Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
27 hits were found for UCUACCUCCAUCUGGUCCG (10 guide strand hits and 17 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 | |||||||||||||
NR_003141 | SNHG4 | 164 | 182 | U | C | U | A | C | C | U | C | C | A | U | C | a | G | G | a | C | C | c | 58 | 3 | 12 | false | <90% | 681 | |||
NM_199189 | MATR3 | 192 | 210 | U | C | U | A | C | C | U | C | C | A | U | C | a | G | G | a | C | C | c | 58 | 3 | 12 | false | <90% | 4031 | |||
NM_016596 | HDAC7A | 3543 | 3561 | c | a | g | c | C | C | U | C | C | A | U | C | U | G | G | U | C | C | G | 30 | 4 | 15 | bc | false | <90% | 4086 | ||
NM_015401 | HDAC7A | 3663 | 3681 | c | a | g | c | C | C | U | C | C | A | U | C | U | G | G | U | C | C | G | 30 | 4 | 15 | bc | false | <90% | 4206 | ||
NM_198149 | TMEM58 | 747 | 765 | U | g | U | A | C | C | U | g | C | A | U | C | U | G | G | U | C | C | u | 21 | 3 | 10 | bc | false | <90% | 1141 | ||
NM_014953 | DIS3 | 6070 | 6088 | g | u | U | A | C | C | U | C | C | A | c | C | U | G | G | U | C | C | c | 20 | 4 | 8 | c | false | <90% | 7320 | ||
NM_016263 | FZR1 | 597 | 615 | U | C | U | A | C | C | U | C | a | A | U | C | U | G | G | U | g | g | a | 8 | 4 | 8 | c | false | <90% | 5008 | ||
NM_019888 | MC3R | 884 | 902 | U | C | U | u | C | C | U | C | C | A | c | C | U | G | G | U | C | C | u | -3 | 3 | 7 | c | false | <90% | 1083 | ||
NM_014721 | PHACTR2 | 509 | 527 | U | C | U | A | C | C | U | C | C | u | U | C | U | G | c | U | C | C | u | -12 | 3 | 9 | c | false | <90% | 4318 | ||
NM_002319 | LRCH4 | 658 | 676 | g | g | g | A | C | C | U | C | C | c | U | C | U | G | G | U | C | C | G | -15 | 4 | 9 | bc | false | <90% | 3201 |
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_002811 | PSMD7 | 895 | 913 | a | u | G | A | C | C | A | G | A | U | G | G | u | G | G | U | A | G | u | 71 | 4 | 10 | false | <90% | 1678 | |||
NM_004501 | HNRPU | 522 | 540 | g | c | G | A | C | C | A | G | A | U | G | G | A | G | c | U | A | G | g | 56 | 4 | 12 | c | false | <90% | 6789 | ||
NM_031844 | HNRPU | 522 | 540 | g | c | G | A | C | C | A | G | A | U | G | G | A | G | c | U | A | G | g | 56 | 4 | 12 | c | false | <90% | 6846 | ||
NM_003309 | TSPYL1 | 849 | 867 | a | G | G | A | g | C | A | G | A | U | G | G | A | G | G | U | A | G | A | 46 | 2 | 14 | bc | false | <90% | 3537 | ||
NM_005915 | MCM6 | 2093 | 2111 | a | G | a | u | C | C | A | G | A | U | G | G | A | G | G | U | A | G | A | 41 | 3 | 15 | bc | false | <90% | 3769 | ||
NM_000616 | CD4 | 1687 | 1705 | C | G | G | A | C | C | A | G | A | U | G | a | A | u | G | U | A | G | c | 41 | 3 | 11 | false | <90% | 3103 | |||
NM_002591 | PCK1 | 335 | 353 | u | G | G | g | C | C | A | G | A | U | G | G | A | G | G | a | A | G | A | 35 | 3 | 11 | c | false | <90% | 2688 | ||
NM_021082 | SLC15A2 | 1057 | 1075 | C | G | G | A | C | C | A | G | A | U | G | c | A | G | G | U | u | c | u | 35 | 4 | 11 | false | <90% | 2846 | |||
XR_016901 | LOC440304 | 3639 | 3657 | g | G | G | A | C | C | A | G | c | U | G | G | A | G | G | U | A | G | c | 32 | 3 | 9 | bc | false | <90% | 5213 | ||
XR_016202 | LOC440300 | 4086 | 4104 | g | G | G | A | C | C | A | G | c | U | G | G | A | G | G | U | A | G | c | 32 | 3 | 9 | bc | false | <90% | 5332 | ||
XR_015206 | LOC728121 | 3985 | 4003 | g | G | G | A | C | C | A | G | c | U | G | G | A | G | G | U | A | G | c | 32 | 3 | 9 | bc | false | <90% | 5459 | ||
XR_017409 | LOC440297 | 3978 | 3996 | g | G | G | A | C | C | A | G | c | U | G | G | A | G | G | U | A | G | c | 32 | 3 | 9 | bc | false | <90% | 5552 | ||
XR_016119 | LOC642288 | 4067 | 4085 | g | G | G | A | C | C | A | G | c | U | G | G | A | G | G | U | A | G | c | 32 | 3 | 9 | bc | false | <90% | 5641 | ||
XR_016146 | LOC390627 | 4068 | 4086 | g | G | G | A | C | C | A | G | c | U | G | G | A | G | G | U | A | G | c | 32 | 3 | 9 | bc | false | <90% | 5642 | ||
XR_016917 | LOC645306 | 3693 | 3711 | g | G | G | A | C | C | A | G | c | U | G | G | A | G | G | U | A | G | c | 32 | 3 | 9 | bc | false | <90% | 5803 | ||
NM_032821 | HYDIN | 4779 | 4797 | a | u | c | u | C | C | A | G | A | U | G | G | A | G | G | U | A | G | A | 30 | 4 | 15 | bc | false | <90% | 15729 | ||
NM_003777 | DNAH11 | 4091 | 4109 | u | G | G | A | a | C | A | G | A | U | G | G | A | u | G | U | A | G | A | 27 | 3 | 8 | c | false | <90% | 14188 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2050
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