Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
41 hits were found for AGAUGAAGGCGAAGGCGUC (20 guide strand hits and 21 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_003904 | ZNF259 | 1476 | 1494 | g | G | A | U | G | A | A | G | G | C | G | A | A | G | G | C | u | g | g | 66 | 4 | 15 | ac | false | <90% | 1810 | ||
NM_015716 | MINK1 | 2596 | 2614 | g | G | A | g | G | A | A | G | G | C | G | A | A | G | G | C | G | g | g | 53 | 4 | 13 | c | false | <90% | 4878 | ||
NM_170663 | MINK1 | 2620 | 2638 | g | G | A | g | G | A | A | G | G | C | G | A | A | G | G | C | G | g | g | 53 | 4 | 13 | c | false | <90% | 4902 | ||
NM_001024937 | MINK1 | 2647 | 2665 | g | G | A | g | G | A | A | G | G | C | G | A | A | G | G | C | G | g | g | 53 | 4 | 13 | c | false | <90% | 4929 | ||
NM_153827 | MINK1 | 2707 | 2725 | g | G | A | g | G | A | A | G | G | C | G | A | A | G | G | C | G | g | g | 53 | 4 | 13 | c | false | <90% | 4989 | ||
NM_017934 | PHIP | 2661 | 2679 | A | G | A | U | G | A | A | G | G | C | G | A | A | G | u | a | G | U | u | 44 | 3 | 14 | c | false | <90% | 5817 | ||
NM_001039111 | TRIM71 | 1124 | 1142 | A | G | A | U | G | A | A | G | G | C | G | A | A | G | G | u | u | g | u | 42 | 4 | 15 | c | false | <90% | 3138 | ||
NM_015871 | ZNF593 | 112 | 130 | A | G | A | U | G | A | A | G | G | C | G | A | A | G | c | g | G | c | g | 41 | 4 | 14 | c | false | <90% | 648 | ||
XM_001132947 | LOC732354 | 108 | 126 | A | G | A | U | G | g | A | G | G | C | G | A | A | G | G | C | a | c | g | 5 | 4 | 10 | c | false | <90% | 486 | ||
XM_001132851 | LOC730189 | 108 | 126 | A | G | A | U | G | g | A | G | G | C | G | A | A | G | G | C | a | c | g | 5 | 4 | 10 | c | false | <90% | 645 | ||
NM_024302 | MMP28 | 2305 | 2323 | g | G | A | U | G | A | A | G | G | C | a | c | A | G | G | C | G | U | C | 2 | 3 | 9 | false | <90% | 2480 | |||
NM_207332 | ERICH1 | 653 | 671 | c | a | A | U | G | A | A | G | G | g | G | A | A | G | G | C | G | U | g | -1 | 4 | 8 | bc | false | <90% | 1836 | ||
XM_001129982 | LOC731538 | 108 | 126 | A | G | A | U | G | A | A | G | G | a | G | A | A | G | G | C | a | g | g | -13 | 4 | 9 | c | false | <90% | 645 | ||
XM_001129982 | LOC731538 | 221 | 239 | A | G | A | U | G | A | A | G | G | a | G | A | A | G | G | C | a | g | u | -13 | 4 | 9 | c | false | <90% | 645 | ||
XM_001129982 | LOC731538 | 383 | 401 | A | G | A | U | G | A | A | G | G | a | G | A | A | G | G | C | a | g | g | -13 | 4 | 9 | c | false | <90% | 645 | ||
XM_001129536 | LOC729167 | 108 | 126 | A | G | A | U | G | A | A | G | G | a | G | A | A | G | G | C | a | g | g | -13 | 4 | 9 | c | false | <90% | 645 | ||
XM_001129536 | LOC729167 | 221 | 239 | A | G | A | U | G | A | A | G | G | a | G | A | A | G | G | C | a | g | u | -13 | 4 | 9 | c | false | <90% | 645 | ||
XM_001129536 | LOC729167 | 383 | 401 | A | G | A | U | G | A | A | G | G | a | G | A | A | G | G | C | a | g | g | -13 | 4 | 9 | c | false | <90% | 645 | ||
NM_015286 | DMN | 1787 | 1805 | A | G | A | U | G | A | A | G | G | a | G | A | A | G | G | C | u | a | a | -13 | 4 | 9 | c | false | <90% | 6419 | ||
NM_145728 | DMN | 1787 | 1805 | A | G | A | U | G | A | A | G | G | a | G | A | A | G | G | C | u | a | a | -13 | 4 | 9 | c | false | <90% | 7355 |
