Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
46 hits were found for GACUUCAACCCCAACAAGG (35 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_152727 | CPNE2 | 1367 | 1385 | a | A | C | U | U | C | A | A | C | C | C | C | A | c | C | A | A | c | c | 70 | 4 | 12 | c | false | <90% | 2182 | ||
NM_133378 | TTN | 61508 | 61526 | a | A | C | U | U | C | A | A | C | C | C | C | A | A | C | A | u | c | u | 66 | 4 | 15 | ac | false | <90% | 101519 | ||
NM_133437 | TTN | 42593 | 42611 | a | A | C | U | U | C | A | A | C | C | C | C | A | A | C | A | u | c | u | 66 | 4 | 15 | ac | false | <90% | 82604 | ||
NM_133432 | TTN | 42392 | 42410 | a | A | C | U | U | C | A | A | C | C | C | C | A | A | C | A | u | c | u | 66 | 4 | 15 | ac | false | <90% | 82403 | ||
NM_003319 | TTN | 42017 | 42035 | a | A | C | U | U | C | A | A | C | C | C | C | A | A | C | A | u | c | u | 66 | 4 | 15 | ac | false | <90% | 82028 | ||
NM_182635 | C9orf164 | 1062 | 1080 | G | A | C | c | U | C | A | A | C | C | C | C | A | A | C | A | A | G | a | 58 | 2 | 14 | bc | false | <90% | 1837 | ||
NM_005561 | LAMP1 | 1050 | 1068 | a | A | C | a | U | C | A | A | C | C | C | C | A | A | C | A | A | G | a | 56 | 3 | 14 | bc | false | <90% | 2560 | ||
NM_001079843 | CASZ1 | 3936 | 3954 | c | A | C | a | U | C | A | A | C | C | C | C | A | A | C | A | A | c | a | 53 | 4 | 13 | c | false | <90% | 7938 | ||
NR_000034 | TMEM185B | 457 | 475 | G | A | C | U | U | C | A | A | C | C | C | C | A | g | u | A | A | G | u | 50 | 3 | 13 | c | false | <90% | 2131 | ||
NM_015512 | DNAH1 | 11513 | 11531 | c | A | C | a | U | C | A | A | C | C | C | C | g | A | C | A | A | G | G | 50 | 3 | 8 | false | <90% | 13114 | |||
NM_001834 | CLTB | 719 | 737 | G | A | C | U | U | C | A | A | C | C | C | C | A | A | g | A | g | c | a | 44 | 4 | 14 | c | false | <90% | 1130 | ||
NM_007097 | CLTB | 773 | 791 | G | A | C | U | U | C | A | A | C | C | C | C | A | A | g | A | g | c | a | 44 | 4 | 14 | c | false | <90% | 1184 | ||
XR_019125 | LOC389160 | 2691 | 2709 | G | A | C | a | U | C | A | A | C | C | C | C | A | A | C | A | u | a | G | 37 | 3 | 12 | c | false | <90% | 3173 | ||
NM_000607 | ORM1 | 280 | 298 | u | A | C | U | U | C | A | c | C | C | C | C | A | A | C | A | A | G | a | 30 | 3 | 10 | bc | false | <90% | 803 | ||
NM_198889 | ANKRD17 | 5259 | 5277 | a | A | C | U | U | C | A | A | g | C | C | C | A | A | C | A | A | c | u | 30 | 4 | 8 | c | false | <90% | 8637 | ||
NM_032217 | ANKRD17 | 6012 | 6030 | a | A | C | U | U | C | A | A | g | C | C | C | A | A | C | A | A | c | u | 30 | 4 | 8 | c | false | <90% | 9390 | ||
NM_052896 | CSMD2 | 2853 | 2871 | G | A | C | U | U | C | u | A | C | C | C | C | A | A | C | A | A | c | u | 26 | 3 | 10 | c | false | <90% | 13108 | ||
XM_940071 | LOC131873 | 2827 | 2845 | u | A | C | U | U | C | A | g | C | C | C | C | A | c | C | A | A | G | G | 16 | 3 | 6 | c | false | <90% | 9089 | ||
XM_067585 | LOC131873 | 2827 | 2845 | u | A | C | U | U | C | A | g | C | C | C | C | A | c | C | A | A | G | G | 16 | 3 | 6 | c | false | <90% | 9089 | ||
NM_021952 | ELAVL4 | 1215 | 1233 | G | A | C | U | U | C | A | A | C | a | C | C | A | A | C | A | A | G | u | 12 | 2 | 9 | bc | false | <90% | 1591 | ||
NM_001419 | ELAVL1 | 999 | 1017 | G | A | C | U | U | C | A | A | C | a | C | C | A | A | C | A | A | G | u | 12 | 2 | 9 | bc | false | <90% | 6075 | ||
NM_001005920 | LOC339123 | 733 | 751 | G | A | g | U | U | C | c | A | C | C | C | C | A | A | C | A | A | G | a | 9 | 3 | 11 | bc | false | <90% | 2074 | ||
NM_002078 | GOLGA4 | 388 | 406 | u | u | C | U | U | C | A | A | C | a | C | C | A | A | C | A | A | G | a | -1 | 4 | 8 | bc | false | <90% | 7717 | ||
