Automatic recommendation
Not OK - siRNA is not specific
37 hits were found for CUGCACCAUGAUCAUCGAC (28 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 | |||||||||||||
XM_290842 | LRFN1 | 1599 | 1617 | C | g | G | C | A | C | C | A | U | G | A | U | C | A | U | C | G | c | C | 85 | 2 | 15 | ac | false | <90% | 3381 | ||
XM_940573 | LRFN1 | 1599 | 1617 | C | g | G | C | A | C | C | A | U | G | A | U | C | A | U | C | G | c | C | 85 | 2 | 15 | ac | false | <90% | 3381 | ||
NM_000746 | CHRNA7 | 966 | 984 | C | a | G | C | A | C | C | A | U | G | A | U | C | A | U | C | G | u | g | 80 | 3 | 15 | ac | false | <90% | 2171 | ||
NM_148911 | CHRFAM7A | 1126 | 1144 | C | a | G | C | A | C | C | A | U | G | A | U | C | A | U | C | G | u | g | 80 | 3 | 15 | ac | false | <90% | 2794 | ||
NM_139320 | CHRFAM7A | 1190 | 1208 | C | a | G | C | A | C | C | A | U | G | A | U | C | A | U | C | G | u | g | 80 | 3 | 15 | ac | false | <90% | 2858 | ||
XR_015707 | LOC732073 | 45 | 63 | g | U | G | C | A | C | C | A | U | G | A | U | C | A | U | C | u | g | C | 71 | 3 | 15 | ac | false | <90% | 1274 | ||
XR_015718 | LOC729945 | 45 | 63 | g | U | G | C | A | C | C | A | U | G | A | U | C | A | U | C | u | g | C | 71 | 3 | 15 | ac | false | <90% | 1274 | ||
NM_020134 | DPYSL5 | 441 | 459 | C | a | c | C | A | C | C | A | U | G | A | U | C | A | U | C | G | g | C | 66 | 3 | 14 | c | false | <90% | 3074 | ||
NM_004352 | CBLN1 | 551 | 569 | u | c | G | C | A | C | C | A | U | G | A | U | C | A | U | C | u | A | C | 63 | 3 | 14 | ac | false | <90% | 1524 | ||
NM_030629 | CMIP | 1160 | 1178 | C | a | G | C | A | C | C | A | U | G | A | g | C | A | U | C | G | A | g | 49 | 3 | 9 | false | <90% | 4128 | |||
NM_198390 | CMIP | 1267 | 1285 | C | a | G | C | A | C | C | A | U | G | A | g | C | A | U | C | G | A | g | 49 | 3 | 9 | false | <90% | 4235 | |||
NM_001387 | DPYSL3 | 410 | 428 | C | a | c | C | A | C | C | A | U | G | A | U | C | A | U | u | G | A | C | 42 | 3 | 12 | c | false | <90% | 5066 | ||
NM_015292 | FAM62A | 920 | 938 | u | g | a | C | A | C | C | A | U | G | A | U | C | A | U | g | G | A | C | 40 | 4 | 12 | c | false | <90% | 4190 | ||
NM_012284 | KCNH3 | 1709 | 1727 | C | U | G | C | A | C | C | A | U | G | c | U | C | A | U | C | G | g | C | 36 | 2 | 10 | c | false | <90% | 3853 | ||
XM_935531 | LOC641765 | 684 | 702 | C | g | G | C | u | C | C | A | U | G | A | U | C | A | U | C | G | A | g | 32 | 3 | 13 | bc | false | <90% | 1053 | ||
XM_001129421 | LOC641765 | 708 | 726 | C | g | G | C | u | C | C | A | U | G | A | U | C | A | U | C | G | A | g | 32 | 3 | 13 | bc | false | <90% | 1077 | ||
XM_939157 | LOC650070 | 699 | 717 | C | g | G | C | u | C | C | A | U | G | A | U | C | A | U | C | G | A | g | 32 | 3 | 13 | bc | false | <90% | 1119 | ||
NM_032890 | DISP1 | 732 | 750 | g | U | G | C | A | C | C | A | U | G | u | U | C | A | U | C | G | u | a | 29 | 4 | 9 | c | false | <90% | 4743 | ||
