Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for GGGCAACUCUGCAGCGGAA (17 guide strand hits and 5 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_020761 | KIAA1303 | 2686 | 2704 | G | G | G | C | A | A | C | U | C | U | G | C | A | G | a | G | a | g | g | 44 | 4 | 14 | c | false | <90% | 6856 | ||
XM_939505 | LOC285556 | 431 | 449 | G | G | G | C | A | A | C | U | C | U | G | C | A | G | C | c | c | c | u | 42 | 4 | 15 | c | false | <90% | 10186 | ||
XM_373030 | LOC285556 | 431 | 449 | G | G | G | C | A | A | C | U | C | U | G | C | A | G | C | c | c | c | u | 42 | 4 | 15 | c | false | <90% | 10186 | ||
NM_181492 | TCF20 | 2183 | 2201 | u | G | G | C | c | A | C | U | C | U | G | C | A | G | C | G | G | g | c | 38 | 4 | 12 | c | false | <90% | 7279 | ||
NM_005650 | TCF20 | 2183 | 2201 | u | G | G | C | c | A | C | U | C | U | G | C | A | G | C | G | G | g | c | 38 | 4 | 12 | c | false | <90% | 7407 | ||
NM_145345 | UBXD5 | 627 | 645 | a | G | G | C | A | A | C | c | C | U | G | C | A | G | C | G | G | c | A | 33 | 3 | 9 | c | false | <90% | 1864 | ||
NM_183008 | UBXD5 | 632 | 650 | a | G | G | C | A | A | C | c | C | U | G | C | A | G | C | G | G | c | A | 33 | 3 | 9 | c | false | <90% | 1869 | ||
XM_001125744 | LOC92154 | 1181 | 1199 | G | c | G | C | c | A | C | U | C | U | G | C | A | G | C | G | G | A | g | 32 | 3 | 13 | bc | false | <90% | 2852 | ||
NM_138383 | ABBA-1 | 1426 | 1444 | G | c | G | C | c | A | C | U | C | U | G | C | A | G | C | G | G | A | g | 32 | 3 | 13 | bc | false | <90% | 4977 | ||
XM_001132632 | LOC732298 | 700 | 718 | G | G | G | C | c | A | C | U | C | U | G | C | A | G | C | G | a | A | A | 25 | 2 | 11 | c | false | <90% | 747 | ||
XM_001130865 | LOC729636 | 700 | 718 | G | G | G | C | c | A | C | U | C | U | G | C | A | G | C | G | a | A | A | 25 | 2 | 11 | c | false | <90% | 747 | ||
NR_002723 | GABPAP | 114902 | 114920 | u | G | G | C | A | A | C | c | C | U | G | C | g | G | C | G | G | A | A | 25 | 3 | 6 | false | <90% | 194142 | |||
NM_001540 | HSPB1 | 342 | 360 | c | G | G | C | A | A | C | U | C | a | G | C | A | G | C | G | G | g | g | 7 | 4 | 8 | c | false | <90% | 865 | ||
NM_001002262 | ZFYVE27 | 875 | 893 | G | G | G | C | A | u | C | U | C | U | G | C | A | G | C | a | G | A | g | 5 | 3 | 9 | c | false | <90% | 3009 | ||
NM_144588 | ZFYVE27 | 875 | 893 | G | G | G | C | A | u | C | U | C | U | G | C | A | G | C | a | G | A | g | 5 | 3 | 9 | c | false | <90% | 3030 | ||
NM_001002261 | ZFYVE27 | 875 | 893 | G | G | G | C | A | u | C | U | C | U | G | C | A | G | C | a | G | A | g | 5 | 3 | 9 | c | false | <90% | 3045 | ||
NM_016478 | ZC3HC1 | 5 | 23 | a | a | G | C | A | A | C | U | C | g | G | C | A | G | C | G | G | A | c | -1 | 4 | 8 | bc | false | <90% | 1945 |
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_025219 | DNAJC5 | 2291 | 2309 | g | g | C | C | G | C | U | G | C | A | G | A | G | U | U | G | C | a | g | 78 | 4 | 15 | ac | false | <90% | 3286 | ||
NM_018553 | C17orf85 | 1370 | 1388 | U | U | u | C | G | C | U | G | C | A | G | A | G | U | U | G | u | a | g | 49 | 4 | 13 | c | false | <90% | 2708 | ||
NM_004321 | KIF1A | 2601 | 2619 | c | c | g | C | G | C | U | G | C | A | G | A | G | g | U | G | C | C | C | 47 | 4 | 10 | c | false | <90% | 8843 | ||
NM_015886 | PI15 | 4208 | 4226 | U | c | a | C | G | C | a | G | C | A | G | A | G | U | U | G | C | C | C | 2 | 3 | 12 | bc | false | <90% | 6732 | ||
XM_001133002 | LOC728804 | 2642 | 2660 | U | U | C | a | G | C | c | G | C | A | G | A | G | U | U | G | C | C | C | -3 | 2 | 12 | bc | false | <90% | 4812 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1607
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