Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
35 hits were found for CCUGGGAAAUGCAGAGAUA (20 guide strand hits and 15 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_015429 | ABI3BP | 137 | 155 | C | C | U | G | G | G | A | A | A | U | G | C | A | c | A | G | A | a | A | 77 | 2 | 13 | c | false | <90% | 4533 | ||
NM_001023565 | LOC401286 | 355 | 373 | g | C | U | G | G | G | A | A | A | U | G | C | A | c | A | G | A | a | A | 75 | 3 | 12 | c | false | <90% | 4518 | ||
NM_004360 | CDH1 | 2807 | 2825 | g | C | U | G | G | G | A | A | A | U | G | C | A | G | A | a | A | U | c | 66 | 3 | 14 | c | false | <90% | 4828 | ||
NM_014938 | MLXIP | 915 | 933 | u | C | U | G | G | G | A | A | A | U | G | C | A | G | A | c | A | U | g | 66 | 3 | 14 | c | false | <90% | 5400 | ||
NM_020549 | CHAT | 22 | 40 | a | C | U | G | G | G | A | A | A | U | G | C | u | G | A | G | c | U | A | 64 | 3 | 11 | false | <90% | 2485 | |||
NM_033401 | CNTNAP4 | 3299 | 3317 | g | g | a | G | G | G | A | A | A | U | G | C | A | G | A | G | A | a | A | 64 | 4 | 14 | c | false | <90% | 4867 | ||
NM_021785 | RAI2 | 1839 | 1857 | C | a | U | G | G | G | A | A | A | U | G | C | A | G | A | G | c | c | c | 57 | 4 | 14 | ac | false | <90% | 2338 | ||
XM_001130457 | LOC729501 | 391 | 409 | u | a | U | G | G | G | A | A | A | U | G | C | A | G | A | c | A | U | g | 55 | 4 | 13 | c | false | <90% | 1377 | ||
XR_015683 | LOC729863 | 286 | 304 | u | a | U | G | G | G | A | A | A | U | G | C | A | G | A | c | A | U | g | 55 | 4 | 13 | c | false | <90% | 3840 | ||
XR_016118 | LOC644734 | 400 | 418 | u | a | U | G | G | G | A | A | A | U | G | C | A | G | A | c | A | U | g | 55 | 4 | 13 | c | false | <90% | 4077 | ||
NM_000351 | STS | 4925 | 4943 | g | C | U | G | a | G | A | A | A | U | G | C | A | G | A | G | A | a | g | 38 | 4 | 12 | c | false | <90% | 6366 | ||
XR_015324 | LOC730944 | 315 | 333 | C | C | U | G | G | G | A | A | c | U | G | C | A | G | A | G | A | g | g | 32 | 3 | 8 | c | false | <90% | 1976 | ||
NM_153697 | ANKRD44 | 152 | 170 | u | C | U | G | G | G | A | g | A | U | G | C | A | G | A | G | A | U | c | 30 | 3 | 10 | bc | false | <90% | 3686 | ||
NM_018098 | ECT2 | 3552 | 3570 | u | C | U | G | u | G | A | A | A | U | G | C | A | u | A | G | A | U | A | 27 | 3 | 8 | c | false | <90% | 3916 | ||
XR_017286 | LOC653772 | 21 | 39 | g | C | U | G | G | G | g | A | A | U | G | C | A | G | A | G | A | a | c | 24 | 4 | 10 | c | false | <90% | 1362 | ||
NM_005443 | PAPSS1 | 140 | 158 | a | C | U | G | G | G | g | A | A | U | G | C | A | G | A | G | A | g | c | 24 | 4 | 10 | c | false | <90% | 2558 | ||
XM_001133958 | LOC731891 | 705 | 723 | C | C | U | G | a | G | A | A | A | U | G | C | A | G | A | G | g | a | u | 17 | 4 | 11 | c | false | <90% | 2023 | ||
