Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
35 hits were found for CUGCUCUUGGACUGCAUGA (15 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_020826 | SYT13 | 2132 | 2150 | C | U | G | C | U | C | U | U | G | G | A | C | U | G | a | A | U | u | u | 67 | 3 | 14 | c | false | <90% | 5108 | ||
XM_001129280 | LOC729086 | 213 | 231 | C | U | G | C | U | C | U | U | G | G | A | g | U | G | C | A | c | a | g | 35 | 4 | 11 | false | <90% | 2950 | |||
NM_030796 | ECOP | 226 | 244 | C | U | G | C | U | C | U | U | G | G | A | g | U | G | C | A | c | a | g | 35 | 4 | 11 | false | <90% | 2962 | |||
NM_080751 | TMC2 | 2850 | 2868 | C | c | u | C | U | C | U | U | G | G | A | a | U | G | C | A | U | G | A | 35 | 3 | 8 | false | <90% | 3169 | |||
XM_001131778 | KIAA0368 | 1030 | 1048 | C | U | G | C | U | u | U | U | G | G | A | C | U | u | C | A | U | G | c | 12 | 3 | 7 | c | false | <90% | 7391 | ||
NM_001080398 | KIAA0368 | 1030 | 1048 | C | U | G | C | U | u | U | U | G | G | A | C | U | u | C | A | U | G | c | 12 | 3 | 7 | c | false | <90% | 7391 | ||
NM_152795 | HIF3A | 5260 | 5278 | C | U | G | C | U | C | c | U | G | G | A | C | U | u | C | A | U | G | c | 9 | 3 | 6 | c | false | <90% | 5850 | ||
NM_152794 | HIF3A | 5274 | 5292 | C | U | G | C | U | C | c | U | G | G | A | C | U | u | C | A | U | G | c | 9 | 3 | 6 | c | false | <90% | 5864 | ||
NM_022462 | HIF3A | 5318 | 5336 | C | U | G | C | U | C | c | U | G | G | A | C | U | u | C | A | U | G | c | 9 | 3 | 6 | c | false | <90% | 5908 | ||
NM_173647 | RNF149 | 36 | 54 | C | U | G | C | U | C | U | U | c | G | A | C | U | G | C | A | c | c | g | 8 | 4 | 8 | c | false | <90% | 2452 | ||
NM_003634 | NIPSNAP1 | 654 | 672 | g | c | c | C | U | C | a | U | G | G | A | C | U | G | C | A | U | G | A | 0 | 4 | 12 | bc | false | <90% | 2233 | ||
NM_005104 | BRD2 | 2837 | 2855 | C | U | G | C | a | C | U | U | G | G | c | C | U | G | C | A | U | G | A | -12 | 2 | 8 | c | false | <90% | 4693 | ||
NM_144686 | TMC4 | 557 | 575 | g | U | G | C | U | C | a | U | G | G | c | C | U | G | C | A | U | G | A | -29 | 3 | 8 | c | false | <90% | 2434 | ||
NM_001401 | EDG2 | 2803 | 2821 | C | U | G | C | U | u | U | U | G | u | A | C | U | G | C | A | U | G | g | -51 | 3 | 8 | bc | false | <90% | 3104 | ||
NM_057159 | EDG2 | 2881 | 2899 | C | U | G | C | U | u | U | U | G | u | A | C | U | G | C | A | U | G | g | -51 | 3 | 8 | bc | false | <90% | 3182 |
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_020845 | PITPNM2 | 744 | 762 | g | C | A | U | G | C | A | G | U | C | C | A | A | G | A | u | C | g | a | 64 | 4 | 14 | c | false | <90% | 6754 | ||
NM_005382 | NEFM | 971 | 989 | a | g | c | U | G | C | A | G | U | C | C | A | A | G | A | G | C | A | u | 62 | 4 | 15 | bc | false | <90% | 3238 | ||
