Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
24 hits were found for UGGCUUGGGAUAUGAUGAU (12 guide strand hits and 12 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_199487 | C20orf44 | 619 | 637 | g | a | u | C | U | U | G | G | G | A | U | A | U | G | A | U | G | A | g | 62 | 4 | 15 | bc | false | <90% | 2257 | ||
NM_018244 | C20orf44 | 700 | 718 | g | a | u | C | U | U | G | G | G | A | U | A | U | G | A | U | G | A | g | 62 | 4 | 15 | bc | false | <90% | 2338 | ||
NM_182476 | COQ6 | 236 | 254 | U | G | c | C | U | U | G | G | G | A | U | A | U | G | A | U | a | u | U | 54 | 3 | 13 | c | false | <90% | 1609 | ||
NM_001033662 | C8orf15 | 1093 | 1111 | U | u | G | C | U | U | G | G | G | A | U | u | U | G | A | U | G | A | a | 49 | 3 | 9 | false | <90% | 1743 | |||
NM_014909 | VASH1 | 4995 | 5013 | g | G | a | C | U | U | G | G | G | A | U | g | U | G | A | U | G | A | U | 44 | 3 | 8 | false | <90% | 5746 | |||
NM_001045477 | FAM22G | 2463 | 2481 | g | u | G | u | U | U | G | G | G | A | U | A | U | G | A | U | G | A | g | 44 | 4 | 14 | bc | false | <90% | 4888 | ||
NM_000632 | ITGAM | 890 | 908 | U | c | c | C | U | U | G | G | G | A | U | A | U | G | A | g | G | A | U | 42 | 3 | 12 | c | false | <90% | 4742 | ||
NM_015335 | THRAP2 | 978 | 996 | c | G | a | g | U | U | G | G | G | A | U | A | U | G | A | U | G | A | U | 41 | 3 | 15 | bc | false | <90% | 9546 | ||
NM_052843 | OBSCN | 13288 | 13306 | U | G | G | C | U | g | G | G | G | A | U | A | U | G | g | U | G | A | c | 7 | 3 | 8 | c | false | <90% | 20431 | ||
NM_033414 | ZNF622 | 1236 | 1254 | g | a | a | C | U | U | G | G | a | A | U | A | U | G | A | U | G | A | U | 6 | 4 | 10 | bc | false | <90% | 1710 | ||
XM_001132352 | LOC730090 | 303 | 321 | a | G | G | C | U | U | G | a | G | A | g | A | U | G | A | U | G | A | U | -25 | 3 | 8 | c | false | <90% | 1527 | ||
XM_001131553 | LOC732001 | 303 | 321 | a | G | G | C | U | U | G | a | G | A | g | A | U | G | A | U | G | A | U | -25 | 3 | 8 | c | false | <90% | 1527 |
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_144594 | FAM112B | 246 | 264 | g | U | C | A | U | C | A | U | A | U | C | u | C | A | A | G | C | u | g | 56 | 4 | 10 | false | <90% | 785 | |||
NM_004119 | FLT3 | 230 | 248 | A | U | C | A | U | C | A | U | A | U | C | C | C | A | u | G | g | u | A | 49 | 3 | 14 | c | false | <90% | 3848 | ||
XM_001132608 | LOC731317 | 580 | 598 | c | U | C | A | U | C | A | c | A | U | C | C | C | A | A | G | u | C | A | 12 | 3 | 8 | c | false | <90% | 881 | ||
XM_001133094 | LOC729121 | 580 | 598 | c | U | C | A | U | C | A | c | A | U | C | C | C | A | A | G | u | C | A | 12 | 3 | 8 | c | false | <90% | 881 | ||
NM_020530 | OSM | 1258 | 1276 | c | U | C | A | U | C | A | U | g | U | C | C | C | A | A | a | C | C | A | 11 | 3 | 7 | c | false | <90% | 1880 | ||
NM_033016 | PDGFB | 1694 | 1712 | c | U | C | A | U | C | A | U | A | U | u | C | C | A | A | c | C | C | A | 10 | 3 | 9 | c | false | <90% | 2378 | ||
NM_002608 | PDGFB | 2689 | 2707 | c | U | C | A | U | C | A | U | A | U | u | C | C | A | A | c | C | C | A | 10 | 3 | 9 | c | false | <90% | 3373 | ||
NM_014470 | RND1 | 997 | 1015 | A | c | C | A | U | C | A | U | A | c | C | C | C | A | A | G | C | C | A | 5 | 2 | 9 | bc | false | <90% | 1681 | ||
NM_181268 | CMTM1 | 229 | 247 | u | U | C | A | U | C | A | U | c | a | C | C | C | A | A | G | C | C | A | -44 | 3 | 9 | bc | false | <90% | 764 | ||
NM_181270 | CMTM1 | 232 | 250 | u | U | C | A | U | C | A | U | c | a | C | C | C | A | A | G | C | C | A | -44 | 3 | 9 | bc | false | <90% | 768 | ||
NM_052999 | CMTM1 | 229 | 247 | u | U | C | A | U | C | A | U | c | a | C | C | C | A | A | G | C | C | A | -44 | 3 | 9 | bc | false | <90% | 780 | ||
NM_181269 | CMTM1 | 232 | 250 | u | U | C | A | U | C | A | U | c | a | C | C | C | A | A | G | C | C | A | -44 | 3 | 9 | bc | false | <90% | 784 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2393
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