NM_181699 | PPP2R1B | 2043 | 2061 | g | C | U | G | G | G | A | A | u | U | G | C | A | G | A | G | c | U | A | 14 | 3 | 7 | c | false | <90% | 2161 | ||
NM_002767 | PRPSAP2 | 823 | 841 | C | C | U | G | G | G | A | A | u | U | G | C | A | G | u | G | A | U | u | 10 | 3 | 8 | c | false | <90% | 1890 | ||
NM_001305 | CLDN4 | 1454 | 1472 | C | C | U | G | G | G | A | A | g | U | G | C | A | G | A | G | u | g | g | 8 | 4 | 8 | c | false | <90% | 1846 |
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_020972 | ZFYVE28 | 1174 | 1192 | a | A | c | C | U | C | U | G | C | A | U | U | U | C | C | C | A | a | G | 75 | 3 | 14 | c | false | <90% | 4110 | ||
NM_020773 | TBC1D14 | 1551 | 1569 | a | A | U | C | U | C | U | G | C | A | U | U | U | u | C | C | A | G | c | 73 | 3 | 12 | c | false | <90% | 4941 | ||
NM_024659 | GTDC1 | 138 | 156 | U | A | U | C | U | C | U | G | C | A | U | U | a | g | C | C | A | G | a | 65 | 3 | 12 | false | <90% | 2459 | |||
NM_001006636 | GTDC1 | 131 | 149 | U | A | U | C | U | C | U | G | C | A | U | U | a | g | C | C | A | G | a | 65 | 3 | 12 | false | <90% | 2692 | |||
NM_033132 | ZIC5 | 2674 | 2692 | g | c | c | C | U | C | U | G | C | A | U | U | U | C | C | C | A | G | a | 62 | 4 | 15 | bc | false | <90% | 4607 | ||
NM_174902 | LDLRAD3 | 1202 | 1220 | U | A | U | C | U | C | U | G | C | A | U | U | c | C | C | C | u | c | c | 58 | 4 | 12 | false | <90% | 2969 | |||
NM_001009992 | ZNF648 | 131 | 149 | g | c | U | g | U | C | U | G | C | A | U | U | U | C | C | C | A | G | G | 49 | 3 | 15 | bc | false | <90% | 3649 | ||
NM_006011 | ST8SIA2 | 3062 | 3080 | U | A | U | C | U | C | U | G | C | A | U | U | U | u | C | C | c | u | u | 49 | 4 | 13 | c | false | <90% | 5626 | ||
NM_014955 | KIAA0859 | 489 | 507 | U | A | U | C | U | C | U | G | C | A | U | c | U | C | C | C | u | G | G | 42 | 2 | 11 | false | <90% | 3096 | |||
NM_015935 | KIAA0859 | 814 | 832 | U | A | U | C | U | C | U | G | C | A | U | c | U | C | C | C | u | G | G | 42 | 2 | 11 | false | <90% | 3421 | |||
NM_199452 | ZNF365 | 1725 | 1743 | U | A | U | g | U | C | U | G | C | A | U | U | U | C | C | C | u | u | c | 32 | 4 | 12 | c | false | <90% | 2695 | ||
NM_199451 | ZNF365 | 2406 | 2424 | U | A | U | g | U | C | U | G | C | A | U | U | U | C | C | C | u | u | c | 32 | 4 | 12 | c | false | <90% | 3376 | ||
NM_031277 | RNF17 | 4257 | 4275 | c | A | U | C | U | C | U | G | C | c | U | U | c | C | C | C | A | G | G | 4 | 3 | 8 | false | <90% | 5120 | |||
NM_130847 | AMOTL1 | 6190 | 6208 | U | A | U | u | U | C | U | G | C | A | c | U | U | C | C | C | A | G | a | -3 | 3 | 7 | c | false | <90% | 8999 | ||
NM_006804 | STARD3 | 1942 | 1960 | a | A | U | C | U | C | U | G | C | c | U | c | U | C | C | C | A | G | G | -18 | 3 | 8 | false | <90% | 2073 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4140
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