Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for AUGUAUCCCUCCUGUUGCU (15 guide strand hits and 2 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_052875 | VPS26B | 3207 | 3225 | c | U | G | U | A | U | C | C | C | U | C | C | U | u | U | U | c | C | U | 54 | 3 | 12 | c | false | <90% | 3685 | ||
NM_001006937 | TCEAL4 | 937 | 955 | A | g | G | c | A | U | C | C | C | U | C | C | U | G | U | U | G | C | U | 51 | 2 | 15 | bc | false | <90% | 1289 | ||
NM_001006936 | TCEAL4 | 941 | 959 | A | g | G | c | A | U | C | C | C | U | C | C | U | G | U | U | G | C | U | 51 | 2 | 15 | bc | false | <90% | 1293 | ||
NM_001006935 | TCEAL4 | 942 | 960 | A | g | G | c | A | U | C | C | C | U | C | C | U | G | U | U | G | C | U | 51 | 2 | 15 | bc | false | <90% | 1294 | ||
NM_024863 | TCEAL4 | 1001 | 1019 | A | g | G | c | A | U | C | C | C | U | C | C | U | G | U | U | G | C | U | 51 | 2 | 15 | bc | false | <90% | 1353 | ||
NM_001996 | FBLN1 | 2219 | 2237 | g | g | G | U | c | U | C | C | C | U | C | C | U | G | U | U | G | C | U | 35 | 3 | 14 | bc | false | <90% | 2313 | ||
NM_001035507 | AGBL5 | 1279 | 1297 | c | U | G | U | c | U | C | C | C | U | C | C | U | G | a | U | G | C | U | 21 | 3 | 9 | c | false | <90% | 2460 | ||
NM_033215 | PPP1R3F | 2364 | 2382 | g | U | G | U | g | U | C | C | C | U | C | C | U | G | g | U | G | C | U | 21 | 3 | 9 | c | false | <90% | 2941 | ||
NM_021831 | AGBL5 | 1279 | 1297 | c | U | G | U | c | U | C | C | C | U | C | C | U | G | a | U | G | C | U | 21 | 3 | 9 | c | false | <90% | 3254 | ||
NM_018121 | C10orf6 | 6293 | 6311 | u | U | G | U | c | U | C | C | C | U | C | C | U | G | c | U | G | C | U | 21 | 3 | 9 | c | false | <90% | 7284 | ||
NM_152735 | ZBTB9 | 414 | 432 | A | U | G | U | g | U | C | C | C | U | C | C | U | G | g | U | G | C | a | 18 | 3 | 9 | c | false | <90% | 2730 | ||
NM_024557 | RIC3 | 1282 | 1300 | A | U | G | U | A | U | C | C | u | U | C | C | U | G | g | U | G | C | U | 15 | 2 | 8 | c | false | <90% | 2907 | ||
NM_003024 | ITSN1 | 5814 | 5832 | A | U | G | U | A | a | C | C | C | U | C | C | U | G | U | U | u | C | U | 13 | 2 | 10 | c | false | <90% | 6439 | ||
XM_044434 | KIAA1458 | 3016 | 3034 | A | U | G | U | A | U | C | C | a | U | C | a | U | G | U | U | G | C | a | 1 | 3 | 8 | false | <90% | 6472 | |||
XM_941571 | KIAA1458 | 3016 | 3034 | A | U | G | U | A | U | C | C | a | U | C | a | U | G | U | U | G | C | a | 1 | 3 | 8 | false | <90% | 6472 |
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_001076786 | QSER1 | 7897 | 7915 | c | u | u | A | A | C | A | G | c | A | G | G | G | A | U | A | C | A | U | 6 | 4 | 10 | bc | false | <90% | 9271 | ||
NM_006197 | PCM1 | 5549 | 5567 | A | G | C | A | A | C | u | G | G | A | G | u | G | A | U | A | C | A | a | -5 | 3 | 6 | false | <90% | 8788 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1883
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