Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
24 hits were found for GUUCAGGCAACUCUUGUGG (15 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_032373 | PCGF5 | 3668 | 3686 | G | U | a | C | A | G | G | C | A | A | C | U | u | U | U | G | U | G | G | 70 | 2 | 9 | false | <90% | 7179 | |||
NM_017990 | PDPR | 739 | 757 | c | c | c | C | A | G | G | C | A | A | C | U | g | U | U | G | U | G | G | 56 | 4 | 9 | false | <90% | 7999 | |||
NM_005065 | SEL1L | 4190 | 4208 | c | U | U | u | A | G | G | C | A | A | C | U | C | U | U | G | U | a | a | 53 | 4 | 13 | c | false | <90% | 7885 | ||
NM_015305 | ANGEL1 | 2984 | 3002 | c | U | U | C | A | G | G | a | A | A | C | U | C | U | U | G | U | u | u | 28 | 4 | 9 | c | false | <90% | 4072 | ||
XM_001127437 | LOC730839 | 1373 | 1391 | G | U | U | C | A | G | G | C | u | A | C | U | C | U | U | c | U | G | G | 13 | 2 | 8 | c | false | <90% | 6652 | ||
NM_001009931 | HRNR | 1449 | 1467 | G | U | U | C | A | G | G | C | u | A | C | U | C | U | U | c | U | G | G | 13 | 2 | 8 | c | false | <90% | 9623 | ||
NM_004285 | H6PD | 4696 | 4714 | G | U | U | C | A | G | G | C | A | A | u | U | C | U | c | G | U | G | c | 9 | 3 | 10 | c | false | <90% | 9117 | ||
NM_006459 | ERLIN1 | 2434 | 2452 | G | U | U | a | A | G | a | C | A | A | C | U | C | U | U | G | U | G | u | -8 | 3 | 11 | bc | false | <90% | 3115 | ||
NM_016038 | SBDS | 1234 | 1252 | c | U | U | g | A | G | G | C | A | g | C | U | C | U | U | G | U | G | G | -21 | 3 | 9 | bc | false | <90% | 1605 | ||
NM_138390 | TMEM169 | 2109 | 2127 | G | U | U | C | A | a | G | C | A | A | u | U | C | U | U | G | U | G | c | -29 | 3 | 7 | c | false | <90% | 3307 | ||
NR_003135 | CEP170L | 65516 | 65534 | G | U | U | C | A | a | G | C | A | A | u | U | C | U | U | G | U | G | c | -29 | 3 | 7 | c | false | <90% | 90477 | ||
NM_021629 | GNB4 | 4079 | 4097 | G | U | U | C | A | a | G | C | A | A | u | U | C | U | U | G | U | G | c | -29 | 3 | 7 | c | false | <90% | 6428 | ||
NM_001080975 | REPS2 | 4071 | 4089 | G | U | U | C | A | a | G | C | A | A | u | U | C | U | U | G | U | G | c | -29 | 3 | 7 | c | false | <90% | 7961 | ||
NM_004726 | REPS2 | 4074 | 4092 | G | U | U | C | A | a | G | C | A | A | u | U | C | U | U | G | U | G | c | -29 | 3 | 7 | c | false | <90% | 7964 | ||
NM_020375 | C12orf5 | 3028 | 3046 | G | U | U | C | A | a | G | C | A | A | u | U | C | U | U | G | U | G | c | -29 | 3 | 7 | c | false | <90% | 8237 |
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_017576 | KIF27 | 3129 | 3147 | g | a | A | C | A | A | G | A | G | U | U | G | u | C | U | G | A | A | a | 71 | 4 | 10 | false | <90% | 4653 | |||
NM_014472 | C10orf28 | 2893 | 2911 | u | u | c | C | A | A | G | A | G | U | U | G | C | C | U | G | g | A | C | 43 | 4 | 13 | c | false | <90% | 3386 | ||
NM_031490 | LONP2 | 3386 | 3404 | g | C | A | C | A | A | G | A | a | U | U | G | C | C | U | G | A | A | C | 37 | 2 | 10 | bc | false | <90% | 4342 | ||
NM_182569 | GDPD1 | 1728 | 1746 | g | C | A | C | A | A | G | A | a | U | U | G | C | u | U | G | A | A | C | 18 | 3 | 7 | c | false | <90% | 1821 | ||
NM_002268 | KPNA4 | 3503 | 3521 | g | C | A | C | A | A | G | u | G | U | U | G | C | a | U | G | A | A | C | 16 | 3 | 6 | c | false | <90% | 3816 | ||
NM_014149 | HSPC049 | 1916 | 1934 | C | C | A | C | A | A | G | A | G | U | g | G | C | C | U | c | A | A | g | 7 | 3 | 10 | c | false | <90% | 3179 | ||
XM_932802 | LOC645307 | 2174 | 2192 | C | C | A | C | A | A | c | A | G | U | U | G | C | C | U | G | g | g | g | 2 | 4 | 9 | c | false | <90% | 3875 | ||
NM_020805 | KLHL14 | 3395 | 3413 | u | C | A | C | c | A | G | A | G | a | U | G | C | C | U | G | A | A | C | -36 | 3 | 9 | bc | false | <90% | 4261 | ||
NM_014159 | SETD2 | 5403 | 5421 | C | C | A | C | A | A | c | A | G | c | U | G | C | C | U | G | A | A | u | -54 | 3 | 8 | bc | false | <90% | 7987 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1682
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