Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
26 hits were found for GUCCUGGAUCACACAGGGA (7 guide strand hits and 19 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_015225 | KIAA0367 | 1898 | 1916 | G | a | u | C | U | G | G | A | U | C | A | C | A | C | A | u | G | G | A | 42 | 3 | 12 | c | false | <90% | 11690 | ||
NM_022064 | RNF123 | 369 | 387 | G | U | C | C | U | G | G | A | c | C | A | C | A | C | A | G | G | c | g | 32 | 3 | 8 | c | false | <90% | 4272 | ||
NM_025015 | HSPA12A | 1978 | 1996 | c | g | C | C | U | G | G | A | U | C | u | C | A | C | A | G | G | G | A | 25 | 3 | 8 | c | false | <90% | 5739 | ||
NM_001008784 | CD200R2 | 739 | 757 | c | U | C | C | U | G | G | A | U | C | c | C | A | g | A | G | G | G | A | 17 | 3 | 9 | c | false | <90% | 1296 | ||
NM_153754 | C21orf88 | 113 | 131 | G | U | C | C | U | G | G | g | U | C | A | C | A | C | A | G | c | c | A | 11 | 3 | 8 | c | false | <90% | 1088 | ||
NM_001176 | ARHGDIG | 397 | 415 | G | U | C | a | U | G | G | A | U | C | u | C | A | C | A | G | G | G | g | -3 | 3 | 7 | c | false | <90% | 965 | ||
NM_015050 | KIAA0082 | 1192 | 1210 | G | U | C | C | U | G | G | A | U | a | A | C | A | C | A | G | a | u | c | -13 | 4 | 9 | c | false | <90% | 4030 |
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_021012 | KCNJ12 | 1068 | 1086 | a | C | C | C | U | G | U | G | U | G | A | U | g | C | A | G | G | u | g | 79 | 4 | 11 | false | <90% | 5230 | |||
NM_021002 | IFNA6 | 362 | 380 | a | g | C | C | U | G | U | G | U | G | A | U | g | C | A | G | G | A | g | 71 | 4 | 10 | false | <90% | 570 | |||
NM_006900 | IFNA13 | 431 | 449 | a | g | C | C | U | G | U | G | U | G | A | U | g | C | A | G | G | A | g | 71 | 4 | 10 | false | <90% | 653 | |||
NM_024013 | IFNA1 | 429 | 447 | a | g | C | C | U | G | U | G | U | G | A | U | g | C | A | G | G | A | g | 71 | 4 | 10 | false | <90% | 876 | |||
NM_002172 | IFNA14 | 418 | 436 | a | g | C | C | U | G | U | G | U | G | A | U | a | C | A | G | G | A | g | 71 | 4 | 10 | false | <90% | 985 | |||
NM_002170 | IFNA8 | 392 | 410 | g | u | C | C | U | G | U | G | U | G | A | U | g | C | A | G | G | A | a | 71 | 4 | 10 | false | <90% | 1039 | |||
NM_152428 | FRMPD2 | 2237 | 2255 | U | g | C | C | U | G | U | G | U | G | A | U | C | C | A | G | a | A | g | 60 | 3 | 14 | ac | false | <90% | 4731 | ||
NM_001018071 | FRMPD2 | 2303 | 2321 | U | g | C | C | U | G | U | G | U | G | A | U | C | C | A | G | a | A | g | 60 | 3 | 14 | ac | false | <90% | 4797 | ||
NM_004943 | DMWD | 945 | 963 | g | g | C | C | U | G | U | G | U | G | A | g | C | C | A | G | G | A | u | 47 | 4 | 9 | false | <90% | 3308 | |||
NM_016376 | ANKFY1 | 7182 | 7200 | U | C | C | C | U | G | U | G | U | G | A | U | C | C | c | a | G | A | g | 44 | 3 | 14 | c | false | <90% | 7959 | ||
NM_023078 | PYCRL | 408 | 426 | g | C | C | C | U | G | U | G | U | G | g | U | C | C | A | G | G | A | a | 31 | 3 | 9 | c | false | <90% | 2331 | ||
NM_007219 | RNF24 | 1424 | 1442 | U | C | C | C | U | G | a | G | U | G | A | U | C | C | A | G | G | A | g | 28 | 2 | 11 | bc | false | <90% | 1692 | ||
NM_024979 | MCF2L | 987 | 1005 | g | C | C | C | a | G | U | G | U | G | A | a | C | C | A | G | G | A | C | 12 | 3 | 7 | false | <90% | 3463 | |||
NM_006238 | PPARD | 938 | 956 | g | C | C | C | U | u | U | G | U | G | A | U | C | C | A | c | G | A | C | 8 | 3 | 9 | c | false | <90% | 3734 | ||
NM_021933 | IIP45 | 572 | 590 | a | g | g | C | U | G | g | G | U | G | A | U | C | C | A | G | G | A | C | 0 | 4 | 12 | bc | false | <90% | 1588 | ||
XR_019468 | LOC646120 | 354 | 372 | U | C | C | C | U | G | U | G | U | a | A | U | C | C | A | G | a | g | a | -13 | 4 | 9 | c | false | <90% | 745 | ||
XR_017575 | LOC646120 | 354 | 372 | U | C | C | C | U | G | U | G | U | a | A | U | C | C | A | G | a | g | a | -13 | 4 | 9 | c | false | <90% | 745 | ||
NM_001031702 | SEMA5B | 1689 | 1707 | g | C | C | C | U | G | U | G | U | c | A | c | C | C | A | G | G | A | C | -18 | 3 | 8 | false | <90% | 4737 | |||
NM_006084 | ISGF3G | 593 | 611 | U | C | C | C | U | c | U | G | U | G | c | U | C | C | A | G | G | A | C | -24 | 2 | 8 | c | false | <90% | 1699 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2599
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)
Motif found in sense strand
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