Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
38 hits were found for GCUGUGCCUUGGGUGGCUU (18 guide strand hits and 20 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_001010908 | C1QL3 | 80 | 98 | u | C | U | G | U | G | C | C | U | U | G | G | G | U | G | c | C | U | a | 66 | 3 | 14 | c | false | <90% | 2493 | ||
NM_000663 | ABAT | 31 | 49 | c | C | U | c | U | G | C | C | U | U | G | G | G | U | G | u | C | U | U | 35 | 3 | 11 | c | false | <90% | 5463 | ||
NM_032296 | FLYWCH1 | 4622 | 4640 | c | u | g | u | U | G | C | C | U | U | G | G | G | U | G | G | C | U | U | 30 | 4 | 15 | bc | false | <90% | 5009 | ||
NM_012346 | NUP62 | 2837 | 2855 | c | C | U | G | U | a | C | C | U | U | G | G | G | U | G | G | C | a | c | 27 | 4 | 11 | c | false | <90% | 3253 | ||
NM_153718 | NUP62 | 2861 | 2879 | c | C | U | G | U | a | C | C | U | U | G | G | G | U | G | G | C | a | c | 27 | 4 | 11 | c | false | <90% | 3277 | ||
NM_016553 | NUP62 | 2983 | 3001 | c | C | U | G | U | a | C | C | U | U | G | G | G | U | G | G | C | a | c | 27 | 4 | 11 | c | false | <90% | 3399 | ||
NM_153719 | NUP62 | 3016 | 3034 | c | C | U | G | U | a | C | C | U | U | G | G | G | U | G | G | C | a | c | 27 | 4 | 11 | c | false | <90% | 3432 | ||
NM_020983 | ADCY6 | 5610 | 5628 | c | C | U | c | a | G | C | C | U | U | G | G | G | U | G | G | C | U | U | 9 | 3 | 14 | bc | false | <90% | 5877 | ||
NM_015270 | ADCY6 | 6327 | 6345 | c | C | U | c | a | G | C | C | U | U | G | G | G | U | G | G | C | U | U | 9 | 3 | 14 | bc | false | <90% | 6594 | ||
NM_015291 | DNAJC16 | 3861 | 3879 | a | a | g | G | U | G | C | C | U | U | u | G | G | U | G | G | C | U | U | 5 | 4 | 8 | c | false | <90% | 6035 | ||
NM_005741 | ZNF263 | 522 | 540 | G | C | U | u | U | G | C | C | a | U | G | G | G | U | G | G | C | U | U | 3 | 2 | 10 | bc | false | <90% | 3303 | ||
XR_017659 | LOC645931 | 1819 | 1837 | G | C | U | G | U | G | u | C | U | U | G | G | G | U | G | G | g | c | a | 2 | 4 | 9 | c | false | <90% | 2028 | ||
XR_018590 | LOC645931 | 1819 | 1837 | G | C | U | G | U | G | u | C | U | U | G | G | G | U | G | G | g | c | a | 2 | 4 | 9 | c | false | <90% | 2028 | ||
NM_004111 | FEN1 | 2063 | 2081 | G | C | U | G | U | G | u | C | U | U | G | G | G | U | G | G | g | c | a | 2 | 4 | 9 | c | false | <90% | 2265 | ||
NM_178003 | PPP2R4 | 532 | 550 | G | C | U | G | U | G | C | C | U | g | a | G | G | U | G | G | C | U | g | -49 | 3 | 9 | c | false | <90% | 2610 | ||
NM_021131 | PPP2R4 | 588 | 606 | G | C | U | G | U | G | C | C | U | g | a | G | G | U | G | G | C | U | g | -49 | 3 | 9 | c | false | <90% | 2666 | ||
NM_178000 | PPP2R4 | 658 | 676 | G | C | U | G | U | G | C | C | U | g | a | G | G | U | G | G | C | U | g | -49 | 3 | 9 | c | false | <90% | 2736 | ||
NM_178001 | PPP2R4 | 763 | 781 | G | C | U | G | U | G | C | C | U | g | a | G | G | U | G | G | C | U | g | -49 | 3 | 9 | c | false | <90% | 2841 |
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_001662 | ARF5 | 514 | 532 | g | u | G | C | C | A | C | C | C | A | A | G | G | C | A | C | A | G | g | 81 | 3 | 16 | abc | false | <90% | 978 | ||
