Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for CCUACCUCUCCAGCUAGGA (6 guide strand hits and 16 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_182554 | C10orf53 | 656 | 674 | C | g | a | A | C | C | U | C | U | C | C | A | G | C | U | A | G | a | u | 61 | 4 | 14 | c | false | <90% | 827 | ||
XM_290540 | MUC6 | 1415 | 1433 | u | C | U | A | C | C | U | C | U | C | C | A | G | g | c | A | G | G | A | 53 | 3 | 12 | c | false | <90% | 6214 | ||
NM_005269 | GLI1 | 1505 | 1523 | a | a | g | A | C | C | U | C | U | C | C | A | G | C | U | u | G | G | A | 40 | 4 | 12 | c | false | <90% | 3600 | ||
NM_006212 | PFKFB2 | 2279 | 2297 | C | C | U | u | C | C | U | C | U | C | C | A | G | C | c | A | G | G | u | 33 | 3 | 10 | c | false | <90% | 7073 | ||
NM_017798 | YTHDF1 | 455 | 473 | C | C | U | A | C | C | U | g | U | C | C | A | G | C | U | A | u | u | A | 11 | 3 | 8 | c | false | <90% | 3265 | ||
NM_152788 | ANKS1B | 5 | 23 | g | C | U | c | C | C | g | C | U | C | C | A | G | C | U | A | G | G | A | -5 | 3 | 12 | bc | false | <90% | 4431 |
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_015206 | KIAA1024 | 5114 | 5132 | c | C | a | U | A | G | C | U | G | G | A | G | A | G | G | U | A | G | u | 73 | 3 | 15 | bc | false | <90% | 6741 | ||
NM_007127 | VIL1 | 470 | 488 | U | g | g | U | A | G | C | U | G | G | A | G | A | G | G | U | A | G | a | 64 | 3 | 15 | bc | false | <90% | 2702 | ||
NM_025188 | TRIM45 | 291 | 309 | g | a | C | U | A | G | C | U | G | G | A | G | A | G | c | U | A | G | a | 56 | 4 | 12 | c | false | <90% | 3584 | ||
NM_005536 | IMPA1 | 150 | 168 | g | a | C | a | A | G | C | U | G | G | A | G | A | G | G | U | A | G | u | 44 | 4 | 14 | bc | false | <90% | 2349 | ||
NM_181798 | KCNQ1 | 2586 | 2604 | U | C | C | U | A | G | C | U | G | G | A | G | A | G | G | a | g | c | c | 42 | 4 | 15 | c | false | <90% | 3029 | ||
NM_000218 | KCNQ1 | 2819 | 2837 | U | C | C | U | A | G | C | U | G | G | A | G | A | G | G | a | g | c | c | 42 | 4 | 15 | c | false | <90% | 3262 | ||
NM_153610 | CMYA5 | 6056 | 6074 | U | C | C | U | A | G | C | U | G | G | A | a | A | u | G | U | A | G | a | 41 | 3 | 11 | false | <90% | 12911 | |||
XM_001127417 | LOC647909 | 3602 | 3620 | c | a | g | U | A | G | C | U | G | G | A | G | A | G | G | c | A | G | G | 40 | 4 | 12 | c | false | <90% | 4124 | ||
XM_929457 | LOC644739 | 3911 | 3929 | c | a | g | U | A | G | C | U | G | G | A | G | A | G | G | c | A | G | G | 40 | 4 | 12 | c | false | <90% | 4444 | ||
NM_013312 | HOOK2 | 875 | 893 | g | C | C | g | A | G | C | U | G | G | A | G | A | G | G | g | A | G | G | 35 | 3 | 11 | c | false | <90% | 2531 | ||
NM_015289 | VPS39 | 2061 | 2079 | U | C | C | c | A | G | C | U | G | G | A | G | A | G | G | a | A | G | a | 32 | 3 | 11 | c | false | <90% | 4851 | ||
NM_058174 | COL6A2 | 1445 | 1463 | g | C | C | U | g | G | C | U | G | G | A | G | A | G | G | U | u | G | G | 23 | 3 | 11 | c | false | <90% | 3168 | ||
NM_001849 | COL6A2 | 1445 | 1463 | g | C | C | U | g | G | C | U | G | G | A | G | A | G | G | U | u | G | G | 23 | 3 | 11 | c | false | <90% | 3455 | ||
NM_058175 | COL6A2 | 1445 | 1463 | g | C | C | U | g | G | C | U | G | G | A | G | A | G | G | U | u | G | G | 23 | 3 | 11 | c | false | <90% | 3461 | ||
NM_001048164 | SLC7A3 | 289 | 307 | U | C | C | U | A | G | C | U | G | G | c | G | A | G | G | U | g | G | c | 10 | 3 | 10 | c | false | <90% | 2285 | ||
NM_032803 | SLC7A3 | 313 | 331 | U | C | C | U | A | G | C | U | G | G | c | G | A | G | G | U | g | G | c | 10 | 3 | 10 | c | false | <90% | 2309 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1946
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