Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
26 hits were found for CUUCUGCUGUCAGUAUCCG (15 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_004440 | EPHA7 | 1505 | 1523 | u | U | g | C | U | G | C | U | G | U | C | A | G | U | A | U | C | a | c | 70 | 4 | 14 | c | false | <90% | 5229 | ||
NM_031431 | COG3 | 2565 | 2583 | C | U | U | C | U | G | C | U | G | U | C | A | G | U | u | U | C | u | a | 67 | 3 | 14 | c | false | <90% | 4500 | ||
NM_018710 | TMEM55A | 107 | 125 | C | c | U | C | U | G | C | U | G | U | C | A | G | c | A | U | C | C | c | 64 | 3 | 11 | c | false | <90% | 2266 | ||
NM_014629 | ARHGEF10 | 4227 | 4245 | C | U | U | C | U | G | C | U | G | U | C | A | G | a | A | U | u | u | G | 54 | 3 | 13 | c | false | <90% | 5595 | ||
NM_018030 | OSBPL1A | 2840 | 2858 | u | U | U | C | U | G | C | a | G | U | C | A | G | U | A | U | C | a | u | 28 | 4 | 9 | c | false | <90% | 3336 | ||
NM_133268 | OSBPL1A | 3615 | 3633 | u | U | U | C | U | G | C | a | G | U | C | A | G | U | A | U | C | a | u | 28 | 4 | 9 | c | false | <90% | 4096 | ||
NM_080597 | OSBPL1A | 3684 | 3702 | u | U | U | C | U | G | C | a | G | U | C | A | G | U | A | U | C | a | u | 28 | 4 | 9 | c | false | <90% | 4165 | ||
NM_014666 | CLINT1 | 2732 | 2750 | C | U | U | C | U | G | C | U | G | U | a | A | u | U | A | U | C | C | u | 23 | 3 | 10 | false | <90% | 3425 | |||
NM_004560 | ROR2 | 269 | 287 | C | U | U | C | U | G | C | U | c | U | C | A | G | U | g | U | C | C | c | 10 | 3 | 8 | c | false | <90% | 4091 | ||
NM_006561 | CUGBP2 | 6926 | 6944 | C | U | U | C | U | G | C | U | u | U | C | A | G | U | c | U | C | C | u | 10 | 3 | 8 | c | false | <90% | 8005 | ||
NM_001083591 | CUGBP2 | 6974 | 6992 | C | U | U | C | U | G | C | U | u | U | C | A | G | U | c | U | C | C | u | 10 | 3 | 8 | c | false | <90% | 8053 | ||
NM_001025076 | CUGBP2 | 6980 | 6998 | C | U | U | C | U | G | C | U | u | U | C | A | G | U | c | U | C | C | u | 10 | 3 | 8 | c | false | <90% | 8059 | ||
NM_001025077 | CUGBP2 | 8177 | 8195 | C | U | U | C | U | G | C | U | u | U | C | A | G | U | c | U | C | C | u | 10 | 3 | 8 | c | false | <90% | 9256 | ||
NM_015235 | CSTF2T | 165 | 183 | g | U | U | C | U | G | u | U | G | U | C | A | G | U | u | U | C | C | G | 6 | 3 | 7 | c | false | <90% | 4127 | ||
XM_001131918 | LOC729968 | 71 | 89 | C | U | U | C | U | G | C | U | G | a | C | A | G | c | A | U | C | C | c | -7 | 3 | 9 | c | false | <90% | 699 |
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_177963 | SYT12 | 2241 | 2259 | a | G | a | A | U | A | C | U | G | A | C | A | G | C | A | G | A | g | G | 75 | 3 | 14 | c | false | <90% | 3520 | ||
NM_001723 | DST | 586 | 604 | C | G | c | A | U | A | C | U | G | A | C | A | a | C | A | G | A | A | c | 65 | 3 | 9 | false | <90% | 8972 | |||
NM_020388 | DST | 586 | 604 | C | G | c | A | U | A | C | U | G | A | C | A | a | C | A | G | A | A | c | 65 | 3 | 9 | false | <90% | 9348 | |||
NM_015548 | DST | 586 | 604 | C | G | c | A | U | A | C | U | G | A | C | A | a | C | A | G | A | A | c | 65 | 3 | 9 | false | <90% | 16384 | |||
NM_183380 | DST | 1982 | 2000 | C | G | c | A | U | A | C | U | G | A | C | A | a | C | A | G | A | A | c | 65 | 3 | 9 | false | <90% | 18036 | |||
NM_017952 | PTCD3 | 2054 | 2072 | g | u | G | A | U | A | C | U | G | A | C | A | G | C | A | G | c | A | G | 63 | 3 | 14 | ac | false | <90% | 6708 | ||
NM_183375 | ESSPL | 222 | 240 | u | u | G | A | U | A | C | U | G | A | C | A | G | C | A | G | c | A | c | 58 | 4 | 14 | ac | false | <90% | 1011 | ||
NM_001013742 | DGKK | 3684 | 3702 | C | G | G | A | c | A | C | U | G | A | C | A | G | u | A | G | A | A | G | 29 | 2 | 8 | c | false | <90% | 3918 | ||
NM_053282 | SH2D1B | 314 | 332 | a | G | G | A | U | A | C | a | G | A | C | u | G | C | A | G | A | A | G | 2 | 3 | 7 | false | <90% | 2553 | |||
NM_173804 | TMEM86B | 1624 | 1642 | C | G | G | u | U | A | a | U | G | A | C | A | G | C | A | G | A | A | a | -8 | 3 | 11 | bc | false | <90% | 1654 | ||
NM_002874 | RAD23B | 3656 | 3674 | u | G | G | A | a | A | g | U | G | A | C | A | G | C | A | G | A | A | G | -19 | 3 | 12 | bc | false | <90% | 4130 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3275
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