Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
52 hits were found for GAACUCUUCUGAAGGAGUU (23 guide strand hits and 29 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 | |||||||||||||
XR_019182 | LOC347028 | 320 | 338 | a | c | A | C | U | C | U | U | C | U | G | A | A | G | G | A | G | g | a | 78 | 4 | 15 | ac | false | <90% | 1871 | ||
XR_016466 | LOC347028 | 320 | 338 | a | c | A | C | U | C | U | U | C | U | G | A | A | G | G | A | G | g | a | 78 | 4 | 15 | ac | false | <90% | 1871 | ||
NR_003227 | AFG3L1 | 683 | 701 | G | A | c | C | U | C | U | U | C | U | G | A | A | G | G | A | G | c | c | 72 | 3 | 14 | c | false | <90% | 2947 | ||
NM_032890 | DISP1 | 1572 | 1590 | G | A | A | C | U | C | U | U | C | U | G | A | c | G | G | c | G | U | g | 58 | 3 | 12 | false | <90% | 4743 | |||
NM_153610 | CMYA5 | 6009 | 6027 | u | u | A | C | U | C | U | U | C | U | G | A | A | G | a | A | G | U | a | 56 | 4 | 12 | c | false | <90% | 12911 | ||
XM_937234 | KIAA1571 | 2189 | 2207 | u | A | A | a | U | C | U | U | C | U | G | A | A | G | G | A | G | a | a | 53 | 4 | 13 | c | false | <90% | 10162 | ||
XM_371590 | KIAA1571 | 2189 | 2207 | u | A | A | a | U | C | U | U | C | U | G | A | A | G | G | A | G | a | a | 53 | 4 | 13 | c | false | <90% | 10162 | ||
NM_152730 | C6orf170 | 1784 | 1802 | G | A | A | C | U | C | U | U | C | U | G | A | A | G | a | A | a | g | U | 49 | 3 | 14 | c | false | <90% | 5132 | ||
XR_018249 | LOC344653 | 1308 | 1326 | c | A | A | C | U | C | U | U | C | U | G | A | A | G | c | u | G | U | U | 47 | 3 | 13 | c | false | <90% | 1867 | ||
XR_016494 | LOC344653 | 1308 | 1326 | c | A | A | C | U | C | U | U | C | U | G | A | A | G | c | u | G | U | U | 47 | 3 | 13 | c | false | <90% | 1867 | ||
NM_015001 | SPEN | 8628 | 8646 | G | A | A | C | a | C | U | U | C | U | G | A | A | G | G | g | G | U | U | 22 | 2 | 10 | c | false | <90% | 12227 | ||
XM_940811 | KIAA1462 | 4617 | 4635 | a | u | g | C | U | C | U | U | g | U | G | A | A | G | G | A | G | U | U | 6 | 4 | 10 | bc | false | <90% | 9282 | ||
XM_929312 | KIAA1462 | 4617 | 4635 | a | u | g | C | U | C | U | U | g | U | G | A | A | G | G | A | G | U | U | 6 | 4 | 10 | bc | false | <90% | 9282 | ||
XM_944819 | KIAA1462 | 4724 | 4742 | a | u | g | C | U | C | U | U | g | U | G | A | A | G | G | A | G | U | U | 6 | 4 | 10 | bc | false | <90% | 9389 | ||
XM_166132 | KIAA1462 | 4724 | 4742 | a | u | g | C | U | C | U | U | g | U | G | A | A | G | G | A | G | U | U | 6 | 4 | 10 | bc | false | <90% | 9389 | ||
XM_941377 | KIAA0748 | 352 | 370 | a | A | A | C | U | C | U | U | C | U | c | c | A | G | G | A | G | U | U | 2 | 3 | 9 | false | <90% | 3672 | |||
XM_374983 | KIAA0748 | 352 | 370 | a | A | A | C | U | C | U | U | C | U | c | c | A | G | G | A | G | U | U | 2 | 3 | 9 | false | <90% | 3673 | |||
NM_018233 | OGFOD1 | 976 | 994 | a | A | A | u | U | C | U | c | C | U | G | A | A | G | G | A | G | U | U | 0 | 3 | 11 | bc | false | <90% | 3020 | ||
NM_001007022 | ODF2L | 1503 | 1521 | a | g | u | C | U | C | a | U | C | U | G | A | A | G | G | A | G | U | U | 0 | 4 | 12 | bc | false | <90% | 2179 | ||
NM_020729 | ODF2L | 1636 | 1654 | a | g | u | C | U | C | a | U | C | U | G | A | A | G | G | A | G | U | U | 0 | 4 | 12 | bc | false | <90% | 2312 | ||
NM_139250 | CTAG1A | 412 | 430 | G | g | g | u | g | C | U | U | C | U | G | A | A | G | G | A | G | U | U | -19 | 4 | 14 | bc | false | <90% | 748 | ||
NM_001327 | CTAG1B | 447 | 465 | G | g | g | u | g | C | U | U | C | U | G | A | A | G | G | A | G | U | U | -19 | 4 | 14 | bc | false | <90% | 806 | ||
XR_016475 | LOC643894 | 262 | 280 | a | A | A | C | U | g | a | U | C | U | G | A | A | G | G | A | G | U | U | -31 | 3 | 12 | bc | false | <90% | 1073 |