XM_001131220 | LOC729762 | 470 | 488 | A | A | G | C | C | A | C | C | C | A | A | G | c | C | A | C | c | c | a | 58 | 4 | 12 | false | <90% | 1242 | |||
XM_001131220 | LOC729762 | 851 | 869 | A | A | G | C | C | A | C | C | C | A | A | G | c | C | A | C | c | c | a | 58 | 4 | 12 | false | <90% | 1242 | |||
XM_498961 | LOC441005 | 662 | 680 | c | A | G | C | C | A | C | C | C | A | A | G | G | a | g | C | A | G | C | 53 | 3 | 12 | c | false | <90% | 1145 | ||
XM_943522 | LOC441005 | 662 | 680 | c | A | G | C | C | A | C | C | C | A | A | G | G | a | g | C | A | G | C | 53 | 3 | 12 | c | false | <90% | 1148 | ||
XM_291001 | MYO7B | 1828 | 1846 | g | A | G | C | C | A | C | C | C | A | A | G | G | a | A | a | A | G | C | 52 | 3 | 12 | c | false | <90% | 3682 | ||
NM_001080527 | MYO7B | 4859 | 4877 | g | A | G | C | C | A | C | C | C | A | A | G | G | a | A | a | A | G | C | 52 | 3 | 12 | c | false | <90% | 6715 | ||
XM_001129005 | MYO7B | 4859 | 4877 | g | A | G | C | C | A | C | C | C | A | A | G | G | a | A | a | A | G | C | 52 | 3 | 12 | c | false | <90% | 6715 | ||
NM_001103 | ACTN2 | 1164 | 1182 | A | A | G | C | C | A | C | C | C | A | A | G | G | u | g | C | A | G | g | 50 | 3 | 13 | c | false | <90% | 4181 | ||
XM_944937 | C14orf72 | 398 | 416 | A | A | G | g | C | A | C | C | C | A | A | G | u | C | A | C | A | G | a | 47 | 3 | 8 | false | <90% | 642 | |||
XM_096733 | C14orf72 | 398 | 416 | A | A | G | g | C | A | C | C | C | A | A | G | u | C | A | C | A | G | a | 47 | 3 | 8 | false | <90% | 642 | |||
NM_018405 | C17orf79 | 346 | 364 | u | g | u | C | C | A | C | C | C | A | A | G | G | a | A | C | A | G | C | 47 | 4 | 10 | c | false | <90% | 861 | ||
NM_198316 | TENC1 | 2226 | 2244 | A | A | G | C | C | A | C | C | C | A | A | G | G | C | A | g | g | c | g | 42 | 4 | 15 | c | false | <90% | 4690 | ||
NM_170754 | TENC1 | 2398 | 2416 | A | A | G | C | C | A | C | C | C | A | A | G | G | C | A | g | g | c | g | 42 | 4 | 15 | c | false | <90% | 4862 | ||
NM_015319 | TENC1 | 2488 | 2506 | A | A | G | C | C | A | C | C | C | A | A | G | G | C | A | g | g | c | g | 42 | 4 | 15 | c | false | <90% | 4952 | ||
NM_013285 | GNL2 | 1461 | 1479 | A | A | G | C | C | A | C | C | C | A | A | u | G | C | A | g | A | G | C | 40 | 2 | 11 | false | <90% | 2331 | |||
NM_182557 | BCL9L | 5009 | 5027 | c | A | G | C | C | c | C | C | C | A | A | G | G | C | u | C | A | G | C | 9 | 3 | 8 | c | false | <90% | 7740 | ||
NM_015642 | ZBTB20 | 1105 | 1123 | g | A | G | C | C | A | C | C | C | A | c | a | G | C | A | C | A | G | C | 2 | 3 | 9 | false | <90% | 2975 | |||
NM_197956 | C9orf90 | 1551 | 1569 | A | c | c | C | C | A | C | C | C | c | A | G | G | C | A | C | A | G | C | -13 | 3 | 9 | bc | false | <90% | 3197 | ||
NM_003253 | TIAM1 | 3351 | 3369 | c | A | G | C | a | A | C | C | C | A | g | G | G | C | A | C | A | G | C | -14 | 3 | 8 | c | false | <90% | 7218 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2511
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