Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
19 hits were found for GACCAGAAGGCUCCGGCGG (8 guide strand hits and 11 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_017520 | HSMPP8 | 2330 | 2348 | u | A | C | C | A | G | A | A | G | G | C | U | C | u | G | G | C | a | u | 70 | 4 | 12 | c | false | <90% | 3234 | ||
NM_199043 | C14orf102 | 2504 | 2522 | u | c | C | C | A | G | A | A | G | G | C | U | C | u | G | G | C | G | a | 62 | 4 | 11 | c | false | <90% | 3480 | ||
NM_017970 | C14orf102 | 2847 | 2865 | u | c | C | C | A | G | A | A | G | G | C | U | C | u | G | G | C | G | a | 62 | 4 | 11 | c | false | <90% | 3824 | ||
NM_014405 | CACNG4 | 1403 | 1421 | c | A | C | C | A | G | A | A | G | G | C | U | C | u | G | c | C | G | G | 52 | 3 | 12 | c | false | <90% | 3397 | ||
NM_015173 | TBC1D1 | 896 | 914 | c | A | C | a | A | G | A | A | G | G | C | U | C | C | G | c | C | G | G | 35 | 3 | 11 | c | false | <90% | 5688 | ||
NM_001005407 | CACNA1H | 3597 | 3615 | G | A | C | C | A | G | A | A | G | c | C | U | C | C | G | G | C | c | a | 9 | 3 | 9 | c | false | <90% | 8079 | ||
NM_021098 | CACNA1H | 3597 | 3615 | G | A | C | C | A | G | A | A | G | c | C | U | C | C | G | G | C | c | a | 9 | 3 | 9 | c | false | <90% | 8097 | ||
NM_145178 | ATOH7 | 945 | 963 | G | c | C | C | A | G | A | A | G | c | C | U | C | C | G | G | C | G | G | 5 | 2 | 9 | bc | false | <90% | 1487 |
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_000932 | PLCB3 | 3562 | 3580 | C | C | G | C | C | G | G | A | G | C | C | U | g | C | U | G | G | g | C | 86 | 2 | 12 | false | <90% | 3705 | |||
NM_015355 | SUZ12 | 96 | 114 | C | C | G | C | C | G | G | A | G | C | C | U | g | C | U | G | G | g | g | 81 | 3 | 12 | false | <90% | 4441 | |||
NM_024646 | ZYG11B | 58 | 76 | u | C | G | C | C | G | G | A | G | C | C | U | c | C | U | G | G | a | g | 79 | 4 | 11 | false | <90% | 6404 | |||
NM_004292 | RIN1 | 1556 | 1574 | g | C | c | C | C | G | G | A | G | C | C | U | U | C | g | G | G | U | C | 53 | 3 | 11 | c | false | <90% | 2698 | ||
NM_014797 | ZBTB24 | 183 | 201 | u | C | G | C | C | a | G | A | G | C | C | U | U | C | U | G | G | g | C | 32 | 3 | 11 | c | false | <90% | 5597 | ||
NM_005631 | SMO | 1814 | 1832 | u | C | G | C | C | c | G | A | G | C | C | U | U | C | U | G | G | U | g | 29 | 3 | 12 | bc | false | <90% | 3772 | ||
NM_002404 | MFAP4 | 633 | 651 | C | C | u | C | a | G | G | A | G | C | C | U | U | C | U | G | G | U | u | 23 | 3 | 13 | bc | false | <90% | 1830 | ||
NM_177999 | ASB6 | 86 | 104 | C | C | G | C | C | G | G | A | G | C | g | U | U | C | c | G | G | U | C | 14 | 2 | 10 | c | false | <90% | 4544 | ||
NM_017873 | ASB6 | 86 | 104 | C | C | G | C | C | G | G | A | G | C | g | U | U | C | c | G | G | U | C | 14 | 2 | 10 | c | false | <90% | 4653 | ||
NM_032098 | PCDHGB4 | 1909 | 1927 | C | C | G | C | C | a | G | c | G | C | C | U | U | C | U | G | G | U | C | -25 | 2 | 11 | bc | false | <90% | 2412 | ||
NM_003736 | PCDHGB4 | 1909 | 1927 | C | C | G | C | C | a | G | c | G | C | C | U | U | C | U | G | G | U | C | -25 | 2 | 11 | bc | false | <90% | 4578 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1784
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