Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
27 hits were found for GCAUAUAUGUGGGCAACUA (1 guide strand hits and 26 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_006952 | UPK1B | 274 | 292 | G | C | A | U | A | U | u | U | G | U | G | G | G | C | A | u | C | U | g | 2 | 3 | 8 | c | false | <90% | 2060 |
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_032448 | FAM120B | 144 | 162 | U | A | c | c | U | G | C | C | C | A | C | A | U | A | U | A | U | G | u | 38 | 3 | 14 | bc | false | <90% | 3261 | ||
XR_016115 | LOC653079 | 121 | 139 | U | g | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 2 | 3 | 12 | bc | false | <90% | 591 | ||
XR_016036 | LOC731892 | 121 | 139 | U | g | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 2 | 3 | 12 | bc | false | <90% | 591 | ||
XR_018788 | LOC650225 | 109 | 127 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 516 | ||
XR_016770 | LOC645157 | 109 | 127 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 516 | ||
XR_015915 | LOC729208 | 120 | 138 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 519 | ||
XR_015894 | LOC731456 | 120 | 138 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 519 | ||
XR_016005 | LOC731706 | 109 | 127 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 536 | ||
XR_016010 | LOC729484 | 109 | 127 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 537 | ||
XM_001127887 | LOC728501 | 122 | 140 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 570 | ||
XM_001126891 | LOC730700 | 122 | 140 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 570 | ||
XM_935700 | RPL21 | 122 | 140 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 570 | ||
XM_001132434 | LOC731125 | 103 | 121 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 571 | ||
XM_928758 | LOC653665 | 103 | 121 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 571 | ||
NM_000982 | RPL21 | 123 | 141 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 582 | ||
XM_001133519 | LOC731567 | 111 | 129 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 583 | ||
XM_001133089 | LOC731640 | 111 | 129 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 590 | ||
XM_370611 | LOC387753 | 123 | 141 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 601 | ||
XM_001133084 | LOC731640 | 123 | 141 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 601 | ||
XM_001133535 | LOC729402 | 131 | 149 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 602 | ||
XM_001133517 | LOC731567 | 131 | 149 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 603 | ||
XM_929340 | LOC653737 | 130 | 148 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 604 | ||
XM_001132436 | LOC731125 | 138 | 156 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 606 | ||
XM_928485 | LOC645452 | 433 | 451 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 845 | ||
XM_939733 | LOC650644 | 433 | 451 | c | c | u | U | U | G | g | C | C | A | C | A | U | A | U | A | U | G | C | 0 | 4 | 12 | bc | false | <90% | 845 | ||
NM_004136 | IREB2 | 5846 | 5864 | U | A | G | U | U | G | C | C | u | g | C | A | U | A | U | A | U | G | g | -47 | 3 | 8 | bc | false | <90% | 6367 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1529
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