Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
28 hits were found for GGAUGGAGCUUAAGAGAAA (13 guide strand hits and 15 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_001633 | AMBP | 508 | 526 | G | u | c | U | G | G | A | G | C | U | U | A | u | G | A | G | A | A | A | 58 | 3 | 9 | false | <90% | 1413 | |||
NM_001010862 | SPIN3 | 1803 | 1821 | u | G | g | U | G | G | A | G | C | U | U | A | A | G | u | G | A | A | A | 53 | 3 | 11 | c | false | <90% | 4479 | ||
NM_199168 | CXCL12 | 1919 | 1937 | u | G | A | U | G | G | A | G | C | U | U | A | A | a | A | a | A | A | A | 52 | 3 | 12 | c | false | <90% | 1937 | ||
NM_001080454 | LOC341392 | 262 | 280 | a | a | A | U | G | G | A | G | C | U | U | c | A | G | A | G | A | A | c | 47 | 4 | 9 | false | <90% | 1743 | |||
XM_937749 | LOC341392 | 262 | 280 | a | a | A | U | G | G | A | G | C | U | U | c | A | G | A | G | A | A | c | 47 | 4 | 9 | false | <90% | 1743 | |||
NM_001011666 | CREB5 | 7084 | 7102 | G | G | A | g | G | G | A | G | u | U | U | A | A | G | A | G | A | A | A | 3 | 2 | 10 | bc | false | <90% | 7772 | ||
NM_182899 | CREB5 | 7500 | 7518 | G | G | A | g | G | G | A | G | u | U | U | A | A | G | A | G | A | A | A | 3 | 2 | 10 | bc | false | <90% | 8188 | ||
NM_004904 | CREB5 | 7525 | 7543 | G | G | A | g | G | G | A | G | u | U | U | A | A | G | A | G | A | A | A | 3 | 2 | 10 | bc | false | <90% | 8213 | ||
NM_182898 | CREB5 | 7844 | 7862 | G | G | A | g | G | G | A | G | u | U | U | A | A | G | A | G | A | A | A | 3 | 2 | 10 | bc | false | <90% | 8532 | ||
NM_199444 | COPE | 539 | 557 | G | G | A | a | G | G | A | G | C | U | g | A | A | G | A | G | A | A | u | -3 | 3 | 7 | c | false | <90% | 978 | ||
NM_199442 | COPE | 386 | 404 | G | G | A | a | G | G | A | G | C | U | g | A | A | G | A | G | A | A | u | -3 | 3 | 7 | c | false | <90% | 981 | ||
NM_007263 | COPE | 539 | 557 | G | G | A | a | G | G | A | G | C | U | g | A | A | G | A | G | A | A | u | -3 | 3 | 7 | c | false | <90% | 1134 | ||
NM_002144 | HOXB1 | 551 | 569 | G | G | A | U | G | a | A | G | g | U | U | A | A | G | A | G | A | A | A | -23 | 2 | 10 | bc | false | <90% | 1014 |
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 | |||||||||||||
XM_938482 | ZC3H12C | 268 | 286 | U | U | g | C | U | C | U | U | A | A | G | C | U | u | C | A | U | C | C | 60 | 2 | 10 | c | false | <90% | 9542 | ||
XM_001125098 | LOC730417 | 1355 | 1373 | U | U | U | C | c | C | U | U | A | A | G | C | U | C | C | A | U | u | u | 40 | 3 | 12 | c | false | <90% | 6329 | ||
NM_207371 | FLJ45187 | 1353 | 1371 | U | U | U | C | c | C | U | U | A | A | G | C | U | C | C | A | U | u | u | 40 | 3 | 12 | c | false | <90% | 6339 | ||
NM_014399 | TSPAN13 | 912 | 930 | U | U | U | C | U | g | U | U | A | A | G | C | U | C | C | A | U | u | u | 29 | 3 | 11 | c | false | <90% | 1912 | ||
NM_032664 | FUT10 | 3198 | 3216 | U | a | U | C | U | C | U | U | A | A | c | C | U | C | C | A | U | C | g | 22 | 3 | 8 | c | false | <90% | 3549 | ||
NM_053052 | C1orf142 | 736 | 754 | U | U | U | a | U | C | U | U | c | A | G | C | U | C | C | A | U | C | a | -1 | 3 | 9 | bc | false | <90% | 2401 | ||
NM_183048 | ZMYND8 | 3306 | 3324 | a | U | U | C | U | C | U | U | A | g | G | C | U | C | C | A | a | C | C | -8 | 3 | 8 | c | false | <90% | 4493 | ||
NM_012408 | ZMYND8 | 3381 | 3399 | a | U | U | C | U | C | U | U | A | g | G | C | U | C | C | A | a | C | C | -8 | 3 | 8 | c | false | <90% | 4568 | ||
NM_183047 | ZMYND8 | 3381 | 3399 | a | U | U | C | U | C | U | U | A | g | G | C | U | C | C | A | a | C | C | -8 | 3 | 8 | c | false | <90% | 4652 | ||
NM_000104 | CYP1B1 | 1814 | 1832 | U | U | U | C | U | C | U | U | c | A | u | C | U | C | C | A | U | C | C | -21 | 2 | 8 | c | false | <90% | 5128 | ||
NM_053042 | KIAA1729 | 6654 | 6672 | U | U | U | C | U | C | a | c | A | A | G | C | U | C | C | A | U | C | C | -28 | 2 | 11 | bc | false | <90% | 6936 | ||
XM_939083 | TTC28 | 9211 | 9229 | g | U | U | C | U | C | c | U | g | A | G | C | U | C | C | A | U | C | C | -28 | 3 | 10 | bc | false | <90% | 11652 | ||
XM_929318 | TTC28 | 9211 | 9229 | g | U | U | C | U | C | c | U | g | A | G | C | U | C | C | A | U | C | C | -28 | 3 | 10 | bc | false | <90% | 11653 | ||
NM_198264 | C1orf2 | 1404 | 1422 | g | U | U | C | U | C | U | U | u | c | G | C | U | C | C | A | U | C | C | -44 | 3 | 9 | bc | false | <90% | 2921 | ||
NM_006589 | C1orf2 | 1692 | 1710 | g | U | U | C | U | C | U | U | u | c | G | C | U | C | C | A | U | C | C | -44 | 3 | 9 | bc | false | <90% | 3209 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2247
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