Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
29 hits were found for CCAAAGAGGUAGUGGACAA (23 guide strand hits and 6 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_012328 | DNAJB9 | 499 | 517 | a | C | A | A | A | G | A | G | G | U | A | G | U | G | G | A | a | g | u | 66 | 4 | 15 | ac | false | <90% | 2371 | ||
NM_003688 | CASK | 1253 | 1271 | C | C | A | A | A | G | A | G | G | U | A | u | U | G | G | A | a | g | A | 40 | 3 | 11 | false | <90% | 3122 | |||
NM_017934 | PHIP | 2268 | 2286 | a | C | u | A | A | G | A | c | G | U | A | G | U | G | G | A | C | A | A | 16 | 3 | 11 | bc | false | <90% | 5817 | ||
NR_003132 | HSP90AB2P | 3658 | 3676 | u | C | A | A | A | G | A | a | G | U | A | G | U | G | G | A | g | A | A | 12 | 3 | 8 | c | false | <90% | 4889 | ||
NM_199037 | SCN1B | 619 | 637 | a | C | A | u | u | G | A | G | G | U | A | G | U | G | G | A | C | A | A | 9 | 3 | 14 | bc | false | <90% | 1170 | ||
NM_001037 | SCN1B | 619 | 637 | a | C | A | u | u | G | A | G | G | U | A | G | U | G | G | A | C | A | A | 9 | 3 | 14 | bc | false | <90% | 1521 | ||
NM_174938 | FRMD3 | 1215 | 1233 | C | C | A | A | A | G | A | G | G | U | g | G | U | G | G | A | g | g | c | 7 | 4 | 10 | c | false | <90% | 2529 | ||
NM_206862 | TACC2 | 1730 | 1748 | C | C | A | A | A | G | A | G | G | U | g | G | U | G | G | A | u | g | c | 7 | 4 | 10 | c | false | <90% | 9706 | ||
NM_012160 | FBXL4 | 522 | 540 | C | C | A | A | A | G | A | a | G | U | A | G | U | G | G | A | u | u | u | 6 | 4 | 8 | c | false | <90% | 2777 | ||
NM_000937 | POLR2A | 4201 | 4219 | a | g | g | A | A | G | A | G | G | U | g | G | U | G | G | A | C | A | A | 5 | 4 | 8 | c | false | <90% | 6732 | ||
XR_016901 | LOC440304 | 3788 | 3806 | C | C | c | A | A | G | A | G | G | c | A | G | U | G | G | A | C | A | c | -7 | 3 | 8 | bc | false | <90% | 5213 | ||
XR_016202 | LOC440300 | 4235 | 4253 | C | C | c | A | A | G | A | G | G | c | A | G | U | G | G | A | C | A | c | -7 | 3 | 8 | bc | false | <90% | 5332 | ||
XR_015206 | LOC728121 | 4134 | 4152 | C | C | c | A | A | G | A | G | G | c | A | G | U | G | G | A | C | A | c | -7 | 3 | 8 | bc | false | <90% | 5459 | ||
XR_017409 | LOC440297 | 4127 | 4145 | C | C | c | A | A | G | A | G | G | c | A | G | U | G | G | A | C | A | c | -7 | 3 | 8 | bc | false | <90% | 5552 | ||
XR_016119 | LOC642288 | 4216 | 4234 | C | C | c | A | A | G | A | G | G | c | A | G | U | G | G | A | C | A | c | -7 | 3 | 8 | bc | false | <90% | 5641 | ||
XR_016146 | LOC390627 | 4217 | 4235 | C | C | c | A | A | G | A | G | G | c | A | G | U | G | G | A | C | A | c | -7 | 3 | 8 | bc | false | <90% | 5642 | ||
XR_016917 | LOC645306 | 3842 | 3860 | C | C | c | A | A | G | A | G | G | c | A | G | U | G | G | A | C | A | c | -7 | 3 | 8 | bc | false | <90% | 5803 | ||
NM_032974 | CASP10 | 711 | 729 | C | C | A | A | A | G | A | G | G | a | A | G | U | G | G | A | g | c | g | -13 | 4 | 9 | c | false | <90% | 2288 | ||
NM_001230 | CASP10 | 711 | 729 | C | C | A | A | A | G | A | G | G | a | A | G | U | G | G | A | g | c | g | -13 | 4 | 9 | c | false | <90% | 5777 | ||
NM_032977 | CASP10 | 711 | 729 | C | C | A | A | A | G | A | G | G | a | A | G | U | G | G | A | g | c | g | -13 | 4 | 9 | c | false | <90% | 5906 | ||
NM_152422 | PTPDC1 | 2190 | 2208 | C | C | A | A | A | G | A | G | G | a | u | G | U | G | G | A | C | A | u | -49 | 3 | 9 | c | false | <90% | 4398 | ||
NM_177995 | PTPDC1 | 2307 | 2325 | C | C | A | A | A | G | A | G | G | a | u | G | U | G | G | A | C | A | u | -49 | 3 | 9 | c | false | <90% | 4515 | ||
NM_003006 | SELPLG | 1813 | 1831 | C | C | A | A | A | c | A | G | G | a | A | G | U | G | G | A | C | A | u | -51 | 3 | 8 | bc | false | <90% | 2550 |
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_001408 | CELSR2 | 7831 | 7849 | U | c | u | U | C | C | A | C | U | A | C | C | U | C | U | U | U | G | c | 64 | 3 | 15 | bc | false | <90% | 10531 | ||
NM_002111 | HD | 4785 | 4803 | U | a | G | U | C | C | A | C | g | A | C | C | U | C | U | U | U | G | u | 23 | 3 | 9 | bc | false | <90% | 13481 | ||
NM_006569 | CGREF1 | 487 | 505 | U | U | c | U | C | C | u | C | U | A | C | C | U | C | U | U | U | G | c | 9 | 3 | 11 | bc | false | <90% | 1886 | ||
NM_000834 | GRIN2B | 6115 | 6133 | c | c | c | U | C | C | A | C | c | A | C | C | U | C | U | U | U | G | G | 6 | 4 | 10 | bc | false | <90% | 6240 | ||
NM_014762 | DHCR24 | 1182 | 1200 | U | c | u | U | C | C | g | C | U | A | C | C | U | C | U | U | U | G | G | 2 | 3 | 12 | bc | false | <90% | 4286 | ||
NM_173598 | KSR2 | 10988 | 11006 | U | U | G | U | C | C | A | C | U | g | C | C | U | C | U | U | c | u | u | -13 | 4 | 9 | c | false | <90% | 16655 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2902
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