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_014390 | SND1 | 2613 | 2631 | u | A | u | G | C | C | U | U | C | G | C | C | U | U | C | A | U | C | c | 73 | 3 | 15 | bc | false | <90% | 3522 | ||
NM_015232 | IQSEC3 | 1849 | 1867 | c | u | C | G | C | C | U | U | C | G | C | C | a | U | C | A | U | C | c | 71 | 4 | 10 | false | <90% | 2699 | |||
NM_000835 | GRIN2C | 645 | 663 | a | g | C | G | C | C | U | U | C | G | C | C | g | U | C | A | U | C | a | 71 | 4 | 10 | false | <90% | 4298 | |||
XM_936831 | IQSEC3 | 1929 | 1947 | c | u | C | G | C | C | U | U | C | G | C | C | a | U | C | A | U | C | c | 71 | 4 | 10 | false | <90% | 6758 | |||
XM_372922 | LOC391359 | 239 | 257 | G | u | g | G | C | C | U | U | C | G | C | C | U | U | C | A | c | C | U | 45 | 3 | 13 | c | false | <90% | 297 | ||
XM_372922 | LOC391359 | 249 | 267 | G | u | g | G | C | C | U | U | C | G | C | C | U | U | C | A | c | C | U | 45 | 3 | 13 | c | false | <90% | 297 | ||
XM_940561 | LOC391359 | 239 | 257 | G | u | g | G | C | C | U | U | C | G | C | C | U | U | C | A | c | C | U | 45 | 3 | 13 | c | false | <90% | 297 | ||
XM_940561 | LOC391359 | 249 | 267 | G | u | g | G | C | C | U | U | C | G | C | C | U | U | C | A | c | C | U | 45 | 3 | 13 | c | false | <90% | 297 | ||
NM_003979 | GPRC5A | 893 | 911 | c | u | C | a | C | C | U | U | C | G | C | C | U | U | C | A | U | C | a | 44 | 4 | 14 | bc | false | <90% | 2856 | ||
NM_006841 | SLC38A3 | 1009 | 1027 | a | u | g | G | C | C | U | U | C | G | C | C | U | U | C | g | U | C | U | 40 | 4 | 12 | c | false | <90% | 2559 | ||
NM_019594 | LRRC8A | 1306 | 1324 | a | A | C | G | a | C | U | U | C | G | C | C | U | U | C | A | U | g | c | 38 | 4 | 12 | c | false | <90% | 4296 | ||
NM_153835 | GPR113 | 1789 | 1807 | c | A | C | c | C | C | U | U | C | G | C | C | U | U | C | A | g | C | U | 37 | 3 | 12 | c | false | <90% | 3499 | ||
NM_000234 | LIG1 | 2094 | 2112 | u | A | C | G | C | C | U | U | C | G | a | C | c | U | C | A | U | C | U | 26 | 3 | 9 | false | <90% | 3083 | |||
NM_006618 | JARID1B | 246 | 264 | G | A | C | c | C | C | U | U | C | G | C | u | U | U | C | A | U | C | c | 24 | 3 | 7 | false | <90% | 6393 | |||
NM_021075 | NDUFV3 | 513 | 531 | G | u | C | G | C | C | U | U | C | G | u | C | U | U | C | A | U | C | c | 22 | 3 | 8 | c | false | <90% | 2151 | ||
NM_198883 | MTX1 | 1059 | 1077 | G | A | C | G | C | C | U | U | C | G | u | C | U | U | C | A | g | C | U | 15 | 2 | 10 | c | false | <90% | 1552 | ||
NM_002455 | MTX1 | 1152 | 1170 | G | A | C | G | C | C | U | U | C | G | u | C | U | U | C | A | g | C | U | 15 | 2 | 10 | c | false | <90% | 1655 | ||
NM_182527 | CABP7 | 649 | 667 | u | u | C | G | C | C | a | U | C | G | C | C | U | U | C | A | U | C | a | 15 | 4 | 11 | bc | false | <90% | 3044 | ||
NM_172344 | KCNG3 | 798 | 816 | G | A | g | G | C | C | U | U | C | G | g | C | U | U | C | A | U | C | c | 14 | 3 | 7 | c | false | <90% | 3791 | ||
NM_133329 | KCNG3 | 798 | 816 | G | A | g | G | C | C | U | U | C | G | g | C | U | U | C | A | U | C | c | 14 | 3 | 7 | c | false | <90% | 3824 | ||
NM_030782 | CLPTM1L | 1484 | 1502 | G | A | C | G | u | C | U | U | u | G | C | C | U | U | C | A | U | C | a | -16 | 3 | 9 | bc | false | <90% | 2164 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3063
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