Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
27 hits were found for GAACCACUGCAACUUUGGU (7 guide strand hits and 20 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_022553 | VPS52 | 322 | 340 | G | A | A | C | C | A | C | U | G | C | A | A | C | U | U | g | G | G | g | 68 | 2 | 15 | c | false | <90% | 2990 | ||
NM_024105 | ALG12 | 2235 | 2253 | c | c | A | C | C | A | C | U | G | C | A | A | C | U | U | U | u | G | U | 63 | 3 | 14 | ac | false | <90% | 2387 | ||
NM_001982 | ERBB3 | 1783 | 1801 | G | A | c | C | C | A | C | U | G | C | A | A | C | U | U | U | c | u | g | 49 | 4 | 13 | c | false | <90% | 5511 | ||
NM_001003937 | TSPYL6 | 2693 | 2711 | G | A | A | a | C | A | C | U | G | C | A | A | u | U | U | U | G | G | g | 47 | 3 | 8 | false | <90% | 3080 | |||
NM_014679 | CEP57 | 2696 | 2714 | G | A | A | a | C | A | C | U | G | C | A | A | C | U | U | U | c | c | U | 37 | 3 | 12 | c | false | <90% | 3158 | ||
NM_000857 | GUCY1B3 | 1877 | 1895 | G | A | A | C | C | A | a | U | G | C | A | A | g | U | U | U | G | G | U | 23 | 2 | 6 | false | <90% | 2443 | |||
NM_031954 | KCTD10 | 1665 | 1683 | a | g | A | C | C | A | g | U | G | C | A | A | C | U | U | U | G | G | g | 15 | 4 | 11 | bc | false | <90% | 4057 |
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_199053 | FLJ12716 | 574 | 592 | A | C | a | A | A | A | G | U | U | G | C | A | G | U | G | G | U | U | C | 80 | 1 | 16 | bc | false | <90% | 4442 | ||
NM_021942 | FLJ12716 | 574 | 592 | A | C | a | A | A | A | G | U | U | G | C | A | G | U | G | G | U | U | C | 80 | 1 | 16 | bc | false | <90% | 4561 | ||
NM_021110 | COL14A1 | 3474 | 3492 | A | C | C | c | A | A | G | U | U | G | C | A | a | U | G | G | U | U | C | 52 | 2 | 8 | false | <90% | 6463 | |||
NM_001013693 | LDLRAD2 | 3821 | 3839 | A | C | C | A | A | A | G | U | a | G | C | A | G | U | G | G | U | a | g | 32 | 3 | 8 | c | false | <90% | 4012 | ||
NM_025209 | EPC1 | 1989 | 2007 | g | u | a | A | A | A | G | U | a | G | C | A | G | U | G | G | U | U | C | 6 | 4 | 10 | bc | false | <90% | 2913 | ||
NM_002745 | MAPK1 | 1625 | 1643 | u | u | g | A | A | A | G | a | U | G | C | A | G | U | G | G | U | U | C | 4 | 4 | 11 | bc | false | <90% | 5916 | ||
XM_001128702 | SGPP2 | 791 | 809 | A | C | C | A | A | A | u | U | U | G | C | A | G | U | G | G | g | a | a | 2 | 4 | 9 | c | false | <90% | 1190 | ||
NM_152386 | SGPP2 | 974 | 992 | A | C | C | A | A | A | u | U | U | G | C | A | G | U | G | G | g | a | a | 2 | 4 | 9 | c | false | <90% | 1200 | ||
NM_016329 | SFMBT1 | 1757 | 1775 | A | g | g | A | A | A | a | U | U | G | C | A | G | U | G | G | U | U | C | 2 | 3 | 12 | bc | false | <90% | 3512 | ||
NM_001005158 | SFMBT1 | 1876 | 1894 | A | g | g | A | A | A | a | U | U | G | C | A | G | U | G | G | U | U | C | 2 | 3 | 12 | bc | false | <90% | 3631 | ||
NM_001005159 | SFMBT1 | 1957 | 1975 | A | g | g | A | A | A | a | U | U | G | C | A | G | U | G | G | U | U | C | 2 | 3 | 12 | bc | false | <90% | 3712 | ||
NM_020796 | SEMA6A | 1968 | 1986 | A | C | C | A | A | A | a | U | U | G | C | A | G | U | G | G | a | c | a | 2 | 4 | 9 | c | false | <90% | 6860 | ||
XM_001132013 | ANKH | 6072 | 6090 | A | C | C | A | A | A | a | U | U | G | C | A | G | U | G | G | a | g | u | 2 | 4 | 9 | c | false | <90% | 8316 | ||
NM_017573 | PCSK4 | 352 | 370 | c | C | C | c | A | A | G | g | U | G | C | A | G | U | G | G | U | U | C | 0 | 3 | 11 | bc | false | <90% | 2674 | ||
NM_001080432 | FTO | 3224 | 3242 | A | C | C | A | g | A | a | U | U | G | C | A | G | U | G | G | U | U | C | -17 | 2 | 12 | bc | false | <90% | 4294 | ||
XM_941142 | FTO | 3224 | 3242 | A | C | C | A | g | A | a | U | U | G | C | A | G | U | G | G | U | U | C | -17 | 2 | 12 | bc | false | <90% | 4294 | ||
NM_018353 | C14orf106 | 2637 | 2655 | A | C | C | A | A | A | G | a | a | G | C | A | G | U | G | G | U | U | C | -22 | 2 | 10 | bc | false | <90% | 4584 | ||
NM_172373 | ELF1 | 1501 | 1519 | A | C | C | c | A | A | G | U | U | c | C | A | G | U | G | G | U | U | g | -24 | 3 | 8 | bc | false | <90% | 3499 | ||
NM_015265 | SATB2 | 4615 | 4633 | g | C | C | A | A | g | u | U | U | G | C | A | G | U | G | G | U | U | C | -31 | 3 | 12 | bc | false | <90% | 4999 | ||
NM_153343 | ENPP6 | 1677 | 1695 | A | C | C | A | A | A | c | U | U | G | g | A | G | U | G | G | U | U | a | -32 | 3 | 7 | c | false | <90% | 3856 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1423
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