Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for CUCAGCCCGGGUACCCUUG (7 guide strand hits and 9 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_173854 | SLC41A1 | 2093 | 2111 | C | U | C | A | G | C | C | C | G | G | G | U | c | C | u | C | U | U | c | 59 | 3 | 12 | false | <90% | 4869 | |||
NM_014855 | KIAA0415 | 570 | 588 | C | U | C | A | G | C | C | C | G | G | G | c | A | C | C | C | U | c | c | 58 | 3 | 11 | false | <90% | 2890 | |||
XM_001129795 | LOC729267 | 499 | 517 | u | c | C | A | G | C | C | C | G | G | G | g | A | C | C | C | U | U | c | 47 | 4 | 9 | false | <90% | 585 | |||
NM_001535 | PRMT2 | 1854 | 1872 | a | U | C | A | G | C | C | C | G | u | G | U | A | C | C | C | U | g | u | 7 | 4 | 8 | c | false | <90% | 2140 | ||
NM_206962 | PRMT2 | 1963 | 1981 | a | U | C | A | G | C | C | C | G | u | G | U | A | C | C | C | U | g | u | 7 | 4 | 8 | c | false | <90% | 2249 | ||
XR_019229 | LOC650438 | 94 | 112 | C | U | C | A | G | C | a | C | u | G | G | U | A | C | C | C | U | U | u | -31 | 3 | 9 | bc | false | <90% | 711 | ||
XR_016282 | LOC402192 | 94 | 112 | C | U | C | A | G | C | a | C | u | G | G | U | A | C | C | C | U | U | u | -31 | 3 | 9 | bc | false | <90% | 711 |
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 | |||||||||||||
XM_001130976 | LOC731831 | 795 | 813 | a | c | g | G | G | G | U | A | C | C | C | G | G | G | C | a | G | A | G | 40 | 4 | 12 | c | false | <90% | 1323 | ||
XM_001129336 | LOC729108 | 795 | 813 | a | c | g | G | G | G | U | A | C | C | C | G | G | G | C | a | G | A | G | 40 | 4 | 12 | c | false | <90% | 1323 | ||
XR_017928 | NANOS3 | 711 | 729 | C | A | A | G | G | G | c | A | C | C | C | G | G | G | C | U | c | g | G | 7 | 3 | 9 | c | false | <90% | 949 | ||
XR_017750 | NANOS3 | 711 | 729 | C | A | A | G | G | G | c | A | C | C | C | G | G | G | C | U | c | g | G | 7 | 3 | 9 | c | false | <90% | 949 | ||
NM_017514 | PLXNA3 | 5867 | 5885 | C | c | u | G | G | G | U | c | C | C | C | G | G | G | C | U | G | A | G | 6 | 3 | 11 | bc | false | <90% | 6762 | ||
NM_006653 | FRS3 | 513 | 531 | u | A | A | G | u | G | U | u | C | C | C | G | G | G | C | U | G | A | G | -15 | 3 | 11 | bc | false | <90% | 2200 | ||
NM_198595 | AFAP1 | 129 | 147 | g | c | g | G | G | G | U | A | C | a | C | G | G | G | C | U | G | A | G | -15 | 4 | 9 | bc | false | <90% | 7534 | ||
XM_001131070 | LOC729697 | 69 | 87 | C | A | A | G | G | G | g | A | C | C | g | G | G | G | C | U | G | A | c | -32 | 3 | 7 | c | false | <90% | 699 | ||
XM_001130499 | LOC731705 | 69 | 87 | C | A | A | G | G | G | g | A | C | C | g | G | G | G | C | U | G | A | c | -32 | 3 | 7 | c | false | <90% | 699 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4453
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