Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
24 hits were found for CGGAGACAUCAGACAACUA (13 guide strand hits and 11 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_291020 | LOC339809 | 3236 | 3254 | a | G | G | A | G | A | C | A | U | C | A | G | c | C | A | A | C | a | u | 79 | 4 | 11 | false | <90% | 5135 | |||
XM_936940 | LOC339809 | 3240 | 3258 | a | G | G | A | G | A | C | A | U | C | A | G | c | C | A | A | C | a | u | 79 | 4 | 11 | false | <90% | 5139 | |||
NM_002844 | PTPRK | 2859 | 2877 | u | G | a | A | G | A | C | A | U | C | A | G | A | C | A | g | C | U | A | 52 | 3 | 12 | c | false | <90% | 5982 | ||
NM_203388 | RNH1 | 809 | 827 | g | u | G | u | G | A | C | A | U | C | A | G | A | C | A | A | C | U | g | 44 | 4 | 14 | bc | false | <90% | 1764 | ||
NM_203384 | RNH1 | 861 | 879 | g | u | G | u | G | A | C | A | U | C | A | G | A | C | A | A | C | U | g | 44 | 4 | 14 | bc | false | <90% | 1816 | ||
NM_203389 | RNH1 | 877 | 895 | g | u | G | u | G | A | C | A | U | C | A | G | A | C | A | A | C | U | g | 44 | 4 | 14 | bc | false | <90% | 1832 | ||
NM_203385 | RNH1 | 929 | 947 | g | u | G | u | G | A | C | A | U | C | A | G | A | C | A | A | C | U | g | 44 | 4 | 14 | bc | false | <90% | 1884 | ||
NM_203386 | RNH1 | 982 | 1000 | g | u | G | u | G | A | C | A | U | C | A | G | A | C | A | A | C | U | g | 44 | 4 | 14 | bc | false | <90% | 1937 | ||
NM_203383 | RNH1 | 1034 | 1052 | g | u | G | u | G | A | C | A | U | C | A | G | A | C | A | A | C | U | g | 44 | 4 | 14 | bc | false | <90% | 1989 | ||
NM_203387 | RNH1 | 1050 | 1068 | g | u | G | u | G | A | C | A | U | C | A | G | A | C | A | A | C | U | g | 44 | 4 | 14 | bc | false | <90% | 2005 | ||
NM_002939 | RNH1 | 1102 | 1120 | g | u | G | u | G | A | C | A | U | C | A | G | A | C | A | A | C | U | g | 44 | 4 | 14 | bc | false | <90% | 2057 | ||
NM_001011725 | LOC144983 | 302 | 320 | a | G | G | A | G | A | C | u | U | C | A | G | A | C | A | A | C | c | A | 33 | 3 | 9 | c | false | <90% | 2224 | ||
NM_001011724 | LOC144983 | 302 | 320 | a | G | G | A | G | A | C | u | U | C | A | G | A | C | A | A | C | c | A | 33 | 3 | 9 | c | false | <90% | 2365 |
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_000204 | CFI | 715 | 733 | a | A | G | U | U | G | U | C | U | G | A | U | c | U | C | U | C | u | a | 79 | 4 | 11 | false | <90% | 2160 | |||
NM_015074 | KIF1B | 4869 | 4887 | a | A | G | U | U | G | U | C | U | G | A | U | a | U | C | U | C | u | c | 79 | 4 | 11 | false | <90% | 10551 | |||
NM_001001395 | LMO3 | 3192 | 3210 | U | u | G | U | U | G | U | C | U | G | A | U | G | c | C | U | C | C | a | 64 | 3 | 11 | c | false | <90% | 3450 | ||
NM_018640 | LMO3 | 3469 | 3487 | U | u | G | U | U | G | U | C | U | G | A | U | G | c | C | U | C | C | a | 64 | 3 | 11 | c | false | <90% | 3727 | ||
NM_194314 | ZBTB41 | 8335 | 8353 | U | g | G | U | U | G | U | C | U | G | A | U | G | U | u | U | C | C | u | 58 | 3 | 12 | c | false | <90% | 8474 | ||
NM_003899 | ARHGEF7 | 4286 | 4304 | c | u | c | U | U | G | U | C | U | G | A | U | c | U | C | U | C | C | G | 56 | 4 | 9 | false | <90% | 5032 | |||
NM_004740 | TIAF1 | 996 | 1014 | U | g | G | g | U | G | U | C | U | G | A | U | G | U | C | U | C | C | a | 46 | 3 | 14 | bc | false | <90% | 2110 | ||
NM_203318 | MYO18A | 6434 | 6452 | U | g | G | g | U | G | U | C | U | G | A | U | G | U | C | U | C | C | a | 46 | 3 | 14 | bc | false | <90% | 7546 | ||
NM_078471 | MYO18A | 6479 | 6497 | U | g | G | g | U | G | U | C | U | G | A | U | G | U | C | U | C | C | a | 46 | 3 | 14 | bc | false | <90% | 7591 | ||
NM_024293 | C2orf17 | 1117 | 1135 | c | A | G | c | U | G | a | C | U | G | A | U | G | U | C | U | C | C | G | -5 | 3 | 12 | bc | false | <90% | 2614 | ||
NM_007348 | ATF6 | 442 | 460 | U | A | G | U | U | c | U | C | a | G | A | U | G | U | C | U | C | C | c | -28 | 3 | 9 | bc | false | <90% | 2488 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 465
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