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_170709 | SGK3 | 1582 | 1600 | A | c | C | U | C | C | U | U | C | A | G | A | A | G | A | c | U | U | a | 57 | 3 | 13 | c | false | <90% | 4059 | ||
NM_013257 | SGK3 | 1678 | 1696 | A | c | C | U | C | C | U | U | C | A | G | A | A | G | A | c | U | U | a | 57 | 3 | 13 | c | false | <90% | 4155 | ||
NM_001033578 | SGK3 | 1763 | 1781 | A | c | C | U | C | C | U | U | C | A | G | A | A | G | A | c | U | U | a | 57 | 3 | 13 | c | false | <90% | 4241 | ||
XM_944280 | SETD5 | 2539 | 2557 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 5170 | |||
XM_931417 | SETD5 | 2539 | 2557 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 5170 | |||
XM_944303 | SETD5 | 4253 | 4271 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 6306 | |||
XM_931455 | SETD5 | 4253 | 4271 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 6306 | |||
XM_931478 | SETD5 | 3925 | 3943 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 6556 | |||
XM_944276 | SETD5 | 3926 | 3944 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 6557 | |||
XM_944298 | SETD5 | 4522 | 4540 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 6575 | |||
XM_931447 | SETD5 | 4522 | 4540 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 6575 | |||
NM_001080517 | SETD5 | 4196 | 4214 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 6827 | |||
XM_939712 | SETD5 | 4196 | 4214 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 6827 | |||
XM_944295 | SETD5 | 5007 | 5025 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 7060 | |||
XM_931444 | SETD5 | 5007 | 5025 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 7060 | |||
XM_944260 | SETD5 | 4440 | 4458 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 7071 | |||
XM_931376 | SETD5 | 4479 | 4497 | g | c | C | U | C | C | U | U | C | A | G | c | A | G | A | G | U | U | C | 52 | 3 | 9 | false | <90% | 7110 | |||
NM_053028 | MYLK | 1293 | 1311 | c | g | g | U | C | C | U | U | C | A | G | A | A | G | A | c | U | U | C | 40 | 4 | 12 | c | false | <90% | 7492 | ||
NM_053026 | MYLK | 1293 | 1311 | c | g | g | U | C | C | U | U | C | A | G | A | A | G | A | c | U | U | C | 40 | 4 | 12 | c | false | <90% | 7645 | ||
NM_053027 | MYLK | 1293 | 1311 | c | g | g | U | C | C | U | U | C | A | G | A | A | G | A | c | U | U | C | 40 | 4 | 12 | c | false | <90% | 7699 | ||
NM_053025 | MYLK | 1293 | 1311 | c | g | g | U | C | C | U | U | C | A | G | A | A | G | A | c | U | U | C | 40 | 4 | 12 | c | false | <90% | 7852 | ||
NM_170724 | PKHD1 | 6986 | 7004 | A | A | C | U | C | C | U | U | C | A | G | u | A | G | A | G | g | c | C | 40 | 3 | 11 | false | <90% | 11604 | |||
NM_138694 | PKHD1 | 6986 | 7004 | A | A | C | U | C | C | U | U | C | A | G | u | A | G | A | G | g | c | C | 40 | 3 | 11 | false | <90% | 16235 | |||
NM_001012981 | ZKSCAN2 | 2058 | 2076 | A | A | a | g | C | C | U | U | C | A | G | A | A | G | A | G | U | U | a | 38 | 3 | 14 | bc | false | <90% | 7124 | ||
NM_021127 | PMAIP1 | 364 | 382 | g | A | C | U | C | C | U | U | C | A | a | A | A | G | A | G | U | U | u | 31 | 3 | 9 | c | false | <90% | 1885 | ||
NM_006633 | IQGAP2 | 2195 | 2213 | g | u | C | U | g | C | U | U | C | A | G | A | A | G | A | G | U | U | g | 30 | 4 | 13 | bc | false | <90% | 5769 | ||
NM_152431 | PIWIL4 | 1661 | 1679 | A | A | C | U | g | C | U | U | g | A | G | A | A | G | A | G | U | U | g | -16 | 3 | 9 | bc | false | <90% | 3138 | ||
XM_001132402 | LOC646892 | 667 | 685 | c | A | C | U | C | C | c | U | g | A | G | A | A | G | A | G | U | U | C | -28 | 3 | 10 | bc | false | <90% | 1892 | ||
XM_937092 | LOC646892 | 667 | 685 | c | A | C | U | C | C | c | U | g | A | G | A | A | G | A | G | U | U | C | -28 | 3 | 10 | bc | false | <90% | 1892 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1979
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