Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
25 hits were found for GAGGACUCUUGGACUCUCU (14 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 | |||||||||||||
NM_004575 | POU4F2 | 1478 | 1496 | G | A | a | G | A | C | U | C | U | U | G | G | c | C | U | C | U | C | c | 65 | 3 | 9 | false | <90% | 3141 | |||
NM_000913 | OPRL1 | 1710 | 1728 | u | g | u | G | A | C | U | C | U | U | G | G | c | C | U | C | U | C | U | 56 | 4 | 9 | false | <90% | 3208 | |||
NM_182647 | OPRL1 | 1861 | 1879 | u | g | u | G | A | C | U | C | U | U | G | G | c | C | U | C | U | C | U | 56 | 4 | 9 | false | <90% | 3359 | |||
NM_003439 | ZKSCAN1 | 2214 | 2232 | a | g | G | c | A | C | U | C | U | U | G | G | A | C | U | C | U | C | g | 44 | 4 | 14 | bc | false | <90% | 5494 | ||
NM_000644 | AGL | 627 | 645 | G | c | a | G | A | C | U | C | U | U | G | G | A | C | U | a | U | C | U | 42 | 3 | 12 | c | false | <90% | 7109 | ||
NM_000643 | AGL | 687 | 705 | G | c | a | G | A | C | U | C | U | U | G | G | A | C | U | a | U | C | U | 42 | 3 | 12 | c | false | <90% | 7169 | ||
NM_000645 | AGL | 700 | 718 | G | c | a | G | A | C | U | C | U | U | G | G | A | C | U | a | U | C | U | 42 | 3 | 12 | c | false | <90% | 7182 | ||
NM_000646 | AGL | 700 | 718 | G | c | a | G | A | C | U | C | U | U | G | G | A | C | U | a | U | C | U | 42 | 3 | 12 | c | false | <90% | 7182 | ||
NM_000642 | AGL | 889 | 907 | G | c | a | G | A | C | U | C | U | U | G | G | A | C | U | a | U | C | U | 42 | 3 | 12 | c | false | <90% | 7371 | ||
NM_000028 | AGL | 967 | 985 | G | c | a | G | A | C | U | C | U | U | G | G | A | C | U | a | U | C | U | 42 | 3 | 12 | c | false | <90% | 7449 | ||
NR_002948 | KLKP1 | 987 | 1005 | c | A | G | G | A | C | U | C | c | U | G | G | A | u | U | C | U | C | U | 18 | 3 | 7 | c | false | <90% | 1146 | ||
NM_033112 | C6orf153 | 923 | 941 | G | A | G | G | g | C | U | C | U | U | G | G | A | C | U | a | U | C | c | 17 | 3 | 10 | c | false | <90% | 1177 | ||
NM_144707 | PROM2 | 303 | 321 | c | A | G | G | A | C | U | C | c | U | G | G | A | C | U | C | c | C | U | 14 | 3 | 7 | c | false | <90% | 3822 | ||
NM_006640 | SEPT9 | 441 | 459 | c | g | G | G | A | C | U | C | U | g | G | G | A | C | U | C | U | C | g | -1 | 4 | 8 | bc | false | <90% | 4452 |
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_006691 | XLKD1 | 1114 | 1132 | g | a | A | G | A | G | U | C | C | A | A | G | A | G | U | C | C | a | a | 78 | 4 | 15 | ac | false | <90% | 2436 | ||
NM_031935 | HMCN1 | 112 | 130 | A | G | A | G | A | u | U | C | C | A | A | G | A | G | U | C | u | g | a | 5 | 4 | 10 | c | false | <90% | 18212 | ||
NM_001008536 | TCHHL1 | 2413 | 2431 | A | G | A | G | A | G | a | C | C | A | A | G | A | G | c | C | C | U | g | 4 | 3 | 7 | c | false | <90% | 3603 | ||
NM_006534 | NCOA3 | 1902 | 1920 | c | a | g | G | A | u | U | C | C | A | A | G | A | G | U | C | C | U | C | 3 | 4 | 13 | bc | false | <90% | 7923 | ||
NM_181659 | NCOA3 | 1902 | 1920 | c | a | g | G | A | u | U | C | C | A | A | G | A | G | U | C | C | U | C | 3 | 4 | 13 | bc | false | <90% | 7935 | ||
NM_023070 | ZNF643 | 937 | 955 | A | G | A | G | A | G | g | C | C | A | A | G | A | G | U | C | u | a | a | 2 | 4 | 9 | c | false | <90% | 1976 | ||
XR_018226 | LOC442063 | 291 | 309 | A | G | A | G | A | a | U | C | C | A | g | G | A | G | U | C | C | U | g | -29 | 3 | 7 | c | false | <90% | 716 | ||
XR_016985 | LOC442063 | 291 | 309 | A | G | A | G | A | a | U | C | C | A | g | G | A | G | U | C | C | U | g | -29 | 3 | 7 | c | false | <90% | 716 | ||
XR_016669 | LOC402182 | 293 | 311 | A | G | A | G | A | a | U | C | C | A | g | G | A | G | U | C | C | U | a | -29 | 3 | 7 | c | false | <90% | 982 | ||
XR_019628 | LOC650605 | 293 | 311 | A | G | A | G | A | a | U | C | C | A | g | G | A | G | U | C | C | U | a | -29 | 3 | 7 | c | false | <90% | 982 | ||
NM_019013 | FAM64A | 342 | 360 | A | G | A | G | A | a | U | C | C | A | g | G | A | G | U | C | C | U | g | -29 | 3 | 7 | c | false | <90% | 1483 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1829
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