 | 4324 | c | U | u | C | U | C | C | C | C | U | U | U | C | u | A | A | A | C | A | 58 | 3 | 10 | c | false | <90% | 7085 | ||
| XM_001128444 | ZNF66 | 1365 | 1383 | c | c | u | C | U | C | C | C | C | U | U | U | C | u | A | A | A | C | A | 47 | 4 | 10 | c | false | <90% | 2097 | ||
| XM_001132102 | ZNF66 | 1368 | 1386 | c | c | u | C | U | C | C | C | C | U | U | U | C | u | A | A | A | C | A | 47 | 4 | 10 | c | false | <90% | 2100 | ||
| NM_145693 | LPIN1 | 196 | 214 | A | U | G | C | U | C | C | C | C | U | U | U | C | C | A | c | g | u | c | 42 | 4 | 15 | c | false | <90% | 5363 | ||
| NM_181337 | KAAG1 | 1283 | 1301 | g | U | G | C | U | a | C | C | C | U | U | U | C | C | A | A | A | C | A | 34 | 2 | 13 | bc | false | <90% | 1382 | ||
| NM_003155 | STC1 | 623 | 641 | g | U | G | C | U | C | C | a | C | U | U | U | C | C | A | A | A | g | g | 28 | 4 | 9 | c | false | <90% | 3897 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3332
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