NM_052813 | CARD9 | 447 | 465 | C | U | u | C | u | C | C | A | U | G | A | U | C | A | U | C | G | A | C | 28 | 2 | 14 | bc | false | <90% | 2136 | ||
NM_014550 | CARD10 | 360 | 378 | C | U | G | C | u | C | C | A | U | G | A | U | C | c | U | C | G | A | u | 24 | 3 | 8 | c | false | <90% | 3912 | ||
NM_002218 | ITIH4 | 279 | 297 | C | U | u | C | u | C | C | A | U | G | A | U | C | A | U | C | G | A | u | 23 | 3 | 13 | bc | false | <90% | 3260 | ||
NM_005481 | THRAP5 | 1900 | 1918 | C | U | G | C | A | C | C | A | a | G | A | U | C | A | c | C | G | A | C | 15 | 2 | 8 | c | false | <90% | 2952 | ||
XM_001130102 | THRAP5 | 1891 | 1909 | C | U | G | C | A | C | C | A | a | G | A | U | C | A | c | C | G | A | C | 15 | 2 | 8 | c | false | <90% | 3218 | ||
NM_019849 | SLC7A10 | 234 | 252 | C | U | G | C | A | C | C | A | U | c | A | U | C | A | U | C | G | g | g | 9 | 3 | 9 | c | false | <90% | 1918 | ||
NM_015448 | RP11-529I10.4 | 494 | 512 | C | U | G | C | A | C | C | c | U | G | A | U | C | A | U | C | u | c | u | 6 | 4 | 8 | c | false | <90% | 858 | ||
NM_014030 | GIT1 | 1233 | 1251 | u | g | c | C | A | C | C | u | U | G | A | U | C | A | U | C | G | A | C | 4 | 4 | 11 | bc | false | <90% | 3758 | ||
NM_002088 | GRIK5 | 668 | 686 | g | U | c | C | A | C | C | A | U | c | A | U | C | A | U | C | G | A | C | -4 | 3 | 9 | bc | false | <90% | 3555 | ||
NM_000400 | ERCC2 | 1270 | 1288 | C | U | u | C | A | C | C | A | U | c | A | U | C | A | U | C | G | A | g | -7 | 3 | 8 | bc | false | <90% | 2355 |
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_000434 | NEU1 | 828 | 846 | a | g | C | G | A | U | G | A | U | C | A | U | G | G | U | G | C | c | u | 78 | 4 | 15 | ac | false | <90% | 1943 | ||
NM_003032 | ST6GAL1 | 916 | 934 | a | U | C | G | A | U | G | A | U | C | A | U | G | a | c | G | C | A | G | 53 | 3 | 12 | c | false | <90% | 4295 | ||
NM_173216 | ST6GAL1 | 1038 | 1056 | a | U | C | G | A | U | G | A | U | C | A | U | G | a | c | G | C | A | G | 53 | 3 | 12 | c | false | <90% | 4403 | ||
NM_182489 | STRA8 | 946 | 964 | a | g | a | G | A | U | G | A | U | C | A | U | G | u | U | G | C | A | G | 47 | 4 | 10 | c | false | <90% | 993 | ||
NM_012287 | CENTB2 | 4877 | 4895 | a | a | a | G | A | U | G | A | U | C | A | U | G | G | U | u | C | A | G | 40 | 4 | 12 | c | false | <90% | 7102 | ||
NM_001079538 | LOC653216 | 161 | 179 | G | a | a | G | A | U | G | A | U | C | A | g | G | G | U | G | C | A | G | 35 | 3 | 8 | false | <90% | 336 | |||
NM_130775 | XAGE5 | 218 | 236 | G | a | a | G | A | U | G | A | U | C | A | g | G | G | U | G | C | A | G | 35 | 3 | 8 | false | <90% | 478 | |||
NM_130777 | XAGE2 | 449 | 467 | G | a | a | G | A | U | G | A | U | C | A | g | G | G | U | G | C | A | G | 35 | 3 | 8 | false | <90% | 720 | |||
NM_020853 | KIAA1467 | 362 | 380 | c | U | C | G | A | U | G | A | U | C | c | U | G | G | U | G | C | u | c | 29 | 4 | 9 | c | false | <90% | 4725 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2474
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