Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
27 hits were found for GGUGGCAAUGGUAGAGAUG (9 guide strand hits and 18 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_032790 | TMEM142A | 476 | 494 | G | G | U | G | G | C | A | A | U | G | G | U | g | G | A | G | g | U | G | 66 | 2 | 12 | false | <90% | 1497 | |||
NM_015089 | PARC | 402 | 420 | a | G | U | G | G | C | A | A | U | G | G | g | A | G | A | G | A | U | G | 64 | 2 | 10 | false | <90% | 7771 | |||
NM_003496 | TRRAP | 1521 | 1539 | a | G | U | G | G | C | A | A | U | G | G | g | A | G | A | G | A | c | G | 61 | 3 | 10 | false | <90% | 12563 | |||
NM_030665 | RAI1 | 4223 | 4241 | a | G | U | G | G | C | A | A | U | G | G | g | g | G | A | G | A | U | G | 53 | 3 | 10 | false | <90% | 7668 | |||
NM_003528 | HIST2H2BE | 1640 | 1658 | G | G | U | G | G | C | A | A | U | G | G | U | A | G | A | u | c | c | a | 42 | 4 | 15 | c | false | <90% | 2223 | ||
XR_018020 | LOC641787 | 185 | 203 | G | G | U | u | G | C | A | A | U | G | G | c | A | G | A | G | A | U | c | 24 | 3 | 7 | false | <90% | 794 | |||
XR_016633 | LOC644236 | 185 | 203 | G | G | U | u | G | C | A | A | U | G | G | c | A | G | A | G | A | U | c | 24 | 3 | 7 | false | <90% | 794 | |||
XR_018010 | LOC641727 | 185 | 203 | G | G | U | u | G | C | A | A | U | G | G | c | A | G | A | G | A | U | c | 24 | 3 | 7 | false | <90% | 794 | |||
XR_017230 | LOC646476 | 185 | 203 | G | G | U | u | G | C | A | A | U | G | G | c | A | G | A | G | A | U | c | 24 | 3 | 7 | false | <90% | 794 |
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_001031666 | MS4A3 | 382 | 400 | C | A | U | C | U | C | U | A | C | C | A | U | a | G | C | C | A | u | g | 81 | 3 | 12 | false | <90% | 1356 | |||
NM_001031809 | MS4A3 | 553 | 571 | C | A | U | C | U | C | U | A | C | C | A | U | a | G | C | C | A | u | g | 81 | 3 | 12 | false | <90% | 1527 | |||
NM_006138 | MS4A3 | 691 | 709 | C | A | U | C | U | C | U | A | C | C | A | U | a | G | C | C | A | u | g | 81 | 3 | 12 | false | <90% | 1665 | |||
NR_002714 | REGL | 8 | 26 | C | A | U | C | U | C | U | A | C | C | A | U | U | a | C | C | u | a | g | 49 | 4 | 13 | c | false | <90% | 2925 | ||
NM_145029 | C6orf136 | 437 | 455 | g | g | a | C | U | C | U | A | C | C | A | U | U | c | C | C | A | C | C | 47 | 4 | 10 | c | false | <90% | 1496 | ||
NM_001010870 | TDRD6 | 890 | 908 | g | A | a | C | U | C | U | A | C | C | A | g | U | G | C | C | A | C | C | 44 | 3 | 8 | false | <90% | 6817 | |||
NM_003773 | HYAL2 | 1034 | 1052 | C | A | U | C | U | C | U | A | C | C | A | U | U | G | g | C | g | a | g | 44 | 4 | 14 | c | false | <90% | 1848 | ||
NM_033158 | HYAL2 | 1077 | 1095 | C | A | U | C | U | C | U | A | C | C | A | U | U | G | g | C | g | a | g | 44 | 4 | 14 | c | false | <90% | 1909 | ||
NM_080591 | PTGS1 | 1280 | 1298 | C | A | U | C | U | C | U | A | C | C | A | c | U | G | g | C | A | C | C | 41 | 2 | 11 | false | <90% | 4982 | |||
NM_000962 | PTGS1 | 1280 | 1298 | C | A | U | C | U | C | U | A | C | C | A | c | U | G | g | C | A | C | C | 41 | 2 | 11 | false | <90% | 5093 | |||
NM_052906 | LRRC62 | 1604 | 1622 | g | A | U | C | U | C | c | A | C | C | A | U | U | G | C | C | A | a | g | 24 | 4 | 10 | c | false | <90% | 7579 | ||
NM_145176 | SLC2A12 | 606 | 624 | C | c | U | C | U | C | U | u | C | C | A | U | U | G | C | C | A | C | u | 21 | 3 | 10 | bc | false | <90% | 5599 | ||
NM_006203 | PDE4D | 3441 | 3459 | u | A | U | C | a | C | U | A | C | C | A | U | U | G | u | C | A | C | C | 21 | 3 | 9 | c | false | <90% | 5876 | ||
NM_019062 | RNF186 | 841 | 859 | C | A | U | C | U | C | U | u | C | C | A | U | U | G | C | C | u | g | a | 6 | 4 | 8 | c | false | <90% | 1268 | ||
NM_005835 | SLC17A2 | 1536 | 1554 | C | A | U | C | U | C | U | u | C | C | A | c | U | G | C | C | A | C | u | 0 | 3 | 7 | false | <90% | 2281 | |||
NM_031965 | GSG2 | 1245 | 1263 | C | A | U | C | U | a | U | A | C | C | A | c | U | G | C | C | A | C | u | -2 | 3 | 6 | false | <90% | 2797 | |||
NM_005730 | CTDSP2 | 2958 | 2976 | C | A | U | C | c | C | U | u | C | C | A | U | U | G | C | C | A | C | a | -18 | 3 | 10 | bc | false | <90% | 5038 | ||
NM_024662 | NAT10 | 3502 | 3520 | C | A | U | C | U | C | U | A | g | a | A | U | U | G | C | C | A | C | g | -47 | 3 | 8 | bc | false | <90% | 4002 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2635
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