NM_002474 | MYH11 | 3899 | 3917 | a | g | c | U | G | C | A | G | U | C | C | A | A | G | u | G | C | A | G | 42 | 4 | 11 | c | false | <90% | 6882 | ||
NM_001040114 | MYH11 | 3920 | 3938 | a | g | c | U | G | C | A | G | U | C | C | A | A | G | u | G | C | A | G | 42 | 4 | 11 | c | false | <90% | 6903 | ||
NM_022844 | MYH11 | 3899 | 3917 | a | g | c | U | G | C | A | G | U | C | C | A | A | G | u | G | C | A | G | 42 | 4 | 11 | c | false | <90% | 6921 | ||
NM_001040113 | MYH11 | 3920 | 3938 | a | g | c | U | G | C | A | G | U | C | C | A | A | G | u | G | C | A | G | 42 | 4 | 11 | c | false | <90% | 6942 | ||
NM_014793 | LCMT2 | 2473 | 2491 | c | C | A | U | G | C | A | G | U | C | C | g | A | G | A | G | g | A | G | 40 | 3 | 10 | false | <90% | 2931 | |||
NM_173851 | SLC30A8 | 2180 | 2198 | U | C | A | U | u | C | A | G | U | C | C | A | c | G | A | G | C | A | u | 33 | 3 | 7 | false | <90% | 5373 | |||
XM_001130956 | ANKS6 | 2103 | 2121 | a | u | c | g | G | C | A | G | U | C | C | A | A | G | A | G | C | A | G | 30 | 4 | 15 | bc | false | <90% | 3492 | ||
NM_173551 | ANKS6 | 2299 | 2317 | a | u | c | g | G | C | A | G | U | C | C | A | A | G | A | G | C | A | G | 30 | 4 | 15 | bc | false | <90% | 7147 | ||
NM_001076786 | QSER1 | 3165 | 3183 | U | C | A | U | G | a | A | G | U | C | C | A | g | G | A | G | C | A | a | 21 | 3 | 6 | false | <90% | 9271 | |||
NM_001066 | TNFRSF1B | 1638 | 1656 | a | C | c | U | G | C | A | G | g | C | C | A | A | G | A | G | C | A | G | 18 | 3 | 10 | bc | false | <90% | 3682 | ||
NM_024731 | C16orf44 | 986 | 1004 | U | C | A | U | G | C | A | G | a | C | C | A | A | G | c | G | C | A | c | 10 | 3 | 8 | c | false | <90% | 2211 | ||
NM_001105 | ACVR1 | 1416 | 1434 | U | C | A | U | G | C | A | u | U | C | C | c | A | G | A | G | C | A | c | 0 | 3 | 7 | false | <90% | 2952 | |||
NM_004807 | HS6ST1 | 1055 | 1073 | U | C | A | U | G | C | A | G | U | a | C | A | A | u | A | G | C | A | c | -7 | 3 | 9 | c | false | <90% | 2051 | ||
XM_001132928 | LOC728969 | 1062 | 1080 | U | C | A | U | G | C | A | G | U | a | C | A | A | c | A | G | C | A | c | -7 | 3 | 9 | c | false | <90% | 4055 | ||
NM_003978 | PSTPIP1 | 1164 | 1182 | U | C | A | U | c | C | A | G | g | C | C | A | A | G | A | G | C | A | c | -16 | 3 | 9 | bc | false | <90% | 1781 | ||
NM_152843 | HPS4 | 1932 | 1950 | g | C | A | U | G | g | A | G | c | C | C | A | A | G | A | G | C | A | G | -25 | 3 | 10 | bc | false | <90% | 2950 | ||
NM_152841 | HPS4 | 1499 | 1517 | g | C | A | U | G | g | A | G | c | C | C | A | A | G | A | G | C | A | G | -25 | 3 | 10 | bc | false | <90% | 4069 | ||
NM_022081 | HPS4 | 1969 | 1987 | g | C | A | U | G | g | A | G | c | C | C | A | A | G | A | G | C | A | G | -25 | 3 | 10 | bc | false | <90% | 4539 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3621
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