NM_004230 | EDG5 | 133 | 151 | u | A | C | c | U | g | A | A | C | C | C | C | A | A | C | A | A | G | G | -2 | 3 | 13 | bc | false | <90% | 3589 | ||
NM_001009606 | HS3ST6 | 742 | 760 | u | A | C | U | U | C | A | A | C | g | C | C | A | c | C | A | A | G | G | -4 | 3 | 8 | c | false | <90% | 1063 | ||
XM_001130338 | LOC650913 | 709 | 727 | G | A | C | U | g | C | A | g | C | C | C | C | A | A | C | A | A | G | a | -18 | 3 | 10 | bc | false | <90% | 1780 | ||
XM_001131554 | LOC392242 | 709 | 727 | G | A | C | U | g | C | A | g | C | C | C | C | A | A | C | A | A | G | a | -18 | 3 | 10 | bc | false | <90% | 1780 | ||
XM_496985 | REXO1L7P | 709 | 727 | G | A | C | U | g | C | A | g | C | C | C | C | A | A | C | A | A | G | a | -18 | 3 | 10 | bc | false | <90% | 1780 | ||
XM_496984 | REXO1L2P | 715 | 733 | G | A | C | U | g | C | A | g | C | C | C | C | A | A | C | A | A | G | a | -18 | 3 | 10 | bc | false | <90% | 1786 | ||
XM_926387 | LOC653185 | 787 | 805 | G | A | C | U | g | C | A | g | C | C | C | C | A | A | C | A | A | G | a | -18 | 3 | 10 | bc | false | <90% | 1858 | ||
XM_496981 | REXO1L3P | 991 | 1009 | G | A | C | U | g | C | A | g | C | C | C | C | A | A | C | A | A | G | a | -18 | 3 | 10 | bc | false | <90% | 2062 | ||
XM_001125700 | LOC653042 | 991 | 1009 | G | A | C | U | g | C | A | g | C | C | C | C | A | A | C | A | A | G | a | -18 | 3 | 10 | bc | false | <90% | 2062 | ||
XM_496983 | REXO1L5P | 991 | 1009 | G | A | C | U | g | C | A | g | C | C | C | C | A | A | C | A | A | G | a | -18 | 3 | 10 | bc | false | <90% | 2062 | ||
XM_376784 | REXO1L6P | 991 | 1009 | G | A | C | U | g | C | A | g | C | C | C | C | A | A | C | A | A | G | a | -18 | 3 | 10 | bc | false | <90% | 2062 | ||
NM_172239 | REXO1L1 | 991 | 1009 | G | A | C | U | g | C | A | g | C | C | C | C | A | A | C | A | A | G | a | -18 | 3 | 10 | bc | false | <90% | 7032 |
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_004845 | PCYT1B | 2877 | 2895 | u | C | U | U | G | U | U | G | G | G | G | U | U | G | A | A | c | U | a | 69 | 3 | 15 | ac | false | <90% | 5447 | ||
NM_138728 | ST7L | 2213 | 2231 | g | g | c | U | G | U | U | G | G | G | G | U | U | G | A | A | G | U | C | 67 | 3 | 16 | bc | false | <90% | 4459 | ||
NM_138727 | ST7L | 2255 | 2273 | g | g | c | U | G | U | U | G | G | G | G | U | U | G | A | A | G | U | C | 67 | 3 | 16 | bc | false | <90% | 4502 | ||
NM_017744 | ST7L | 2306 | 2324 | g | g | c | U | G | U | U | G | G | G | G | U | U | G | A | A | G | U | C | 67 | 3 | 16 | bc | false | <90% | 4552 | ||
NM_030645 | SH3BP5L | 2539 | 2557 | C | C | a | U | G | U | U | G | G | G | G | g | U | G | A | A | G | U | C | 46 | 2 | 8 | false | <90% | 3182 | |||
NM_012308 | FBXL11 | 4287 | 4305 | a | C | U | U | a | U | U | G | G | G | G | U | U | G | A | A | G | c | u | 38 | 4 | 12 | c | false | <90% | 6210 | ||
XM_371491 | LOC388946 | 1095 | 1113 | C | C | U | U | G | a | U | G | G | G | G | U | U | G | A | A | a | c | C | 10 | 3 | 10 | c | false | <90% | 1137 | ||
XM_941345 | LOC388946 | 1095 | 1113 | C | C | U | U | G | a | U | G | G | G | G | U | U | G | A | A | a | c | C | 10 | 3 | 10 | c | false | <90% | 1137 | ||
NM_006083 | IK | 1752 | 1770 | a | g | c | U | G | a | U | G | G | G | G | U | U | G | A | A | G | U | C | 3 | 4 | 13 | bc | false | <90% | 1955 | ||
NM_021230 | MLL3 | 5656 | 5674 | C | C | U | U | G | a | g | G | G | G | G | U | U | G | A | A | G | U | C | -29 | 2 | 12 | bc | false | <90% | 14358 | ||
NM_170606 | MLL3 | 8329 | 8347 | C | C | U | U | G | a | g | G | G | G | G | U | U | G | A | A | G | U | C | -29 | 2 | 12 | bc | false | <90% | 16872 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2146
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